diff --git a/Changelog b/Changelog index d01d9f1d..f7ed1ef9 100644 --- a/Changelog +++ b/Changelog @@ -1,3 +1,10 @@ +2018-02-01 Youri Hoogstrate v0.16.0 + * Adds the exons before the break and exons after the break to the + integrate results. Remark that the offset to match an exon is + [-2,+2] because STAR may introduce slight offset errors. + * Fixes bug in integrate where rather similar fusions in opposite + strands were still bundled together. + 2018-02-01 Youri Hoogstrate v0.15.2 * Makes mismatches per base classification more stringent unless `--ffpe` is used. Using `--ffpe` the old behaviour diff --git a/bin/dr-disco b/bin/dr-disco index b3000255..54d8c9a1 100755 --- a/bin/dr-disco +++ b/bin/dr-disco @@ -140,8 +140,8 @@ def CLI_classify(table_input_file, table_output_file, only_valid, blacklist_regi @CLI.command(name='integrate', short_help='Maps junctions back together that are likely to correspond to the same fusion event.') @click.argument('table_input_file', type=click.Path(exists=True)) @click.argument('table_output_file') -@click.option('--gtf', help="Use gene annotation (GTF file)") -@click.option('--fasta', help="Use FASTA sequence file to estimate edit distances to splice junction motifs") +@click.option('--gtf', help="Use gene annotation for estimating fusion genes and improve classification of exonic (GTF file)") +@click.option('--fasta', help="Use reference sequences to estimate edit distances to splice junction motifs (FASTA file)") def CLI_integrate(table_input_file, table_output_file, gtf, fasta): cl = DetectOutput(table_input_file) diff --git a/drdisco/ChimericAlignment.py b/drdisco/ChimericAlignment.py index 7039fac5..06da8f0f 100644 --- a/drdisco/ChimericAlignment.py +++ b/drdisco/ChimericAlignment.py @@ -530,6 +530,8 @@ def randstr(n): if len(alignments) > 0: self.reconstruct_alignments(alignments, sam_file_discordant, fh) else: + os.remove(basename + ".name-sorted.bam") + os.remove(basename + ".name-sorted.fixed.sam") err = "No reads were found, fixing empty sam/bam file: " + self.input_alignment_file log.error(err) raise Exception(err) diff --git a/drdisco/DetectFrameShifts.py b/drdisco/DetectFrameShifts.py index 5fccd089..1dd2f189 100644 --- a/drdisco/DetectFrameShifts.py +++ b/drdisco/DetectFrameShifts.py @@ -90,7 +90,7 @@ def load_gtf_per_transcript(): transcript_idx[transcript_id][exon_number][gtf_type] = feature except KeyError: - log.warn("Warning: GTF file misses certain attributes (gene_name, transcript_id or transcript_version) and is therefore skipping the frameshift detection.") + log.warn("Warning: GTF file misses certain attributes (gene_name, transcript_id or transcript_version) and is therefore skipping the frameshift detection. Ensembl GTF files are known to be compatible.") # there is no GFF_Reader.close() so break it dirty: break @@ -229,6 +229,9 @@ def evaluate(self, _from, _to, offset): results = {0: [], 1: [], 2: [], 'fgd': []} + all_from = sorted(list(set([_ for _ in from_l_fgd] + [_[0] for _ in from_l]))) + all_to = sorted(list(set([_ for _ in to_l_fgd] + [_[0] for _ in to_l]))) + for from_l_i in from_l_fgd: for to_l_i in to_l_fgd: results['fgd'].append((from_l_i, to_l_i)) @@ -238,4 +241,4 @@ def evaluate(self, _from, _to, offset): frame_shift = ((from_l_i[1] + to_l_i[1]) % 3) results[frame_shift].append((from_l_i, to_l_i)) - return results + return all_from, all_to, results diff --git a/drdisco/DetectOutput.py b/drdisco/DetectOutput.py index d99bf445..b38d1f69 100644 --- a/drdisco/DetectOutput.py +++ b/drdisco/DetectOutput.py @@ -125,6 +125,9 @@ def parse(self): self.edit_dist_to_splice_motif = "" + self.exons_from = [] + self.exons_to = [] + self.structure = self.line[46] inv = {'-': '+', '+': '-'} @@ -464,12 +467,12 @@ def insert_in_index(index, entries, score, i): if score not in index: index[score] = {} - key = entries[0].chrA + ':' + str(entries[0].posA) + '(' + entries[0].strandA + ')-' + entries[0].chrB + ':' + str(entries[0].posB) + '(' + entries[0].strandB + ')_' + str(i) + key = entries[0].chrA + ':' + str(entries[0].posA) + '(' + entries[0].strandA + ')-' + entries[0].chrB + ':' + str(entries[0].posB) + '(' + entries[0].strandB + ')|' + str(i) index[score][key] = entries with open(output_table, 'w') as fh_out: header = self.header.split("\t") - header = "\t".join(header[:-5] + ['full-gene-dysregulation', 'frameshift=0', 'frameshift=+1', 'frameshift=+2', 'splice-motif-edit-distance'] + header[-5:]) + header = "\t".join(header[:-5] + ['full-gene-dysregulation', 'frameshift=0', 'frameshift=+1', 'frameshift=+2', 'splice-motif-edit-distance', "exons from (5')", "exons to (3')"] + header[-5:]) fh_out.write("shared-id\tfusion\t" + header) @@ -492,9 +495,9 @@ def insert_in_index(index, entries, score, i): done_breaks = set([]) if e.donorA > e.donorB: - frame_shifts = dfs.evaluate([e.chrA, e.posA, e.RNAstrandA], [e.chrB, e.posB, e.RNAstrandB], 2) + exons_from, exons_to, frame_shifts = dfs.evaluate([e.chrA, e.posA, e.RNAstrandA], [e.chrB, e.posB, e.RNAstrandB], 2) else: - frame_shifts = dfs.evaluate([e.chrB, e.posB, e.RNAstrandB], [e.chrA, e.posA, e.RNAstrandA], 2) + exons_from, exons_to, frame_shifts = dfs.evaluate([e.chrB, e.posB, e.RNAstrandB], [e.chrA, e.posA, e.RNAstrandA], 2) done_breaks.add(e.chrA + ':' + str(e.posA) + '/' + str(e.posA + 1) + '(' + e.strandA + ')->' + e.chrB + ':' + str(e.posB) + '/' + str(e.posB + 1) + '(' + e.strandB + ')') @@ -513,9 +516,13 @@ def insert_in_index(index, entries, score, i): if params[0] not in done_breaks and n_split_reads > 0: if e.donorA > e.donorB: # nice, use same thing to swap if necessary - frame_shifts = dfs.evaluate([e.chrA, posA, e.RNAstrandA], [e.chrB, posB, e.RNAstrandB], 2) + exons_from_, exons_to_, frame_shifts = dfs.evaluate([e.chrA, posA, e.RNAstrandA], [e.chrB, posB, e.RNAstrandB], 2) else: - frame_shifts = dfs.evaluate([e.chrB, posB, e.RNAstrandB], [e.chrA, posA, e.RNAstrandA], 2) + exons_from_, exons_to_, frame_shifts = dfs.evaluate([e.chrB, posB, e.RNAstrandB], [e.chrA, posA, e.RNAstrandA], 2) + + exons_from += exons_from_ + exons_to += exons_to_ + del(exons_from_, exons_to_) fgd += [x[0] + '->' + x[1] for x in frame_shifts['fgd']] frameshifts_0 += [x[0][0] + '->' + x[1][0] for x in frame_shifts[0]] @@ -524,10 +531,15 @@ def insert_in_index(index, entries, score, i): done_breaks.add(params[0]) + e.exons_from = sorted(list(set(exons_from))) + e.exons_to = sorted(list(set(exons_to))) + del(exons_from, exons_to) + e.fgd = ','.join(sorted(list(set(fgd)))) e.frameshift_0 = ','.join(sorted(list(set(frameshifts_0)))) e.frameshift_1 = ','.join(sorted(list(set(frameshifts_1)))) e.frameshift_2 = ','.join(sorted(list(set(frameshifts_2)))) + del(fgd, frameshifts_0, frameshifts_1, frameshifts_2) if ffs: e.is_on_splice_junction_motif(ffs) @@ -581,7 +593,7 @@ def insert(pos, e): top_result = (None, 9999999999999) for r in sorted(results.keys()): - if results[r] >= 2: + if results[r] >= 2 and r.strandA == e.strandA and r.strandB == e.strandB: d1 = (r.posA - e.posA) d2 = (r.posB - e.posB) sq_d = math.sqrt(pow(d1, 2) + pow(d2, 2)) @@ -596,7 +608,6 @@ def insert(pos, e): insert_in_index(idx2, [e, top_result[0]], e.score + top_result[0].score, q) else: insert_in_index(idx2, [e], e.score, q) - q += 1 for e in remainder: @@ -613,7 +624,7 @@ def insert(pos, e): for entry in idx2[score][key]: if entry not in exported: acceptors_donors = entry.get_donors_acceptors(gene_annotation) - line = entry.line[:-5] + [entry.fgd, entry.frameshift_0, entry.frameshift_1, entry.frameshift_2, entry.edit_dist_to_splice_motif] + entry.line[-5:] + line = entry.line[:-5] + [entry.fgd, entry.frameshift_0, entry.frameshift_1, entry.frameshift_2, entry.edit_dist_to_splice_motif, ",".join(entry.exons_from), ",".join(entry.exons_to)] + entry.line[-5:] fh_out.write(str(i) + "\t" + acceptors_donors + "\t" + "\t".join(line) + "\n") exported.add(entry) diff --git a/drdisco/__init__.py b/drdisco/__init__.py index f0ef6241..462b58a6 100644 --- a/drdisco/__init__.py +++ b/drdisco/__init__.py @@ -31,7 +31,7 @@ import logging import sys -__version_info__ = ('0', '15', '2') +__version_info__ = ('0', '16', '0') __version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3]) + "-" + __version_info__[3] __author__ = 'Youri Hoogstrate' __homepage__ = 'https://github.com/yhoogstrate/dr-disco' diff --git a/tests/chim_overhang/test_01_integrate.out.txt b/tests/chim_overhang/test_01_integrate.out.txt index 7f99ed6b..27ae00e5 100644 --- a/tests/chim_overhang/test_01_integrate.out.txt +++ b/tests/chim_overhang/test_01_integrate.out.txt @@ -1,2 +1,2 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr2:17281790->chr11:5566704 chr2 17281790 + 0 22 chr11 5566704 - 22 0 inf entropy=0.7372<0.7382,chim_overhang=21<25 linear intronic 33 22 11 0 1530 10 1 1 1 0 0 0.7372 0.7372 0.0000 0.0000 0.3818 18.0000 0.8367 0.0013 0.0833 2.0455 38.7727 0.9652 0.0000 0.1847 0.0000 0.3333 2.0000 21 49 21 57 chr2:17281790/17281791(+)->chr11:5566704/5566705(-):(spanning_paired_1:11,spanning_paired_2:11) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr2:17281790->chr11:5566704 chr2 17281790 + 0 22 chr11 5566704 - 22 0 inf entropy=0.7372<0.7382,chim_overhang=21<25 linear intronic 33 22 11 0 1530 10 1 1 1 0 0 0.7372 0.7372 0.0000 0.0000 0.3818 18.0000 0.8367 0.0013 0.0833 2.0455 38.7727 0.9652 0.0000 0.1847 0.0000 0.3333 2.0000 21 49 21 57 chr2:17281790/17281791(+)->chr11:5566704/5566705(-):(spanning_paired_1:11,spanning_paired_2:11) diff --git a/tests/chim_overhang/test_02_integrate.out.txt b/tests/chim_overhang/test_02_integrate.out.txt index 328caaad..135f5c32 100644 --- a/tests/chim_overhang/test_02_integrate.out.txt +++ b/tests/chim_overhang/test_02_integrate.out.txt @@ -1,2 +1,2 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr5:105166412->chr7:12213276 chr5 105166412 + 0 22 chr7 12213276 + 22 0 inf entropy=0.7372<0.7382,chim_overhang=16<25 linear intronic 33 22 11 0 1528 14 1 1 1 0 0 0.7372 0.7372 0.0000 0.0000 0.1273 15.0000 0.8367 0.0013 0.0278 0.6091 53.9545 0.9419 0.0000 0.0724 0.0000 0.3333 2.0000 16 57 16 59 chr5:105166412/105166413(+)->chr7:12213276/12213277(+):(spanning_paired_1:11,spanning_paired_2:11) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr5:105166412->chr7:12213276 chr5 105166412 + 0 22 chr7 12213276 + 22 0 inf entropy=0.7372<0.7382,chim_overhang=16<25 linear intronic 33 22 11 0 1528 14 1 1 1 0 0 0.7372 0.7372 0.0000 0.0000 0.1273 15.0000 0.8367 0.0013 0.0278 0.6091 53.9545 0.9419 0.0000 0.0724 0.0000 0.3333 2.0000 16 57 16 59 chr5:105166412/105166413(+)->chr7:12213276/12213277(+):(spanning_paired_1:11,spanning_paired_2:11) diff --git a/tests/chim_overhang/test_03_integrate.out.txt b/tests/chim_overhang/test_03_integrate.out.txt index 70bb5bf5..60d9da02 100644 --- a/tests/chim_overhang/test_03_integrate.out.txt +++ b/tests/chim_overhang/test_03_integrate.out.txt @@ -1,2 +1,2 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr8:86472668->chr17:40685761 chr8 86472668 - 6 8 chr17 40685761 + 8 6 inf chim_overhang=18<25 linear intronic 21 8 7 0 998 6 1 1 1 0 0 0.8277 0.8277 0.6547 0.0000 0.3214 53.7500 0.9186 0.0035 0.0619 0.2143 16.9286 0.8660 0.0117 0.0553 0.0000 0.1905 2.0000 55 18 56 18 chr8:86472668/86472669(-)->chr17:40685761/40685762(+):(spanning_paired_1:3,spanning_paired_1_t:4,spanning_paired_2:3,spanning_paired_2_t:4) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr8:86472668->chr17:40685761 chr8 86472668 - 6 8 chr17 40685761 + 8 6 inf chim_overhang=18<25 linear intronic 21 8 7 0 998 6 1 1 1 0 0 0.8277 0.8277 0.6547 0.0000 0.3214 53.7500 0.9186 0.0035 0.0619 0.2143 16.9286 0.8660 0.0117 0.0553 0.0000 0.1905 2.0000 55 18 56 18 chr8:86472668/86472669(-)->chr17:40685761/40685762(+):(spanning_paired_1:3,spanning_paired_1_t:4,spanning_paired_2:3,spanning_paired_2_t:4) diff --git a/tests/integrate/test_frameshift-prediction_01-complementary.out.txt b/tests/integrate/test_frameshift-prediction_01-complementary.out.txt index 0fcc81c3..d9dac5b9 100644 --- a/tests/integrate/test_frameshift-prediction_01-complementary.out.txt +++ b/tests/integrate/test_frameshift-prediction_01-complementary.out.txt @@ -1,17 +1,17 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 1:1035203->1:999610 1 1035203 - 0 200 1 999610 + 200 0 2992369 valid linear intronic 500 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 -1 chr1:1035203->chr1:999610 chr1 1035203 + 0 200 chr1 999610 - 200 0 3052497 valid linear exonic 800 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -2 1:1035203->1:999610 1 999610 + 200 0 1 1035203 - 0 200 2992369 valid linear intronic 650 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 -2 chr1:1035203->chr1:999610 chr1 999610 - 200 0 chr1 1035203 + 0 200 3052497 valid linear exonic 550 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -3 1:1035203->1:999610 1 1035203 + 0 200 1 999610 + 200 0 2992369 valid linear intronic 300 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 -4 1:1035203->1:999610 1 999610 + 200 0 1 1035203 + 0 200 2992369 valid linear intronic 250 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 -5 chr1:1035203->chr1:999610 chr1 999610 + 200 0 chr1 1035203 - 0 200 3052497 valid linear exonic 750 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -6 1:1035203->1:999610 1 1035203 + 0 200 1 999610 - 200 0 2992369 valid linear intronic 700 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 -7 chr1:1035203->chr1:999610 chr1 1035203 - 0 200 chr1 999610 + 200 0 3052497 valid linear exonic 600 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -8 1:1035203->1:999610 1 999610 - 200 0 1 1035203 + 0 200 2992369 valid linear intronic 450 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 -9 chr1:1035203->chr1:999610 chr1 1035203 + 0 200 chr1 999610 + 200 0 3052497 valid linear exonic 400 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -10 chr1:1035203->chr1:999610 chr1 999610 + 200 0 chr1 1035203 + 0 200 3052497 valid linear exonic 350 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -11 chr1:999610->chr1:1035203 chr1 1035203 - 200 0 chr1 999610 - 0 200 3052497 valid linear exonic 200 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -12 chr1:999610->chr1:1035203 chr1 999610 - 0 200 chr1 1035203 - 200 0 3052497 valid linear exonic 150 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 -13 1:999610->1:1035203 1 1035203 - 200 0 1 999610 - 0 200 2992369 valid linear intronic 100 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 -14 1:999610->1:1035203 1 999610 - 0 200 1 1035203 - 200 0 2992369 valid linear intronic 50 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 1:1035203->1:999610 1 999610 + 200 0 1 1035203 - 0 200 2992369 valid linear intronic 650 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl 50 50 50 50 +1 chr1:1035203->chr1:999610 chr1 1035203 + 0 200 chr1 999610 - 200 0 3052497 valid linear exonic 800 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +2 1:1035203->1:999610 1 1035203 - 0 200 1 999610 + 200 0 2992369 valid linear intronic 500 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl 50 50 50 50 +2 chr1:1035203->chr1:999610 chr1 999610 - 200 0 chr1 1035203 + 0 200 3052497 valid linear exonic 550 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +3 chr1:1035203->chr1:999610 chr1 999610 + 200 0 chr1 1035203 - 0 200 3052497 valid linear exonic 750 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl 50 50 50 50 +4 1:1035203->1:999610 1 1035203 + 0 200 1 999610 + 200 0 2992369 valid linear intronic 300 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 +4 chr1:1035203->chr1:999610 chr1 1035203 + 0 200 chr1 999610 + 200 0 3052497 valid linear exonic 400 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 +5 1:1035203->1:999610 1 1035203 + 0 200 1 999610 - 200 0 2992369 valid linear intronic 700 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +6 1:1035203->1:999610 1 999610 + 200 0 1 1035203 + 0 200 2992369 valid linear intronic 250 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 +6 chr1:1035203->chr1:999610 chr1 999610 + 200 0 chr1 1035203 + 0 200 3052497 valid linear exonic 350 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 +7 chr1:1035203->chr1:999610 chr1 1035203 - 0 200 chr1 999610 + 200 0 3052497 valid linear exonic 600 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl 50 50 50 50 +8 1:1035203->1:999610 1 999610 - 200 0 1 1035203 + 0 200 2992369 valid linear intronic 450 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +9 chr1:999610->chr1:1035203 chr1 1035203 - 200 0 chr1 999610 - 0 200 3052497 valid linear exonic 200 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 +10 chr1:999610->chr1:1035203 chr1 999610 - 0 200 chr1 1035203 - 200 0 3052497 valid linear exonic 150 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 +11 1:999610->1:1035203 1 1035203 - 200 0 1 999610 - 0 200 2992369 valid linear intronic 100 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 +12 1:999610->1:1035203 1 999610 - 0 200 1 1035203 - 200 0 2992369 valid linear intronic 50 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 diff --git a/tests/integrate/test_frameshift-prediction_01.out.txt b/tests/integrate/test_frameshift-prediction_01.out.txt index 57e271c9..43b82013 100644 --- a/tests/integrate/test_frameshift-prediction_01.out.txt +++ b/tests/integrate/test_frameshift-prediction_01.out.txt @@ -1,5 +1,5 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr1:1035203->chr1:999610 chr1 1035203 - 0 200 chr1 999610 - 200 0 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 -2 chr1:1035203->chr1:999610 chr1 999610 - 200 0 chr1 1035203 - 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 -3 1:1035203->1:999610 1 1035203 - 0 200 1 999610 - 200 0 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 -4 1:1035203->1:999610 1 999610 - 200 0 1 1035203 - 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr1:1035203->chr1:999610 chr1 1035203 - 0 200 chr1 999610 - 200 0 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +2 chr1:1035203->chr1:999610 chr1 999610 - 200 0 chr1 1035203 - 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +3 1:1035203->1:999610 1 1035203 - 0 200 1 999610 - 200 0 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +4 1:1035203->1:999610 1 999610 - 200 0 1 1035203 - 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 diff --git a/tests/integrate/test_frameshift-prediction_02.out.txt b/tests/integrate/test_frameshift-prediction_02.out.txt index 80bc007d..0bd67665 100644 --- a/tests/integrate/test_frameshift-prediction_02.out.txt +++ b/tests/integrate/test_frameshift-prediction_02.out.txt @@ -1,5 +1,5 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr1:1035203->chr1:999020 chr1 1035203 - 0 200 chr1 999020 - 200 0 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) 50 50 50 50 -2 chr1:1035203->chr1:999020 chr1 999020 - 200 0 chr1 1035203 - 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) 50 50 50 50 -3 1:1035203->1:999020 1 1035203 - 0 200 1 999020 - 200 0 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) 50 50 50 50 -4 1:1035203->1:999020 1 999020 - 200 0 1 1035203 - 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) 50 50 50 50 +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr1:1035203->chr1:999020 chr1 1035203 - 0 200 chr1 999020 - 200 0 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +2 chr1:1035203->chr1:999020 chr1 999020 - 200 0 chr1 1035203 - 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +3 1:1035203->1:999020 1 1035203 - 0 200 1 999020 - 200 0 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +4 1:1035203->1:999020 1 999020 - 200 0 1 1035203 - 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl(+0)->HES4(ENST00000304952.10)-ensembl_havana(+2) AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 diff --git a/tests/integrate/test_frameshift-prediction_03.out.txt b/tests/integrate/test_frameshift-prediction_03.out.txt index ce136ba3..904d9bc3 100644 --- a/tests/integrate/test_frameshift-prediction_03.out.txt +++ b/tests/integrate/test_frameshift-prediction_03.out.txt @@ -1,5 +1,5 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr1:1040604->chr1:999020 chr1 1040604 - 0 200 chr1 999020 - 200 0 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 -2 chr1:1040604->chr1:999020 chr1 999020 - 200 0 chr1 1040604 - 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 -3 1:1040604->1:999020 1 1040604 - 0 200 1 999020 - 200 0 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 -4 1:1040604->1:999020 1 999020 - 200 0 1 1040604 - 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr1:1040604->chr1:999020 chr1 1040604 - 0 200 chr1 999020 - 200 0 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +2 chr1:1040604->chr1:999020 chr1 999020 - 200 0 chr1 1040604 - 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +3 1:1040604->1:999020 1 1040604 - 0 200 1 999020 - 200 0 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 +4 1:1040604->1:999020 1 999020 - 200 0 1 1040604 - 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 AGRN(ENST00000620552.4)-ensembl->HES4(ENST00000304952.10)-ensembl_havana AGRN(ENST00000620552.4)-ensembl HES4(ENST00000304952.10)-ensembl_havana 50 50 50 50 diff --git a/tests/integrate/test_in_frame_non_hybrid_protein.out.txt b/tests/integrate/test_in_frame_non_hybrid_protein.out.txt index eb0b0d71..7fa616ea 100644 --- a/tests/integrate/test_in_frame_non_hybrid_protein.out.txt +++ b/tests/integrate/test_in_frame_non_hybrid_protein.out.txt @@ -1,2 +1,2 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr21:41508080->chr21:38445621 chr21 38445621 - 238 0 chr21 41508080 + 0 238 3062459 valid linear exonic 494 318 159 17 10000 0 12 5 8 2 0 0.6676 0.7788 0.2243 0.8525 0.2600 81.0521 0.8788 0.0000 0.0135 0.2575 16.2608 0.8745 0.0000 0.0137 0.1069 0.3219 1.0833 TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000429727.6)-ensembl 50 50 50 50 chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:111,spanning_paired_2:111) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr21:41508080->chr21:38445621 chr21 38445621 - 238 0 chr21 41508080 + 0 238 3062459 valid linear exonic 494 318 159 17 10000 0 12 5 8 2 0 0.6676 0.7788 0.2243 0.8525 0.2600 81.0521 0.8788 0.0000 0.0135 0.2575 16.2608 0.8745 0.0000 0.0137 0.1069 0.3219 1.0833 TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000429727.6)-ensembl TMPRSS2(ENST00000424093.5)-havana ERG(ENST00000429727.6)-ensembl 50 50 50 50 chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:111,spanning_paired_2:111) diff --git a/tests/integrate/test_terg_s041.out.txt b/tests/integrate/test_terg_s041.out.txt index 5d84a9bb..6131b8cd 100644 --- a/tests/integrate/test_terg_s041.out.txt +++ b/tests/integrate/test_terg_s041.out.txt @@ -1,6 +1,6 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 TMPRSS2->ERG chr21 38487350 - 200 0 chr21 41479719 + 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 chr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7) -1 TMPRSS2->ERG chr21 38445621 - 200 0 chr21 41498118 + 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000492833.5)-ensembl_havana TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000442448.5)-ensembl TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1) TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0) 50 50 50 50 chr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2) -2 chr21:36338771->chr21:36344707 chr21 36338771 + 0 10 chr21 36344707 - 10 0 5936 valid circular exonic 117 58 38 3 10000 0 2 2 2 0 0 0.8536 0.8591 2.436 0.871 2.1714 19.1829 0.9605 0 0.1021 2.0941 32.6902 0.9725 0 0.0814 0.0789 0.2479 2 50 50 50 50 chr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1) -3 chr21:29329693->chr21:29321220 chr21 29321220 + 10 0 chr21 29329693 - 0 10 8473 valid circular exonic 49 35 15 4 10000 0 4 4 3 0 0 0.8605 0.8018 0 0.6667 8.3531 34.3077 0.9863 0 0.4412 9.4685 14.5897 0.9701 0 0.749 0.2667 0.3571 1.75 50 50 50 50 chr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4) -4 chr21:33432871<->chr21:33414887 chr21 33414887 + 5 5 chr21 33432871 - 5 5 17984 valid circular exonic 20 12 6 2 10000 0 3 3 2 1 0 0.8277 0.9167 0 0.75 12.6 50.8 0.7995 0.1045 5.4663 12.8 24.2 0.8072 0.0987 5.4049 0.3333 0.3 1.6667 50 50 50 50 chr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 TMPRSS2->ERG chr21 38487350 - 200 0 chr21 41479719 + 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 chr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7) +1 TMPRSS2->ERG chr21 38445621 - 200 0 chr21 41498118 + 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000492833.5)-ensembl_havana TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000442448.5)-ensembl TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000332149.9)-ensembl_havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000398585.7)-ensembl(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+1)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000424093.5)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000454499.5)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000455813.1)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000288319.11)-ensembl_havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398905.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398907.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398910.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398911.5)-havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000398919.6)-ensembl_havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000417133.6)-ensembl_havana(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000429727.6)-ensembl(+1),TMPRSS2(ENST00000458356.5)-havana(+0)->ERG(ENST00000442448.5)-ensembl(+1) TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000332149.9)-ensembl_havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000398585.7)-ensembl(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000424093.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0) TMPRSS2(ENST00000332149.9)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl,TMPRSS2(ENST00000424093.5)-havana,TMPRSS2(ENST00000454499.5)-havana,TMPRSS2(ENST00000455813.1)-havana,TMPRSS2(ENST00000458356.5)-havana,TMPRSS2(ENST00000463138.1)-havana,TMPRSS2(ENST00000497881.5)-havana ERG(ENST00000288319.11)-ensembl_havana,ERG(ENST00000398897.5)-ensembl_havana,ERG(ENST00000398905.5)-havana,ERG(ENST00000398907.5)-havana,ERG(ENST00000398910.5)-havana,ERG(ENST00000398911.5)-havana,ERG(ENST00000398919.6)-ensembl_havana,ERG(ENST00000417133.6)-ensembl_havana,ERG(ENST00000429727.6)-ensembl,ERG(ENST00000442448.5)-ensembl,ERG(ENST00000453032.6)-ensembl_havana,ERG(ENST00000468474.5)-havana,ERG(ENST00000473107.1)-havana,ERG(ENST00000481609.5)-havana,ERG(ENST00000485493.1)-havana,ERG(ENST00000492833.5)-ensembl_havana 50 50 50 50 chr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2) +2 chr21:36338771->chr21:36344707 chr21 36338771 + 0 10 chr21 36344707 - 10 0 5936 valid circular exonic 117 58 38 3 10000 0 2 2 2 0 0 0.8536 0.8591 2.436 0.871 2.1714 19.1829 0.9605 0 0.1021 2.0941 32.6902 0.9725 0 0.0814 0.0789 0.2479 2 50 50 50 50 chr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1) +3 chr21:29329693->chr21:29321220 chr21 29321220 + 10 0 chr21 29329693 - 0 10 8473 valid circular exonic 49 35 15 4 10000 0 4 4 3 0 0 0.8605 0.8018 0 0.6667 8.3531 34.3077 0.9863 0 0.4412 9.4685 14.5897 0.9701 0 0.749 0.2667 0.3571 1.75 50 50 50 50 chr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4) +4 chr21:33432871<->chr21:33414887 chr21 33414887 + 5 5 chr21 33432871 - 5 5 17984 valid circular exonic 20 12 6 2 10000 0 3 3 2 1 0 0.8277 0.9167 0 0.75 12.6 50.8 0.7995 0.1045 5.4663 12.8 24.2 0.8072 0.0987 5.4049 0.3333 0.3 1.6667 50 50 50 50 chr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4) diff --git a/tests/integrate/test_terg_s041_b.out.txt b/tests/integrate/test_terg_s041_b.out.txt index 697bede1..e4975e63 100644 --- a/tests/integrate/test_terg_s041_b.out.txt +++ b/tests/integrate/test_terg_s041_b.out.txt @@ -1,6 +1,6 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr21:41479719->chr21:38487350 chr21 38487350 - 200 0 chr21 41479719 + 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 chr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7) -1 chr21:41498118->chr21:38445621 chr21 38445621 - 200 0 chr21 41498118 + 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 chr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2) -2 chr21:36338771->chr21:36344707 chr21 36338771 + 0 10 chr21 36344707 - 10 0 5936 valid circular exonic 117 58 38 3 10000 0 2 2 2 0 0 0.8536 0.8591 2.436 0.871 2.1714 19.1829 0.9605 0 0.1021 2.0941 32.6902 0.9725 0 0.0814 0.0789 0.2479 2 50 50 50 50 chr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1) -3 chr21:29329693->chr21:29321220 chr21 29321220 + 10 0 chr21 29329693 - 0 10 8473 valid circular exonic 49 35 15 4 10000 0 4 4 3 0 0 0.8605 0.8018 0 0.6667 8.3531 34.3077 0.9863 0 0.4412 9.4685 14.5897 0.9701 0 0.749 0.2667 0.3571 1.75 50 50 50 50 chr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4) -4 chr21:33432871<->chr21:33414887 chr21 33414887 + 5 5 chr21 33432871 - 5 5 17984 valid circular exonic 20 12 6 2 10000 0 3 3 2 1 0 0.8277 0.9167 0 0.75 12.6 50.8 0.7995 0.1045 5.4663 12.8 24.2 0.8072 0.0987 5.4049 0.3333 0.3 1.6667 50 50 50 50 chr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr21:41479719->chr21:38487350 chr21 38487350 - 200 0 chr21 41479719 + 0 200 2992369 valid linear intronic 151 96 48 7 10000 0 1 1 1 0 0 0.869 0.869 0.2887 0.8124 2.1465 5.6435 0.9817 0 0.0571 1.9162 26.2818 0.99 0 0.0376 0.1458 0.3179 2 50 50 50 50 chr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7) +1 chr21:41498118->chr21:38445621 chr21 38445621 - 200 0 chr21 41498118 + 0 200 3052497 valid linear exonic 588 378 189 21 10000 0 14 7 9 2 4 0.7421 0.8197 0 0.7162 0.7344 19.9882 0.9657 0 0.0178 0.7194 21.976 0.9648 0 0.0177 0.1111 0.3214 1.1429 50 50 50 50 chr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2) +2 chr21:36338771->chr21:36344707 chr21 36338771 + 0 10 chr21 36344707 - 10 0 5936 valid circular exonic 117 58 38 3 10000 0 2 2 2 0 0 0.8536 0.8591 2.436 0.871 2.1714 19.1829 0.9605 0 0.1021 2.0941 32.6902 0.9725 0 0.0814 0.0789 0.2479 2 50 50 50 50 chr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1) +3 chr21:29329693->chr21:29321220 chr21 29321220 + 10 0 chr21 29329693 - 0 10 8473 valid circular exonic 49 35 15 4 10000 0 4 4 3 0 0 0.8605 0.8018 0 0.6667 8.3531 34.3077 0.9863 0 0.4412 9.4685 14.5897 0.9701 0 0.749 0.2667 0.3571 1.75 50 50 50 50 chr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4) +4 chr21:33432871<->chr21:33414887 chr21 33414887 + 5 5 chr21 33432871 - 5 5 17984 valid circular exonic 20 12 6 2 10000 0 3 3 2 1 0 0.8277 0.9167 0 0.75 12.6 50.8 0.7995 0.1045 5.4663 12.8 24.2 0.8072 0.0987 5.4049 0.3333 0.3 1.6667 50 50 50 50 chr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4) diff --git a/tests/splice_site_motif/test_splice_site_motif_01.out.dbed b/tests/splice_site_motif/test_splice_site_motif_01.out.dbed index 7d10b731..4ce7fc0f 100644 --- a/tests/splice_site_motif/test_splice_site_motif_01.out.dbed +++ b/tests/splice_site_motif/test_splice_site_motif_01.out.dbed @@ -1,2 +1,2 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr2:189->chr2:999 chr2 189 - 0 14 chr2 999 + 14 0 810 unclassified linear intronic 19 12 6 1 1019 4 1 1 1 0 0 0.7580 0.7580 0.0000 1.0000 8.0357 16.8929 0.9213 0.0032 1.5165 7.5714 22.0000 0.9311 0.0023 1.3263 0.1667 0.3158 2.0000 0 41 34 75 75 chr2:189/190(-)->chr2:999/1000(+):(discordant_mates:2,spanning_paired_1:5,spanning_paired_1_t:1,spanning_paired_2:5,spanning_paired_2_t:1) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr2:189->chr2:999 chr2 189 - 0 14 chr2 999 + 14 0 810 unclassified linear intronic 19 12 6 1 1019 4 1 1 1 0 0 0.7580 0.7580 0.0000 1.0000 8.0357 16.8929 0.9213 0.0032 1.5165 7.5714 22.0000 0.9311 0.0023 1.3263 0.1667 0.3158 2.0000 0 41 34 75 75 chr2:189/190(-)->chr2:999/1000(+):(discordant_mates:2,spanning_paired_1:5,spanning_paired_1_t:1,spanning_paired_2:5,spanning_paired_2_t:1) diff --git a/tests/splice_site_motif/test_splice_site_motif_02.out.dbed b/tests/splice_site_motif/test_splice_site_motif_02.out.dbed index aabf22ef..fa252faa 100644 --- a/tests/splice_site_motif/test_splice_site_motif_02.out.dbed +++ b/tests/splice_site_motif/test_splice_site_motif_02.out.dbed @@ -1,2 +1,2 @@ -shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance median-AS-A median-AS-B max-AS-A max-AS-B data-structure -1 chr21:1730->chr21:589 chr21 589 - 10 0 chr21 1730 + 0 10 1141 unclassified linear intronic 24 14 7 5 2387 4 2 1 2 0 0 0.8277 0.9070 0.0000 0.9398 8.3000 73.6000 0.7947 0.1082 3.6601 8.5000 18.6000 0.8063 0.0993 3.5995 0.7143 0.2917 1.5000 0 95 50 126 120 chr21:589/590(-)->chr21:1730/1731(+):(spanning_paired_1:5,spanning_paired_2:5)&chr21:589/590(-)->chr21:1599/1600(+):(discordant_mates:10,spanning_singleton_1_r:2,spanning_singleton_2_r:2) +shared-id fusion chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge full-gene-dysregulation frameshift=0 frameshift=+1 frameshift=+2 splice-motif-edit-distance exons from (5') exons to (3') median-AS-A median-AS-B max-AS-A max-AS-B data-structure +1 chr21:1730->chr21:589 chr21 589 - 10 0 chr21 1730 + 0 10 1141 unclassified linear intronic 24 14 7 5 2387 4 2 1 2 0 0 0.8277 0.9070 0.0000 0.9398 8.3000 73.6000 0.7947 0.1082 3.6601 8.5000 18.6000 0.8063 0.0993 3.5995 0.7143 0.2917 1.5000 0 95 50 126 120 chr21:589/590(-)->chr21:1730/1731(+):(spanning_paired_1:5,spanning_paired_2:5)&chr21:589/590(-)->chr21:1599/1600(+):(discordant_mates:10,spanning_singleton_1_r:2,spanning_singleton_2_r:2) diff --git a/tests/test_frameshift_prediction.py b/tests/test_frameshift_prediction.py index 6addd193..ba1d9b92 100755 --- a/tests/test_frameshift_prediction.py +++ b/tests/test_frameshift_prediction.py @@ -47,11 +47,14 @@ def test_01(self): # example of in-frame fusion - strands are RNA strand for fusion in fusions: for gtf_file in gtf_files: dfs = DetectFrameShifts(gtf_file) - frameshift_annotation = dfs.evaluate(fusion[0], fusion[1], 0) + exons_from, exons_to, frameshift_annotation = dfs.evaluate(fusion[0], fusion[1], 0) self.assertEqual(str(frameshift_annotation[0]), "[(('AGRN(ENST00000620552.4)-ensembl', 0), ('HES4(ENST00000304952.10)-ensembl_havana', 0))]") self.assertEqual(len(frameshift_annotation[1]), 0) self.assertEqual(len(frameshift_annotation[2]), 0) + self.assertEqual(",".join(exons_from), "AGRN(ENST00000620552.4)-ensembl") + self.assertEqual(",".join(exons_to), "HES4(ENST00000304952.10)-ensembl_havana") + def test_02(self): # 0, +2 fusions = [(['chr1', 1035203, '+'], ['chr1', 999020, '-']), (['1', 1035203, '+'], ['1', 999020, '-'])] # (from), (to) and strands are at RNA level! gtf_files = [TEST_DIR + 'frameshift_example.gtf', TEST_DIR + 'frameshift_example.no_chr_prefix.gtf'] @@ -59,11 +62,14 @@ def test_02(self): # 0, +2 for fusion in fusions: for gtf_file in gtf_files: dfs = DetectFrameShifts(gtf_file) - frameshift_annotation = dfs.evaluate(fusion[0], fusion[1], 0) + exons_from, exons_to, frameshift_annotation = dfs.evaluate(fusion[0], fusion[1], 0) self.assertEqual(len(frameshift_annotation[0]), 0) self.assertEqual(len(frameshift_annotation[1]), 0) self.assertEqual(str(frameshift_annotation[2]), "[(('AGRN(ENST00000620552.4)-ensembl', 0), ('HES4(ENST00000304952.10)-ensembl_havana', 2))]") + self.assertEqual(",".join(exons_from), "AGRN(ENST00000620552.4)-ensembl") + self.assertEqual(",".join(exons_to), "HES4(ENST00000304952.10)-ensembl_havana") + def test_03(self): # +1, +2 -> 0 fusions = [(['chr1', 1040604, '+'], ['chr1', 999020, '-']), (['1', 1040604, '+'], ['1', 999020, '-'])] gtf_files = [TEST_DIR + 'frameshift_example.gtf', TEST_DIR + 'frameshift_example.no_chr_prefix.gtf'] @@ -71,11 +77,14 @@ def test_03(self): # +1, +2 -> 0 for fusion in fusions: for gtf_file in gtf_files: dfs = DetectFrameShifts(gtf_file) - frameshift_annotation = dfs.evaluate(fusion[0], fusion[1], 0) + exons_from, exons_to, frameshift_annotation = dfs.evaluate(fusion[0], fusion[1], 0) self.assertEqual(str(frameshift_annotation[0]), "[(('AGRN(ENST00000620552.4)-ensembl', 1), ('HES4(ENST00000304952.10)-ensembl_havana', 2))]") self.assertEqual(len(frameshift_annotation[1]), 0) self.assertEqual(len(frameshift_annotation[2]), 0) + self.assertEqual(",".join(exons_from), "AGRN(ENST00000620552.4)-ensembl") + self.assertEqual(",".join(exons_to), "HES4(ENST00000304952.10)-ensembl_havana") + if __name__ == '__main__': main() diff --git a/tests/test_splice_site_motif.py b/tests/test_splice_site_motif.py index 42738f53..1d83f3b4 100755 --- a/tests/test_splice_site_motif.py +++ b/tests/test_splice_site_motif.py @@ -42,7 +42,7 @@ os.makedirs(T_TEST_DIR) -class TestIntronicBreakDetection(unittest.TestCase): +class TestSpliceJunctions(unittest.TestCase): def test_sj_01(self): test_id = 'splice_site_motif_01'