PedroBarbosa · PedroBarbosa · Apr 16, 2024 · Apr 16, 2024 · Apr 16, 2024
diff --git a/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_30_archive_logger.csv.gz b/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_30_archive_logger.csv.gz
diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_30_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_30_dataset.csv.gz
diff --git a/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_31_archive_logger.csv.gz b/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_31_archive_logger.csv.gz
diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_31_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_31_dataset.csv.gz
diff --git a/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_32_archive_logger.csv.gz b/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_32_archive_logger.csv.gz
diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_32_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_32_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_33_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_33_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_34_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_34_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_35_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_35_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_36_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_36_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_37_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_37_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_40_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_40_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_44_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_44_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_45_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_45_dataset.csv.gz
diff --git a/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_46_archive_logger.csv.gz b/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_46_archive_logger.csv.gz
diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_46_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_46_dataset.csv.gz
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diff --git a/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_49_archive_logger.csv.gz b/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_49_archive_logger.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_50_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_50_dataset.csv.gz
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diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_58_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_58_dataset.csv.gz
diff --git a/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_59_archive_logger.csv.gz b/...as_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_59_archive_logger.csv.gz
diff --git a/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_59_dataset.csv.gz b/...asets_fas_exon6/bin_filler/chr10_89010439_89012181_ENST00000652046_seed_59_dataset.csv.gz
diff --git a/data/examples/explain/datasets_fas_exon6/bin_filler/preprocessing_extracted_from_cache.bed b/data/examples/explain/datasets_fas_exon6/bin_filler/preprocessing_extracted_from_cache.bed
diff --git a/...amples/explain/datasets_fas_exon6/bin_filler/preprocessing_sequences_trimmed_at_5000bp.fa b/...amples/explain/datasets_fas_exon6/bin_filler/preprocessing_sequences_trimmed_at_5000bp.fa
diff --git a/...xplain/datasets_fas_exon6/bin_filler/preprocessing_sequences_trimmed_at_5000bp_ss_idx.tsv b/...xplain/datasets_fas_exon6/bin_filler/preprocessing_sequences_trimmed_at_5000bp_ss_idx.tsv
diff --git a/tests/data/chr22.fa b/tests/data/chr22.fa
diff --git a/tests/data/chr22.fa.fai b/tests/data/chr22.fa.fai
diff --git a/tests/preprocessing_raw_test.py b/tests/preprocessing_raw_test.py
@@ -1,20 +1,25 @@
 import gzip
+import os
 import shutil
 import pytest
+import tempfile
 from dress.datasetgeneration.os_utils import open_fasta
 from dress.datasetgeneration.preprocessing.utils import tabular_file_to_genomics_df
 from dress.datasetgeneration.preprocessing.gtf_cache import (
     extractGeneStructure,
     generate_pipeline_input,
 )
 
-raw_data = "tests/data/raw_data.tsv"
-cache_dir = "tests/data"
-genome_c = "tests/data/chr22.fa.gz"
-genome = genome_c.replace(".gz", "")
+
+abs_path = os.path.dirname(os.path.abspath(__file__))
+raw_data = os.path.join(abs_path,"data/raw_data.tsv")
+cache_dir = os.path.join(abs_path,"data")
+genome_c =  os.path.join(abs_path, "data/chr22.fa.gz")
 level = 2
 
 with gzip.open(genome_c, "rb") as f_in:
+    tmp_f = tempfile.NamedTemporaryFile()
+    genome = tmp_f.name
     with open(genome, "wb") as f_out:
         shutil.copyfileobj(f_in, f_out)
 
@@ -214,4 +219,4 @@ def test_trimmed_sequence(self, initial_setup):
                     donor = int(donor)
 
                     assert seq[acceptor - 2 : acceptor] == "AG"
-                    assert seq[donor + 1 : donor + 3] == "GT"
+                    assert seq[donor + 1 : donor + 3] == "GT"