Fix requantify.py for cases where no reads map to a given input seque…

…nce.
TRON-Bioinformatics · Nov 25, 2020 · 9f7c983 · 9f7c983
1 parent c1422ab
commit 9f7c983
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/requantify.py b/requantify.py
@@ -95,6 +95,10 @@ def count_reads(seq_to_pos, cash, bp_dist):
         # initialize anchor
         anchor: int = 0
 
+        # test if there are no reads for this sequence
+        if seq_name not in cash:
+            continue
+
         # iterate over all reads (read group):
         for read_name in cash[seq_name]:
 

diff --git a/run_test.sh b/run_test.sh
@@ -2,11 +2,12 @@
 module load  python/2.7.15
 
 # Test run for requantify.py
-/code/Anaconda/3/2019/bin/python requantify.py \
+# /code/Anaconda/3/2019/bin/python requantify.py \
+python requantify.py \
   -i star_aln/Aligned.sortedByCoord.out.bam \
   -t example_data/CLDN18_Context_seq.csv \
   -d 10 \
-  -o CLDN18_Context_seq.csv.counts_new4_star.tsv
+  -o CLDN18_Context_seq.csv.counts_new5_star.tsv
 
 # Test rund for easy_qant.py on example data
 python easy_quant.py \