Generate proviral_landscape for HIVIntact runs too

cfe-lab · Jul 21, 2023 · 7e15cf0 · 7e15cf0
1 parent 6ad62bd
commit 7e15cf0
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/gene_splicer/sample.py b/gene_splicer/sample.py
@@ -115,7 +115,7 @@ def main():
     for file in fasta_files:
         gene_splicer.run(file, outdir=outpath)
     utils.generate_table_precursor(name=run_name, outpath=outpath)
-    utils.generate_proviral_landscape_csv(outpath)
+    utils.generate_proviral_landscape_csv(outpath, is_hivintact=args.hivintact)
     copy_output(outpath / 'outcome_summary.csv', args.outcome_summary_csv)
     copy_output(outpath / (run_name + '_conseqs_primer_analysis.csv'),
                 args.conseqs_primers_csv)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
@@ -558,12 +558,14 @@ def generate_table_precursor_2(hivseqinr_resultsfile, filtered_file,
     return table_precursorfile
 
 
-def generate_proviral_landscape_csv(outpath):
+def generate_proviral_landscape_csv(outpath, is_hivintact):
     proviral_landscape_csv = os.path.join(outpath, 'proviral_landscape.csv')
     landscape_rows = []
 
     table_precursor_csv = os.path.join(outpath, 'table_precursor.csv')
     blastn_csv = glob.glob(
+        os.path.join(outpath, 'hivintact*', 'blast.tsv') \
+        if is_hivintact else \
         os.path.join(
             outpath,
             'hivseqinr*',