Use fixed grep patterns

Novartis · May 26, 2022 · 420f8f0 · 420f8f0
1 parent 67126e4
commit 420f8f0
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/pisces/__init__.py b/pisces/__init__.py
@@ -149,15 +149,15 @@ def fingerprint_sample(args, fastq_1, fastq_2, data_dir, output_dir,
                 kmers2_outname, 'w') as kmers2_out:
             p1 = Popen(
                 [
-                    'zgrep', '-h', '-o', '-f',
+                    'zgrep', '-F', '-h', '-o', '-f',
                     os.path.join(data_dir, 'data/fp_kmers_col1.txt'),
                     ' '.join(fastq_1)
                 ],
                 stdout=kmers1_out,
                 stderr=PIPE)
             p2 = Popen(
                 [
-                    'zgrep', '-h', '-o', '-f',
+                    'zgrep', '-F', '-h', '-o', '-f',
                     os.path.join(data_dir, 'data/fp_kmers_col1.txt'),
                     ' '.join(fastq_2)
                 ],
@@ -169,7 +169,7 @@ def fingerprint_sample(args, fastq_1, fastq_2, data_dir, output_dir,
         with open(kmers1_outname, 'w') as kmers1_out:
             p1 = Popen(
                 [
-                    'zgrep', '-h', '-o', '-f',
+                    'zgrep', '-F', '-h', '-o', '-f',
                     os.path.join(data_dir, 'data/fp_kmers_col1.txt'),
                     ' '.join(fastq_1)
                 ],