Remove gunzip -c and replace with zcat

edilytics · Aug 29, 2024 · ca92dd0 · ca92dd0
1 parent 3eba615
commit ca92dd0
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -133,7 +133,7 @@ def check_program(binary_name, download_url=None, version_flag=None, version_reg
 check_fastp = lambda: check_program('fastp', download_url='http://opengene.org/fastp/fastp', version_flag='--version', version_regex=r'fastp (\d+)\.(\d+)\.(\d+)', version=(0, 19, 8))
 
 def get_avg_read_length_fastq(fastq_filename):
-     cmd = 'gunzip -c' if fastq_filename.endswith('.gz') else 'cat' + \
+     cmd = 'zcat' if fastq_filename.endswith('.gz') else 'cat' + \
         ' < \"%s\"' % fastq_filename + \
         r''' | awk 'BN {n=0;s=0;} NR%4 == 2 {s+=length($0);n++;} END { printf("%d\n",s/n)}' '''
      p = sb.Popen(cmd, shell=True, stdout=sb.PIPE)

diff --git a/CRISPResso2/CRISPRessoShared.py b/CRISPResso2/CRISPRessoShared.py
@@ -724,7 +724,7 @@ def get_command_output(command):
 
 def get_n_reads_fastq(fastq_filename):
     """Count the number of reads from fastq_filename."""
-    p = sb.Popen('gunzip -c' if fastq_filename.endswith('.gz') else 'cat' + ' < "%s" | wc -l' % fastq_filename, shell=True, stdout=sb.PIPE)
+    p = sb.Popen('zcat' if fastq_filename.endswith('.gz') else 'cat' + ' < "%s" | wc -l' % fastq_filename, shell=True, stdout=sb.PIPE)
     return round(float(p.communicate()[0]) / 4.0)