From 293c946d6a9aac5ab8b22f1983d762a315efcd05 Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Wed, 27 Jul 2022 17:50:34 +0200
Subject: [PATCH] added support for gzipped files
---
_modules/functions_PhageTerm.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/_modules/functions_PhageTerm.py b/_modules/functions_PhageTerm.py
index 63db8b3..a20be63 100644
--- a/_modules/functions_PhageTerm.py
+++ b/_modules/functions_PhageTerm.py
@@ -49,6 +49,7 @@ import pandas as pd
# String
#import cStringIO
import io
+import gzip
# PDF report building
import time
@@ -127,11 +128,13 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
sys.stdout.flush()
# Mapping
- filin = open(inRawDArgs.fastq)
+ #filin = open(inRawDArgs.fastq)
+ filin = gzip.open(inRawDArgs.fastq, "rt") if inRawDArgs.fastq.endswith(".gz") else open(inRawDArgs.fastq)
line = filin.readline()
if inRawDArgs.paired != "":
- filin_paired = open(inRawDArgs.paired)
+ #filin_paired = open(inRawDArgs.paired)
+ filin_paired = gzip.open(inRawDArgs.paired, "rt") if inRawDArgs.paired.endswith(".gz") else open(inRawDArgs.paired)
line_paired = filin_paired.readline()
count_line_tmp=0
while line and count_line!=count_line_tmp:
--
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