From bec64eda41401268539e2c1c6c84844eba742a74 Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Thu, 28 Jul 2022 17:38:50 +0200
Subject: [PATCH] added gzip format support for genome
---
_modules/IData_handling.py | 3 ++-
_modules/main_utils.py | 3 ++-
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/_modules/IData_handling.py b/_modules/IData_handling.py
index 4f63c64..5714031 100755
--- a/_modules/IData_handling.py
+++ b/_modules/IData_handling.py
@@ -304,7 +304,8 @@ def genomeFastaRecovery(filin, limit_reference, edge, host_test = 0):
if filin == "":
return "", "", ""
- infile = open(filin, 'r')
+ #infile = open(filin, 'r')
+ infile = gzip.open(filin, "rt") if filin.endswith(".gz") else open(filin, 'r')
name = []
genome = []
genome_line = ""
diff --git a/_modules/main_utils.py b/_modules/main_utils.py
index 2a88196..f6c35d0 100755
--- a/_modules/main_utils.py
+++ b/_modules/main_utils.py
@@ -11,6 +11,7 @@ from __future__ import print_function
from time import gmtime, strftime
import sys
+import gzip
from optparse import OptionParser, OptionGroup
from _modules.utilities import checkReportTitle,changeCase
from _modules.IData_handling import totReads,genomeFastaRecovery
@@ -47,7 +48,7 @@ usage = """\n\nUsage: %prog -f reads.fastq -r phage_sequence.fasta [--report_tit
def checkFastaFile(filin):
"""Check sequence Fasta file given by user"""
first_line = 1
- infil = open(filin, 'r')
+ infil = gzip.open(filin, "rt") if filin.endswith(".gz") else open(filin, 'r')
try:
for line in infil:
# Test '>'
--
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