From 595d9e36a8d97bf57eef1ce6760af96b7732e532 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Wed, 7 Mar 2012 15:27:16 +0000
Subject: [PATCH] added support for reading compressed files
---
modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm
index 67bdbf260..7f6633e6d 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm
@@ -72,7 +72,12 @@ sub fetch_input {
my $self = shift @_;
my $inputfile = $self->param('inputfile') || die "'inputfile' is an obligatory parameter";
- my $input_seqio = Bio::SeqIO->new(-file => '<'.$inputfile) || die "Could not open or parse '$inputfile', please investigate";
+ die "Cannot read '$inputfile'" unless(-r $inputfile);
+
+ if($inputfile=~/\.(?:gz|Z)$/) {
+ $inputfile = "gunzip -c $inputfile |";
+ }
+ my $input_seqio = Bio::SeqIO->new(-file => $inputfile) || die "Could not open or parse '$inputfile', please investigate";
$self->param('input_seqio', $input_seqio);
}
--
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