From 591ffe583776c6d8314fc443455c842271eea19c Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 22 Dec 2017 12:12:37 +0000
Subject: [PATCH] file can already be downloaded
---
.../xref_mapping/XrefParser/RFAMParser.pm | 34 +++++++++++++------
1 file changed, 23 insertions(+), 11 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
index def94e241e..5ec0b98836 100644
--- a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
@@ -42,7 +42,7 @@ sub run_script {
}
$verbose |=0;
- my $wget = "";
+ my $wget;
my $user = "ensro";
my $host;
my $port = 3306;
@@ -120,17 +120,29 @@ sub run_script {
}
$sth->finish;
- my $ua = LWP::UserAgent->new();
- $ua->timeout(10);
- $ua->env_proxy();
- my $request = HTTP::Request->new(GET => $wget);
- my $response = $ua->request($request);
-
- if ( !$response->is_success() ) {
- warn($response->status_line);
- return 1;
+ my @lines;
+ if (defined $wget) {
+ my $ua = LWP::UserAgent->new();
+ $ua->timeout(10);
+ $ua->env_proxy();
+ my $request = HTTP::Request->new(GET => $wget);
+ my $response = $ua->request($request);
+
+ if ( !$response->is_success() ) {
+ warn($response->status_line);
+ return 1;
+ }
+ @lines = split(/\n\n\n/, $response->decoded_content);
+ } else {
+ my $file_io = $self->get_filehandle($file);
+ if ( !defined $file_io ) {
+ print "ERROR: Can't open HGNC file $file\n";
+ return 1;
+ }
+ while (my $line = $file_io->getline()) {
+ push(@lines, $line);
+ }
}
- my @lines = split(/\n\n\n/, $response->decoded_content);
my @xrefs;
my $xref_count = 0;
--
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