Commit d536e753 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Fixes for blast db name change at IGS

parent 9f58015a
......@@ -114,7 +114,7 @@ sub Usage{
print {*STDERR} "
$0 -d refprot -p blastp -i fasta_file
$0 -d refseq_protein -p blastp -i fasta_file
Options disponibles:
-i input multifasta file
......@@ -141,7 +141,7 @@ sub Usage{
mtimonensis
nr
pdbaa
refprot
refseq_protein
sprot
sptr
sptr_nr_ncbi_v => swissprot + trembl avec entete taxonomique
......
......@@ -271,8 +271,8 @@ sub HELP {
-quiet ........ on : do not display all the default/defined blast parameters
Default off
Environement Variables
These variables can be set from the environement
Environment Variables
These variables can be set from the environment
DATABASE......................[Indicates where your database file must be fetched (locally)]
BLAST_DIRECTORY...............[Indicates where your BLAST directory is installed locally]
......@@ -479,7 +479,7 @@ sub WEB_BLAST {
last;
}
elsif ( $response->content =~ /Status=UNKNOWN/im ){
print {*STDERR} "Search $rid expired\n";
print {*STDERR} "Search [$rid] expired\n";
$verif = 1;
last;
}
......@@ -557,7 +557,7 @@ sub LOCAL_BLAST
print {*STDERR} "\nsorry invalid database for gigablast\n";exit 1;
}
if ( $database eq 'pdb') { $database = 'pdbaa';}
if ( $database eq 'refseq_protein') { $database = 'refprot';}
# if ( $database eq 'refseq_protein') { $database = 'refseq_protein';}
if ( $database eq '') { print {*STDERR} "provide a valid database!\n"; exit;}
open (COM,"$runblast -d $database -p blastp -e $Eval -v $align -F F \<$query_file |");
}
......
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