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