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Sebastien Moretti
ProtoGene
Commits
d536e753
Commit
d536e753
authored
Jun 13, 2014
by
Sebastien Moretti
Browse files
Fixes for blast db name change at IGS
parent
9f58015a
Changes
2
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Inline
Side-by-side
runblast.pl
View file @
d536e753
...
...
@@ -114,7 +114,7 @@ sub Usage{
print
{
*STDERR
}
"
$0 -d refprot -p blastp -i fasta_file
$0 -d ref
seq_
prot
ein
-p blastp -i fasta_file
Options disponibles:
-i input multifasta file
...
...
@@ -141,7 +141,7 @@ sub Usage{
mtimonensis
nr
pdbaa
refprot
ref
seq_
prot
ein
sprot
sptr
sptr_nr_ncbi_v => swissprot + trembl avec entete taxonomique
...
...
webblast.pl
View file @
d536e753
...
...
@@ -271,8 +271,8 @@ sub HELP {
-quiet ........ on : do not display all the default/defined blast parameters
Default off
Environ
e
ment Variables
These variables can be set from the environ
e
ment
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
}
"
\n
sorry 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 = 'ref
seq_
prot
ein
';}
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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