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Sebastien Moretti
ProtoGene
Commits
8aba9ba8
Commit
8aba9ba8
authored
Sep 08, 2016
by
Sebastien Moretti
Browse files
Fix for new NCBI BLAST raw format without GI and some other stuffs
parent
b3f4d3ee
Changes
1
Hide whitespace changes
Inline
Side-by-side
webblast.pl
View file @
8aba9ba8
...
...
@@ -631,7 +631,7 @@ sub PARSING {
if
(
$distant
==
1
){
my
$version_d
,
my
$database_d
,
my
$poste_d
;
undef
$/
;
(
$query
,
$length_query
)
=
(
$intra_res
[
0
]
=~
/Query=\s+(\S+)\s+Length=\s*(\d+)/smo
);
undef
$/
;
(
$query
,
$length_query
)
=
(
$intra_res
[
0
]
=~
/Query=\s+(\S+)
.*?
\s+Length=\s*(\d+)/smo
);
$/
=
"
\n
";
open
(
F3
,
'
<
',
'
web_tempo.result
')
or
die
;
while
(
$_
=<
F3
>
){
...
...
@@ -691,15 +691,24 @@ sub PARSING {
}
elsif
(
$method
=~
/^geneid$/i
){
if
(
$database
!~
/pdb/i
&&
$database
!~
/swiss/i
&&
$locale
=~
/1|2/
){
while
(
$intra_res
=~
/>.*?(gb|prf|emb|sp|pir|tpe|ref|prf|dbj|ddbj|pdb)[\|]+([A-Za-z0-9_\.]+?)(\s|\|(.{1}))/sg
){
my
$databank
=
$
1
;
my
$last
=
$
4
;
my
$refseq
=
$
2
;
if
(
$databank
eq
'
pdb
'
){
$refseq
.=
$last
;
if
(
$intra_res
=~
/>.*?[A-Za-z0-9_\.]+?\s+/
){
while
(
$intra_res
=~
/>.*?([A-Za-z0-9_\.]+?)\s+/sg
){
my
$refseq
=
$
1
;
$refseq
=~
s/\.\d+$//
;
push
(
@result_not_sort
,
"
$query
\t
$refseq
\t
$identity
\t
$recouvrement
\t
$bits
\t
$evalue
\t
ncbi
");
}
}
elsif
(
$intra_res
=~
/>.*?(gb|prf|emb|sp|pir|tpe|ref|prf|dbj|ddbj|pdb)[\|]+([A-Za-z0-9_\.]+?)(\s|\|(.{1}))/
){
while
(
$intra_res
=~
/>.*?(gb|prf|emb|sp|pir|tpe|ref|prf|dbj|ddbj|pdb)[\|]+([A-Za-z0-9_\.]+?)(\s|\|(.{1}))/sg
){
my
$databank
=
$
1
;
my
$last
=
$
4
;
my
$refseq
=
$
2
;
if
(
$databank
eq
'
pdb
'
){
$refseq
.=
$last
;
}
$refseq
=~
s/\.\d+$//
;
push
(
@result_not_sort
,
"
$query
\t
$refseq
\t
$identity
\t
$recouvrement
\t
$bits
\t
$evalue
\t
$databank
");
}
$refseq
=~
s/\.\d+$//
;
push
(
@result_not_sort
,
"
$query
\t
$refseq
\t
$identity
\t
$recouvrement
\t
$bits
\t
$evalue
\t
$databank
");
}
}
elsif
(
$database
=~
/pdb|pdbaa/i
&&
(
$locale
==
1
||
$locale
==
2
)
){
...
...
@@ -758,14 +767,23 @@ sub MULTI_EQUIVALENT {
my
(
$query
,
$identity
,
$recouvrement
,
$bits
,
$evalue
,
$intra_res
)
=
@_
;
my
@result
=
();
while
(
$intra_res
=~
/>.*?(gb|prf|emb|sp|pir|tpe|ref|prf|dbj|ddbj|pdb)[\|]+([A-Za-z0-9_\.]+?)(\s|\|(.{1}))/g
){
my
$databank
=
$
1
;
my
$last
=
$
4
;
my
$refseq
=
$
2
;
if
(
$databank
eq
'
pdb
'
){
$refseq
.=
$last
;
}
$refseq
=~
s/\.\d+$//
;
push
(
@result
,
"
$query
\t
$refseq
\t
$identity
\t
$recouvrement
\t
$bits
\t
$evalue
\t
$databank
");
if
(
$intra_res
=~
/>.*?[A-Za-z0-9_\.]+?\s+/
){
while
(
$intra_res
=~
/>.*?([A-Za-z0-9_\.]+?)\s+/sg
){
my
$refseq
=
$
1
;
$refseq
=~
s/\.\d+$//
;
push
(
@result
,
"
$query
\t
$refseq
\t
$identity
\t
$recouvrement
\t
$bits
\t
$evalue
\t
ncbi
");
}
}
elsif
(
$intra_res
=~
/>.*?(gb|prf|emb|sp|pir|tpe|ref|prf|dbj|ddbj|pdb)[\|]+([A-Za-z0-9_\.]+?)(\s|\|(.{1}))/
){
while
(
$intra_res
=~
/>.*?(gb|prf|emb|sp|pir|tpe|ref|prf|dbj|ddbj|pdb)[\|]+([A-Za-z0-9_\.]+?)(\s|\|(.{1}))/g
){
my
$databank
=
$
1
;
my
$last
=
$
4
;
my
$refseq
=
$
2
;
if
(
$databank
eq
'
pdb
'
){
$refseq
.=
$last
;
}
$refseq
=~
s/\.\d+$//
;
push
(
@result
,
"
$query
\t
$refseq
\t
$identity
\t
$recouvrement
\t
$bits
\t
$evalue
\t
$databank
");
}
}
return
(
@result
);
}
...
...
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