Commit e1edc701 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Cleaning + remove unused modules

parent 9b725190
......@@ -3,7 +3,6 @@
package Exonerate;
sub parser{
my ($infile, $debug) = @_;
my %pos_aln;
......
......@@ -453,15 +453,15 @@ if ( exists($tmpFiles[0]) ){
if ( -s "$originalMSA.cds" || -s "$originalMSA.out" ){
print "\n\nTERMINATION STATUS: SUCCESS\n";
print 'OUTPUT RESULTS', "\n";
print " #### File Type= MSA Format= fasta_CDS Name= $originalMSA.cds\n"
print " #### File Type= MSA Format= fasta_CDS Name= $originalMSA.cds\n"
if ( -s "$originalMSA.cds" );
print " #### File Type= MSA Format= fasta_CDS+Query Name= $originalMSA.cdsP\n"
print " #### File Type= MSA Format= fasta_CDS+Query Name= $originalMSA.cdsP\n"
if ( -s "$originalMSA.cdsP" );
print " #### File Type= MSA Format= colored_fasta_CDS Name= $originalMSA.cdsP.html\n"
print " #### File Type= MSA Format= colored_fasta_CDS Name= $originalMSA.cdsP.html\n"
if ( Views::Html("$originalMSA.cdsP") && -s "$originalMSA.cdsP.html" );
print " #### File Type= MSA Format= Rejected_seq Name= $originalMSA.out\n"
print " #### File Type= MSA Format= Rejected_seq Name= $originalMSA.out\n"
if ( -s "$originalMSA.out" );
print " #### File Type= MSA Format= fasta_Exon-Boundaries Name= $originalMSA.boj\n"
print " #### File Type= MSA Format= fasta_Exon-Boundaries Name= $originalMSA.boj\n"
if ( -s "$originalMSA.boj" && -s "$originalMSA.cds" && $hideBOJ==0 );
unlink "$cache/web_tempo.result";
......@@ -1060,7 +1060,7 @@ sub runExonerate{
my @bestAln;
RUN_EXONERATE:
for(my $b=0; $b<=$#gis; $b++){
# Warning: Arbitrarily threshold between genomic and transcript sequence lengths, fixed at 5000 bp here
# Warning: Arbitrarily threshold between genomic and transcript sequence lengths, fixed at 5000 bp here
# To manage short DNA seq, everything pass through --model protein2genome but with --exhaustive for short ones
if ( -s "$cache/$gis[$b].fas" > 5000 ){
# Exonerate prot - genomic or long RNA
......
......@@ -132,9 +132,9 @@ sub Html {
}
else {
s{ _S_ (\w+) }{ _S_ <a href='$ncbi_aa$1' target='_blank'>$1</a> };
}
}
}
print {$CDSHTML} "<span class='$isOdd$isSubOdd'>", $_, "\n";
$isSubOdd = $isSubOdd eq 'odd' ? 'even' : 'odd';
}
......@@ -143,7 +143,6 @@ sub Html {
$isSubOdd = $isSubOdd eq 'odd' ? 'even' : 'odd';
}
elsif ( m/^&gt;.*/ && !m/MATCHES_ON / ){
print {$CDSHTML} "<span class='$isOdd'>", $_, "\n";
$isOdd = $isOdd eq 'odd' ? 'even' : 'odd';
$isSubOdd = 'odd';
......@@ -162,7 +161,7 @@ sub Html {
sub htmlHeader {
my ($jobName) = @_;
$jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};
$jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};
my $css = '';
for my $style ( keys(%css) ){
......
......@@ -267,7 +267,7 @@ sub Html {
elsif ( $match =~ /^(.+?(v|V)ir(us|al))(.*)$/ && $2 !~ /^ resistance/ && $2 !~ /^ oncogene/ ){
$match = $1;
$rest = $2 ||'';
}
}
else {
my $pred = '';
my @desc = split(' ', $match);
......@@ -343,9 +343,9 @@ sub Html {
}
else {
s{ _S_ (\w+) }{ _S_ <a href='$ncbi_aa$1' target='_blank'>$1</a> };
}
}
}
print {$CDSHTML} "<span class='$isOdd$isSubOdd'>", $_, "\n";
$isSubOdd = $isSubOdd eq 'odd' ? 'even' : 'odd';
}
......@@ -354,7 +354,6 @@ sub Html {
$isSubOdd = $isSubOdd eq 'odd' ? 'even' : 'odd';
}
elsif ( m/^&gt;.*/ && !m/MATCHES_ON / ){
print {$CDSHTML} "<span class='$isOdd'>", $_, "\n";
$isOdd = $isOdd eq 'odd' ? 'even' : 'odd';
$isSubOdd = 'odd';
......@@ -373,7 +372,7 @@ sub Html {
sub htmlHeader {
my ($jobName) = @_;
$jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};
$jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};
my $css = '';
for my $style ( keys(%css) ){
......
......@@ -3,11 +3,7 @@
use strict;
use warnings;
use diagnostics;
#use Env qw(HOME);
#use lib "$HOME/.lib_webblast/";
#use HTTP::GHTTP qw/:methods/;
use CGI;
use URI::Escape;
use LWP::UserAgent;
my $ua = LWP::UserAgent->new;
use HTTP::Request::Common qw(POST);
......@@ -47,7 +43,7 @@ $html = 'on' if( $html eq 'T' );
# Build Command script
my @command;
# Add program
push( @command , "Program=$program" );
push( @command , "Program=$program" );
# Add database
push( @command , "$dbtype=$dbname" );
push( @command , "evalue=$evalue" );
......
#!/usr/bin/env perl
#
#
#date : 2007/11/19
#prog : webblast.pl
#subj : make a BLAST/WU-BLAST (by HTTP request or locally) against a database with a file containing sequences in fasta format
####### method genid, pdbid and profile
#
#############################################################################################
#use Env qw(HOME);
#use lib "$HOME/.lib_webblast/";
use LWP::UserAgent;
use HTML::Parser; # @@@@@@@ #
use HTTP::Request::Common qw(POST); # @/^ ^\@ #
use URI::Escape; # @/ - - \@ #
use Getopt::Long; ## \ ^ / ##
use strict; ## | 0 | ##
use warnings; ####### \ _ / #######
use HTTP::Request::Common qw(POST);
use Getopt::Long;
use strict;
use warnings;
##############################################################################################
......
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