Commit fced4bf7 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Remove most STDERR writings of webblast.pl

parent 022bcba2
......@@ -54,7 +54,7 @@ if ( ($database_line || $database_var) && ($blast_line || $blast_var) ){
$locale = 1;
$database = 'expressopdb';
unless ( $quiet=~ /on/i ){
print {*STDERR} "\nRUN BLAST LOCALLY\n";
print "\nRUN BLAST LOCALLY\n";
}
}
else{
......@@ -63,7 +63,7 @@ if ( ($database_line || $database_var) && ($blast_line || $blast_var) ){
$locale = 1;
$blast_way = &CONTROLE_DB_PG($database, $blast_tp, $program);
unless ( $quiet=~ /on/i ){
print {*STDERR} "\nRUN BLAST LOCALLY\n";
print "\nRUN BLAST LOCALLY\n";
}
}
}
......@@ -74,12 +74,12 @@ else{
$locale = 2;
$distant = 0;
unless ( $quiet=~ /on/i ){
print {*STDERR} "\nRUN ON GIGABLASTER\n";
print "\nRUN ON GIGABLASTER\n";
}
}
else{
unless ( $quiet=~ /on/i ){
print {*STDERR} "\nRUN BLAST AT THE NCBI\n";
print "\nRUN BLAST AT THE NCBI\n";
}
}
}
......@@ -153,7 +153,7 @@ unless ( $quiet =~ /on/i ){
}
print {*STDERR} "\n***************************************************************\n\n";
print "\n***************************************************************\n\n";
}
......@@ -437,7 +437,7 @@ sub WEB_BLAST {
}
foreach my $encoded_seq(@list_encoded){
my $nb = 0;
print {*STDERR} "BLAST $names[$i]...";
print "BLAST $names[$i]...";
#-- BUILD THE REQUEST
my ($arguments) = "CMD=Put&ENTREZ_QUERY=$orgn&CDD_SEARCH=off&FILTER=$filter&MATRIX_NAME=$matrix&PROGRAM=$program&DATABASE=$database&QUERY=" . $encoded_seq;
......@@ -462,7 +462,7 @@ sub WEB_BLAST {
die "parse error: $!";
}
for (my $j=0; $j<=$wait/2; $j++){
print {*STDERR} '.';
print '.';
sleep 2;
}
......@@ -470,7 +470,7 @@ sub WEB_BLAST {
while (){
for (my $j=0; $j<=5; $j++){
print {*STDERR} '.';
print '.';
sleep 1;
}
......@@ -496,7 +496,7 @@ sub WEB_BLAST {
last;
}
else {
print {*STDERR} "No hits found.\n";
print {*STDERR} "No hits found\n";
$verif = 1;
last;
}
......@@ -533,7 +533,7 @@ sub WEB_BLAST {
$req = new HTTP::Request GET => "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&FORMAT_TYPE=$format&FILTER=off&EXPECT=$Eval&ALIGNMENTS=$align&DESCRIPTIONS=$align&ALIGNMENT_VIEW=$aln_view&RID=$rid";
$response = $ua -> request($req);
if ($response->content =~ /Altschul/i) { print {*STDERR} "Search Complete\n"; push(@list_pdb,$response -> content);last; }
if ($response->content =~ /Altschul/i) { print "Search Complete\n"; push(@list_pdb,$response -> content);last; }
else { next; }
}
print {$SOR1} (@list_pdb);
......@@ -581,7 +581,7 @@ sub LOCAL_BLAST
open (COM,"$blast_dir -p blastp -d $database -i $query_file -v 1 -b 1 -F $filter -e $Eval -M $matrix -v $align -b $align -a $process |") or die;
}
unless ( $quiet=~ /on/ ) { print {*STDERR} "\nrun BLAST..."; }
unless ( $quiet=~ /on/ ) { print "\nrun BLAST..."; }
my ($name_database, $posted, $version) = ('', '', '');
......@@ -595,12 +595,12 @@ sub LOCAL_BLAST
print {$SOR2} $_;
push (@list_pdb, $_);
# if ( $_=~ /\s*(.+?)\s/ ){
# print {*STDERR} "\n$1 done";
# print "\n$1 done";
# }
}
close COM;
close $SOR2;
# print {*STDERR} "\n";
# print "\n";
$name_database = $database if ( $name_database =~ m{/} );
unless ($quiet=~ /on/i) {
......@@ -869,7 +869,7 @@ sub PROFILE {
unlink("tempo_file_profile");
undef(@list_pdb);
print {*STDERR} "\n**********************************************************************\n\n";
print "\n**********************************************************************\n\n";
#-- OUTFILE /STDOUT
if ($out_file){ open (SOR1,">$out_file") or die "can not open $out_file"; print SOR1 @sortie; }
print {*STDOUT} @sortie;
......
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