Commit 919560fe authored by Sebastien Moretti's avatar Sebastien Moretti
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parent b3cd004b
......@@ -216,8 +216,8 @@ elsif ( exists( $original_seq[0] ) && $original_seq[0] =~ /[acgtu]/i ){
my $non = ($first_seq =~ s{[^aAcCgGtTuUXxNn-]}{}g) || 0;
if ( ($a+$c+$g+$t) >= (($a+$c+$g+$t+$non)*80/100) ){
failure();
print {*STDERR} "\tYour sequences seem already to be nucleotides
\tthe goal of this program is to turn AMINO ACID alignments into CDS nucleotide alignments\n\n";
print {*STDERR} "\tYour sequences look already to be nucleotides
\tThe goal of this program is to turn AMINO ACID alignments into CDS nucleotide alignments\n\n";
exit(1);
}
}
......@@ -227,7 +227,7 @@ undef $fasta_checker;
# Check GigaBlaster status if used
if ( $giga==1 ){
$local = 0;
$local = 2 if ( head('http://www.igs.cnrs-mrs.fr/public_g/remoteblast.cgi') );
$local = 2 if ( head('http://www.igs.cnrs-mrs.fr/public_g/remoteblast.cgi') );
}
......
......@@ -29,6 +29,7 @@ my %species = ( 'alfalfa' => '',
'duck' => '',
'goat' => '',
'gorilla' => '',
#'guina pig' => '', " Works as normal species name
'hamster' => '',
'hamsters' => '',
'hiv-1' => '',
......@@ -78,7 +79,8 @@ my %nonSpecies = ( 'mRNA' => '',
);
#FIXME: fake match if 1st word is a single letter !
my %fakeMatch = ('Bacterial enrichment' => '',
my %fakeMatch = ('Arsenite-oxidising bacterium' => '',
'Bacterial enrichment' => '',
'Boar' => '',
'Expression vector' => '',
'C-terminal' => '',
......@@ -212,7 +214,7 @@ my %longer_species_name = ( 'altaica' => '', #Panthera tigris altaica
'orientalis' => '', #Panthera pardus orientalis
'persica' => '', #Panthera leo persica
'pseudoobscura' => '',
'quinquefasciatus' => '',
'quinquefasciatus' => '', #Culex pipiens quinquefasciatus
'Red Jungle fowl' => '', #Gallus gallus breed Red Jungle fowl
'rubra' => '', #Varecia variegata rubra
'saxicolor' => '', #Panthera pardus saxicolor
......@@ -221,6 +223,7 @@ my %longer_species_name = ( 'altaica' => '', #Panthera tigris altaica
'Sprague-Dawley' => '', #Rattus norvegicus Sprague-Dawley
'sp.' => '',
'sumatrae' => '', #Panthera tigris sumatrae
'SY8' => '', #Achromobacter arsenitoxydans SY8
'variegata' => '', #Varecia variegata variegata
'versicolor' => '', #Anas versicolor versicolor
'verus' => '', #Pan troglodytes verus
......
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