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ProtoGene.pl

@@ -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') );
 }
 
 

Views0.pm

@@ -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