Commit 86815e3e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.3.0

parent 4d2478f1

resfinder.pl

+6 −6
Original line number Diff line number Diff line
@@ -10,7 +10,7 @@ use Try::Tiny::Retry; 


use constant PROGRAM_NAME            => 'ResFinder_v2.pl';

use constant PROGRAM_NAME_LONG       => 'Findes antimicrobial resitance genes for a sequence or genome';

use constant VERSION                 => '2.1';

use constant VERSION                 => '2.3';



#Global variables

my $BLAST;
@@ -465,7 +465,7 @@ foreach my $element(@Antimicrobial){ 
        my $Seqs_genome_ref = grep_ids(-seqs => $Seqs_input, -ids => \@array_for_getting_genome_seq);  

        for (@{ $Seqs_genome_ref }) {

          my $contig = lc($_->seq);

          my $length_contig = length($contig);  #Redundant, da jeg ogsΠv.h.a. bioperl finder hit length

          my $length_contig = length($contig);  #Redundant, da jeg ogs� v.h.a. bioperl finder hit length

          

          # Getting the right sub_contig depends on which strand the hit is on

          # If the hit is on the +1
@@ -490,7 +490,7 @@ foreach my $element(@Antimicrobial){ 
                $variant = 4;

                $major_variants_detector = 1;

                $sub_contig = substr($contig, 0,  ( $HIT_START{$data} + (($QUERY_LENGTH{$data} + $no_gaps_gene) - $QUERY_START{$data})));

                #If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||Ê|||Ê||") should be preceeded by spaces

                #If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||�|||�||") should be preceeded by spaces

                $spaces_hit = $QUERY_START{$data} - $HIT_START{$data} + 1;

                $spaces_match_string = $QUERY_START{$data};

              } else {
@@ -705,7 +705,7 @@ foreach my $element(@Antimicrobial){ 
                $variant = 4;

                $major_variants_detector = 1;

                $sub_contig = substr($contig, 0,  ( $HIT_START{$data} + (($QUERY_LENGTH{$data} + $no_gaps_gene) - $QUERY_START{$data})));

                # If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||Ê|||Ê||") should be preceeded by spaces

                # If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||�|||�||") should be preceeded by spaces

                $spaces_hit = $QUERY_START{$data} - $HIT_START{$data} + 1;

                $spaces_match_string = $QUERY_START{$data};

              }
@@ -860,7 +860,7 @@ foreach my $element(@Antimicrobial){ 
        #print $ABres_substr . "\n";

        push(@{$GENE_ALIGN_QUERY_HASH{$gene}}, $ABres_substr);

   

        #Printing spaces before the match string with the "||Ê||||Ê||Ê||" and the string itself

        #Printing spaces before the match string with the "||�||||�||�||" and the string itself

        #print "                   ";

        my $string_spaces = "";  #For saving the spaces as a string of spaces instead of a number of spaces

        for (my $i = 1 ; $i < $spaces_match_string; ++$i){
@@ -969,7 +969,7 @@ foreach my $key (sort keys %GENE_RESULTS_HASH2) { 
    $outStr = $outStr.": WARNING2, "; 

  }  

  $alignment .= $outStr."ID: ".@$array[1]."%, HSP/Length: ".@$array[3]."/".@$array[2]. ", Contig name: ".@$array[4].", Position: ".@$array[5]."\n\n";

  $hits_in_seq .= ">".$outStr."ID: ".@$array[1]."%, HSP/Length: ".@$array[3]."/".@$array[2]. ", Positions in reference: ".$qStart."..".$qEnd.", Contig name: ".@$array[4].", Position: ".@$array[5]."\n"; #mŒske forkert text

  $hits_in_seq .= ">".$outStr."ID: ".@$array[1]."%, HSP/Length: ".@$array[3]."/".@$array[2]. ", Positions in reference: ".$qStart."..".$qEnd.", Contig name: ".@$array[4].", Position: ".@$array[5]."\n"; #m�ske forkert text

  $resalign .= ">".@$array[7]."\n";

  

  # now print the alleles