debian/changelog

+resfinder (2.3.0-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille@debian.org>  Thu, 07 Jun 2018 21:55:00 +0200

debian/compat

+11

debian/control

+Source: resfinder
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/resfinder
+Vcs-Git: https://salsa.debian.org/med-team/resfinder.git
+Homepage: https://bitbucket.org/genomicepidemiology/resfinder
+
+Package: resfinder
+Architecture: any
+Depends: ${perl:Depends},
+         ${python:Depends},
+         ${misc:Depends},
+         bioperl,
+         ncbi-blast+-legacy
+Description: identifies acquired antimicrobial resistance genes
+ ResFinder identifies acquired antimicrobial resistance genes in total or
+ partial sequenced isolates of bacteria.
+ .
+ ResFinder that uses BLAST for identification of acquired antimicrobial
+ resistance genes in whole-genome data. As input, the method can use both
+ pre-assembled, complete or partial genomes, and short sequence reads
+ from four different sequencing platforms. The method was evaluated on
+ 1862 GenBank files containing 1411 different resistance genes, as well
+ as on 23 de-novo-sequenced isolates.

debian/copyright

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: resfinder
+Source: https://bitbucket.org/genomicepidemiology/resfinder.git
+
+Files: *
+Copyright: 2012-2018 Ole Lund, Technical University of Denmark 
+License: Apache-2.0
+
+Files: debian/*
+Copyright: 2018 Andreas Tille <tille@debian.org>
+License: Apache-2.0
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems you can find the full text of the Apache-2.0
+ license at /usr/share/common-licenses/Apache-2.0.

debian/install

+*_DB	/usr/bin
+*.pl	/usr/bin

debian/lintian-overrides

+# see discussion on Debian Med mailing list
+#   https://lists.debian.org/debian-med/2018/06/msg00042.html
+# and following mails in thread
+resfinder: script-with-language-extension usr/bin/resfinder.pl

debian/rules

+#!/usr/bin/make -f
+
+%:
+	dh $@
+
+override_dh_auto_build:
+override_dh_auto_install:
+	echo "Upstream install target just fetches BioPerl which is now installed via Depends"

debian/source/format

+3.0 (quilt)

debian/upstream/metadata

+Reference:
+  Author: Ea Zankari and Henrik Hasman and Salvatore Cosentino and Martin Vestergaard and Simon Rasmussen and Ole Lund and Frank M. Aarestrup and Mette Voldby Larsen 
+  Title: Identification of acquired antimicrobial resistance genes
+  Journal: Journal of Antimicrobial Chemotherapy
+  Year: 2012
+  Volume: 67
+  Number: 11
+  Pages: 2640-4
+  DOI: 10.1093/jac/dks261
+  PMID: 22782487
+  URL: https://academic.oup.com/jac/article/67/11/2640/707208
+  eprint: https://academic.oup.com/jac/article-pdf/67/11/2640/2085909/dks261.pdf

debian/watch

+version=4
+
+https://bitbucket.org/genomicepidemiology/resfinder/downloads/?tab=tags .*/@ANY_VERSION@@ARCHIVE_EXT@
+
+#opts="mode=git,pretty=2.1+git%cd.%h" \
+#    https://bitbucket.org/genomicepidemiology/resfinder.git HEAD
+
+# In branches is totally different code ov not yet released Python code version 4.x
+# https://bitbucket.org/genomicepidemiology/resfinder/downloads/?tab=branches .*/@ANY_VERSION@@ARCHIVE_EXT@

resfinder.pl

@@ -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