Merge pull request #24 from cancerit/dev

Merge for release

perl/MANIFEST

@@ -20,14 +20,14 @@ docs/pod_html/CN_to_VCF.html
 docs/pod_html/failed_cn_csv.html
 docs/pod_html/index.html
 docs/pod_html/Sanger/CGP/Ascat.html
-docs/reports_html/blib-lib-Sanger-CGP-Ascat-pm--subroutine.html
-docs/reports_html/blib-lib-Sanger-CGP-Ascat-pm.html
 docs/reports_html/common.js
 docs/reports_html/cover.css
 docs/reports_html/coverage.html
 docs/reports_html/css.js
 docs/reports_html/digests
 docs/reports_html/index.html
+docs/reports_html/lib-Sanger-CGP-Ascat-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-Ascat-pm.html
 docs/reports_html/standardista-table-sorting.js
 docs/reports_text/coverage.txt
 lib/Sanger/CGP/Ascat.pm
@@ -37,6 +37,7 @@ MANIFEST			This list of files
 perltidy.LOG
 share/ascat/ascat.R
 share/ascat/runASCAT.R
+share/gender/GRCh37d5_Y.loci
 t/1_pm_compile.t
 t/2_pl_compile.t
 t/CN_to_VCF.t

perl/MYMETA.json

@@ -4,7 +4,7 @@
       "unknown"
    ],
    "dynamic_config" : 0,
-   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560",
+   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690",
    "license" : [
       "agpl_3"
    ],
@@ -37,5 +37,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.4.1"
+   "version" : "v1.5.0"
 }

perl/MYMETA.yml

@@ -3,20 +3,20 @@ abstract: unknown
 author:
   - unknown
 build_requires:
-  ExtUtils::MakeMaker: 0
+  ExtUtils::MakeMaker: '0'
 configure_requires:
-  ExtUtils::MakeMaker: 0
+  ExtUtils::MakeMaker: '0'
 dynamic_config: 0
-generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560'
+generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690'
 license: open_source
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
-  version: 1.4
+  version: '1.4'
 name: AscatNgs
 no_index:
   directory:
     - t
     - inc
 requires:
-  Const::Fast: 0.014
-version: v1.4.1
+  Const::Fast: '0.014'
+version: v1.5.0

perl/bin/ascat.pl

@@ -130,16 +130,6 @@ sub setup {
   delete $opts{'index'} unless(defined $opts{'index'});
   $opts{'minbasequal'} = 20 unless(defined $opts{'minbasequal'});
 
-  if(defined $opts{'gender'}){
-    pod2usage(-message => 'unknown gender value: '.$opts{'gender'}, -verbose => 1) unless(first {$_ eq $opts{'gender'}} @VALID_GENDERS);
-    if($opts{'gender'} eq 'L') {
-      $opts{'gender'} = Sanger::CGP::Ascat::Implement::determine_gender(\%opts);
-    }
-  } else {
-    pod2usage(-message => 'gender not set', -verbose => 1);
-  }
-
-
   if(exists $opts{'process'}) {
     PCAP::Cli::valid_process('process', $opts{'process'}, \@VALID_PROCESS);
     if(exists $opts{'index'}) {
@@ -164,6 +154,15 @@ sub setup {
 
   $opts{'tmp'} = $tmpdir;
 
+  if(defined $opts{'gender'}){
+    pod2usage(-message => 'unknown gender value: '.$opts{'gender'}, -verbose => 1) unless(first {$_ eq $opts{'gender'}} @VALID_GENDERS);
+    if($opts{'gender'} eq 'L') {
+      $opts{'gender'} = Sanger::CGP::Ascat::Implement::determine_gender(\%opts);
+    }
+  } else {
+    pod2usage(-message => 'gender not set', -verbose => 1);
+  }
+
   return \%opts;
 }
 
@@ -206,8 +205,8 @@ =head1 SYNOPSIS
     -minbasequal  -q    Minimum base quality required before allele is used. [20]
     -cpus         -c    Number of cores to use. [1]
                         - recommend max 2 during 'input' process.
-    -locus        -l    Attempt to determine gender using a male specific locus.
-                          e.g. Y:2654896-2655740 (GRCh37)
+    -locus        -l    Using a list of loci, default when '-L' [share/gender/GRCh37d5_Y.loci]
+                        - these are loci that will not present at all in a female sample
     -force        -f    Force completion - solution not possible
                         - adding this will result in successful completion of analysis even
                           when ASCAT can't generate a solution.  A default copynumber of 5/2

perl/lib/Sanger/CGP/Ascat.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.4.1';
+our $VERSION = '1.5.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>

perl/lib/Sanger/CGP/Ascat/Implement.pm

@@ -247,7 +247,7 @@ sub _which {
   return $path;
 }
 
-sub determine_gender {
+sub OLD_determine_gender {
   my $options = shift;
   my $gender = 'XX';
   my $samtools = _which('samtools');
@@ -269,4 +269,57 @@ sub determine_gender {
   return $gender;
 }
 
+sub determine_gender {
+  my $options = shift;
+  my $gender_loci;
+  if(defined $options->{'locus'}) {
+    $gender_loci = $options->{'locus'};
+  }
+  else {
+    my $mod_path = dirname(abs_path($0)).'/../share';
+    $mod_path = module_dir('Sanger::CGP::Ascat::Implement') unless(-e File::Spec->catdir($mod_path, 'gender'));
+
+    my $gender_path = File::Spec->catdir($mod_path, 'gender');
+    $gender_loci = File::Spec->catfile($gender_path,'GRCh37d5_Y.loci');
+  }
+
+  my $command = _which('alleleCounter');
+  $command .= sprintf $ALLELE_COUNT_PARA, $options->{'tumour'}, File::Spec->catfile($options->{'tmp'}, 'tumour_gender.tsv'), $gender_loci;
+  $command .= '-m '.$options->{'minbasequal'} if exists $options->{'minbasequal'};
+  system($command);
+  my $tum_gender = _parse_gender_results(File::Spec->catfile($options->{'tmp'}, 'tumour_gender.tsv'));
+  $command = _which('alleleCounter');
+  $command .= sprintf $ALLELE_COUNT_PARA, $options->{'normal'}, File::Spec->catfile($options->{'tmp'}, 'normal_gender.tsv'), $gender_loci;
+  $command .= '-m '.$options->{'minbasequal'} if exists $options->{'minbasequal'};
+  system($command);
+  my $norm_gender = _parse_gender_results(File::Spec->catfile($options->{'tmp'}, 'normal_gender.tsv'));
+  if($tum_gender ne $norm_gender) {
+    die "Gender loci gacve incolclusive results see $options->{tmp}/*_gender.tsv";
+  }
+  return $tum_gender;
+}
+
+sub _parse_gender_results {
+  my $file = shift @_;
+  my $male_loci = 0;
+  my $total_loci = 0;
+  open my $fh, '<', $file;
+  while(my $line = <$fh>) {
+    next if($line =~ m/^#/);
+    chomp $line;
+    #CHR	POS	Count_A	Count_C	Count_G	Count_T	Good_depth
+    my ($chr, $pos, $a, $c, $g, $t, $depth) = split /\t/, $line;
+    # all we really care about is the depth
+    $male_loci++ if($depth > 5);
+    $total_loci++;
+  }
+  close $fh;
+  my $gender = 'XX';
+  if($male_loci/$total_loci >= 0.5) {
+    $gender = 'XY';
+  }
+  return $gender;
+}
+
+
 1;

perl/share/gender/GRCh37d5_Y.loci

@@ -0,0 +1,4 @@
+Y	4546684
+Y	2934912
+Y	4550107
+Y	4549638

prerelease.sh

@@ -45,7 +45,7 @@ echo '### Running perl tests ###'
 export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-ignore,'t/.*\.t'
 rm -rf docs
 mkdir -p docs/reports_text
-prove --nocolor -I lib t | sed 's/^/  /' # indent output of prove
+prove -w --nocolor -I lib t | sed 's/^/  /' # indent output of prove
 if [[ $? -ne 0 ]] ; then
   echo "\n\tERROR: TESTS FAILED\n"
   exit 1