V1.0.4

.travis.yml

@@ -1,20 +1,37 @@
 sudo: required
-dist: trusty
+language: perl
+perl:
+  - "5.14"
+  - "5.20"
 
 env:
   global:
     - PERL_MM_USE_DEFAULT=1
-    - "PATH=$PATH:/hap1.1"
+    - "PATH=$PATH:$TRAVIS_BUILD_DIR:$TRAVIS_BUILD_DIR/hap1.1:/opt/ngs-tools/bin:$TRAVIS_BUILD_DIR/gfe_submission/bin"
+    - NXF_VER='0.22.4'
+    - NXF_OPTS='-Xms512M -Xmx2G'
 
 before_install:
   - sudo apt-get install -qyy openjdk-7-jre-headless perl-doc wget curl build-essential git libssl-dev
-  - cp docker/hap1.1.tar.gz .
+  - export RELEASE_TESTING=1 AUTOMATED_TESTING=1 AUTHOR_TESTING=1 HARNESS_OPTIONS=c HARNESS_TIMER=1
+  - cp docker/hap1.1.tar.gz docker/ngs-tools_1.9.deb .
+  - sudo dpkg --install ngs-tools_1.9.deb
+  - curl -fsSL get.nextflow.io | bash
   - tar -xvzf hap1.1.tar.gz
   - chmod a+x hap1.1/hap1.1.jar
   - wget http://www.clustal.org/omega/clustalo-1.2.3-Ubuntu-x86_64
   - mv clustalo-1.2.3-Ubuntu-x86_64 hap1.1/clustalo
   - chmod a+x hap1.1/clustalo
-  - sudo cpan YAML Plack Plack::Handler::Starman Template JSON Getopt::Long Data::Dumper LWP::UserAgent REST::Client Test::More 
-  - sudo cpan JSON::Schema::AsType Dancer Moose Math::Round File::Spec IO::Socket::SSL Net::SSLeay Dancer::Plugin::Swagger Log::Log4perl
+  - cd GFE_Submission
+  - cpanm --quiet --notest --installdeps .
+  - cpanm --quiet --notest Devel::Cover::Report::Coveralls
+  - cd ..
+  - mv -i GFE_Submission gfe_submission
+  - cd gfe_submission
 
-script: "./build.sh"
+script:
+    - PERL5OPT=-MDevel::Cover=-coverage,statement,branch,condition,path,subroutine prove -lrsv t
+    - cover
+
+after_success:
+    - cover -report coveralls

GFE_Submission/bin/fasta2gfe

@@ -0,0 +1,156 @@
+#!/usr/bin/env perl
+=head1 NAME
+
+    gfe-submission
+
+=head1 SYNOPSIS
+
+
+=head1 AUTHOR     Mike Halagan <mhalagan@nmdp.org>
+
+    Bioinformatics Scientist
+    3001 Broadway Stree NE
+    Minneapolis, MN 55413
+    ext. 8225
+
+=head1 DESCRIPTION
+
+
+=head1 CAVEATS
+
+
+=head1 LICENSE
+
+    Copyright (c) 2015 National Marrow Donor Program (NMDP)
+
+    This library is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published
+    by the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+
+    This library is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+    License for more details.
+
+    You should have received a copy of the GNU Lesser General Public License
+    along with this library;  if not, write to the Free Software Foundation,
+    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+
+    > http://www.gnu.org/licenses/lgpl.html
+
+=head1 VERSIONS
+
+    Version    Description              Date
+
+
+=head1 TODO
+
+
+=head1 SUBROUTINES
+
+=cut
+use strict;    # always
+use warnings;  # or else
+use FindBin;
+use Data::Dumper;
+use FindBin;
+use lib "$FindBin::Bin/../lib";
+use GFE;
+use GFE::Client;
+use GFE::Annotate;
+use vars qw($USAGE);
+BEGIN{
+
+    $| = 1;
+
+    $USAGE = 
+        qq{./gfe-submission [--fasta] [--uri] [--verbose] [--help]
+            -f/--fasta      Fasta file
+            -u/--uri        URI of feature service
+            -l/--locus      HLA-Locus
+            -v/--verbose    Flag for running in verbose
+            -h/--help
+        };
+
+}   
+use Getopt::Long;
+use Cwd;
+
+our($s_subject_id) = (undef);
+&GetOptions('subject|i=s' => \$s_subject_id );
+
+my $o_gfe = GFE->new();
+
+$o_gfe->verbose(1);
+$o_gfe->return_structure(0);
+
+my %h_seqs;
+my $s_header;
+my $s_seq;
+while (<>) {
+    chomp;
+    if ($_ =~ />/) {
+        if ($s_seq) {    
+            $h_seqs{$s_header} = $s_seq;
+        }              
+        $s_header = $_;
+        $s_header =~ s/^>//; # remove ">"
+        $s_header =~ s/\s+$//; # remove trailing whitespace
+        $s_seq = ""; # clear out old sequence
+    }else {    
+        s/\s+//g; # remove whitespace
+        $s_seq .= $_; # add sequence
+    }
+}
+
+if ($s_seq) { # handle last sequence
+    $h_seqs{$s_header} = $s_seq;
+}
+
+my $s_out_file = $s_subject_id.".txt";
+open(my $fh,">",$s_out_file) or die "CANT OPEN FILE $! $0";
+foreach my $s_typing (keys %h_seqs){
+    $s_typing =~ /(HLA-\D{1,3}\d{0,1})\|/;
+    my $s_locus = $1;
+    $s_locus =~ s/\|//g;
+    next if(!defined $s_locus || $s_locus !~ /\S/);
+    my $rh_gfe = $o_gfe->getGfe($s_locus,$h_seqs{$s_typing});
+    my $s_gfe  = defined $$rh_gfe{gfe} ? $$rh_gfe{gfe} : '';
+    next if !defined $s_gfe || $s_gfe !~ /\S/;
+    my $n_seq  = length($h_seqs{$s_typing});
+    print $fh join(",",$s_subject_id,$s_typing,$s_locus,$s_gfe,$n_seq),"\n";
+}
+close $fh;
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GFE_Submission/bin/gfe_test.pl

@@ -1,46 +1,140 @@
 #!/usr/bin/env perl
-use strict;
-use warnings;
+=head1 NAME
+
+    gfe-submission
+
+=head1 SYNOPSIS
+
+
+=head1 AUTHOR     Mike Halagan <mhalagan@nmdp.org>
+
+    Bioinformatics Scientist
+    3001 Broadway Stree NE
+    Minneapolis, MN 55413
+    ext. 8225
+
+=head1 DESCRIPTION
+
+
+=head1 CAVEATS
+
+
+=head1 LICENSE
+
+    Copyright (c) 2015 National Marrow Donor Program (NMDP)
+
+    This library is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published
+    by the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+
+    This library is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+    License for more details.
+
+    You should have received a copy of the GNU Lesser General Public License
+    along with this library;  if not, write to the Free Software Foundation,
+    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+
+    > http://www.gnu.org/licenses/lgpl.html
+
+=head1 VERSIONS
+
+    Version    Description              Date
+
+
+=head1 TODO
+
+
+=head1 SUBROUTINES
+
+=cut
+use strict;    # always
+use warnings;  # or else
+use FindBin;
 use Data::Dumper;
-use Getopt::Long;
 use FindBin;
 use lib "$FindBin::Bin/../lib";
 use GFE;
 use GFE::Client;
 use GFE::Annotate;
 
-# my $o_client = GFE::Client->new();
-
-# my $s_seq = $o_client->getSequence("HLA-A","exon",1,1);
-# print STDERR $s_seq,"\n";
 
 my $o_gfe  = GFE->new();
-
 $o_gfe->verbose(1);
 $o_gfe->return_structure(0);
-# my $rh_gfe = $o_gfe->getGfe("HLA-A","TCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCGGGGGCGCAGGTCAGGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCTGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGTCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATGAGGCGGAGCAGTTGAGAGCCTACCTGGATGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTGTAGATCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCACCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAATCTCTGAAGGAGTGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGACACCGGCAGCAGCCTTGGGCCCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTGAGTCCAGCACTTCTGAGTCCCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTTCTCAGGGAATAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGTGTCCTGTCCATTCTCAAGATGGCCACATGCGTGCTGGTGGAGTGTCCCATGACAGATGCAAAATGCCTGAATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTCTGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCGTCCACAATCATGGGCCTACCCAGTCTGGGCCCCGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCTCACAGATAGAAAAGGAGGGAGTTACACTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCTCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTTTTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCCCTCACAGCTTGTAAAGGTGAGAGCTTGGAGGACCTAATGTGTGTTGGGTGTTGGGCGGAACAGTGGACACAGCTGTGCTATGGGGTTTCTTTGCATTGGATGTATTGAGCATGCGATGGGCTGTTTAAGGTGTGACCCCTCACTGTGATGGATATGAATTTGTTCATGAATATTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAG");
 
-# print Dumper($rh_gfe),"\n";
+my $s_path = `echo \$PATH`;chomp($s_path);
+foreach my $s_p (split(/:/,$s_path)){
+    print STDERR "PATH: ".$s_p,"\n";
+}
+
+my $s_hml   = "$FindBin::Bin/../t/resources/hmltest1.HML";
+my $rh_gfe  = $o_gfe->getGfeHmlNextflow($s_hml);
+print STDERR "gfe_test.pl output:",Dumper($rh_gfe),"\n";
+# my %h_seqs;
+# my $s_header;
+# my $s_seq;
+# while (<>) {
+#     chomp;
+#     if ($_ =~ />/) {
+#         if ($s_seq) {    
+#             $h_seqs{$s_header} = $s_seq;
+#         }              
+#         $s_header = $_;
+#         $s_header =~ s/^>//; # remove ">"
+#         $s_header =~ s/\s+$//; # remove trailing whitespace
+#         $s_seq = ""; # clear out old sequence
+#     }else {    
+#         s/\s+//g; # remove whitespace
+#         $s_seq .= $_; # add sequence
+#     }
+# }
+
+# if ($s_seq) { # handle last sequence
+#     $h_seqs{$s_header} = $s_seq;
+# }
+
+# foreach my $s_typing (keys %h_seqs){
+#   $s_typing =~ /(HLA-\D+\d{0,1})\*/;
+#   my $s_locus = $1;
+#   next if(!defined $s_locus || $s_locus !~ /\S/);
+#   my $rh_gfe = $o_gfe->getGfe($s_locus,$h_seqs{$s_typing});
+#   my $s_gfe  = defined $$rh_gfe{gfe} ? $$rh_gfe{gfe} : '';
+#   my $n_seq  = length($h_seqs{$s_typing});
+#   print join(",",$s_locus,$s_typing,$n_seq,$s_gfe),"\n";
+# }
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-my $s_fasta_file = "t/resources/HmlTest.HML";
-#my $s_fasta_file = "t/resources/FastaTest.fasta";
 
-my $rh_gfe2 = $o_gfe->getGfeHml($s_fasta_file);
-#my $rh_gfe2 = $o_gfe->getGfeFasta("HLA-A",$s_fasta_file);
-print Dumper($rh_gfe2),"\n";
 
 
-# my $o_annotate = GFE::Annotate->new();
-# $o_annotate->setFasta("HLA-A",$s_fasta_file);
 
 
-# my $s_file = (split(/\//,$s_fasta_file))[  scalar( @{[ $s_fasta_file=~/\//gi ]} ) ];
-# my $s_pref = (split(/\//,$s_file))[0];
-# $o_annotate->fasta($s_fasta_file);
-# $o_annotate->fileId($s_pref);
 
-# print Dumper($o_annotate),"\n";