Merge pull request #33 from mhalagan-nmdp/hackathon-updates

Hackathon updates

.travis.yml

@@ -8,26 +8,26 @@ perl:
 env:
   global:
     - PERL_MM_USE_DEFAULT=1
-    - "PATH=$PATH:$TRAVIS_BUILD_DIR:$TRAVIS_BUILD_DIR/hap1.1:/opt/ngs-tools/bin:$TRAVIS_BUILD_DIR/gfe_submission/bin"
+    - "PATH=$PATH:$TRAVIS_BUILD_DIR:$TRAVIS_BUILD_DIR/hap1.2:/opt/ngs-tools/bin:$TRAVIS_BUILD_DIR/gfe_submission/bin"
     - NXF_VER='0.22.4'
     - NXF_OPTS='-Xms512M -Xmx2G'
 
 cache:
   directories:
   - perl_modules
-  - $TRAVIS_BUILD_DIR/hap1.1
+  - $TRAVIS_BUILD_DIR/hap1.2
 
 before_install:
   - sudo apt-get install -qyy openjdk-7-jre-headless perl-doc wget curl build-essential git libssl-dev
   - 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 .
+  - cp docker/hap1.2.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
+  - tar -xvzf hap1.2.tar.gz
+  - chmod a+x hap1.2/hap1.2.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
+  - mv clustalo-1.2.3-Ubuntu-x86_64 hap1.2/clustalo
+  - chmod a+x hap1.2/clustalo
   - cd GFE_Submission
   - cpanm --quiet --notest --installdeps .
   - cpanm --quiet --notest Devel::Cover::Report::Coveralls

GFE_Submission/bin/app.pl

@@ -52,8 +52,8 @@ =head1 LICENSE
        $tokens->{'login_url'}         = uri_for('/login');
        $tokens->{'logout_url'}        = uri_for('/logout');
        $tokens->{'upload_url'}        = uri_for('/upload');
-       $tokens->{'gfe_url'}           = uri_for('/gfe');
-       $tokens->{'ars_reduxfile_url'} = uri_for('/gfe');
+       $tokens->{'gfe_url'}           = uri_for('/gfe_gui');
+       $tokens->{'ars_reduxfile_url'} = uri_for('/gfe_gui');
 };
 
 dance;

GFE_Submission/bin/breakup-fasta

@@ -0,0 +1,150 @@
+#!/usr/bin/env perl
+=head1 NAME
+
+    breakup-fasta
+
+=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) 2016 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 vars qw($USAGE);
+BEGIN{
+
+    $| = 1;
+
+    $USAGE = 
+        qq{./breakup-fasta [--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 Cwd;
+use Math::Round;
+my $n_id = getID();
+
+
+my %h_seqs;
+my $s_header;
+my $s_seq;
+while (<>) {
+    chomp;
+    if ($_ =~ />/) {
+        if ($s_seq) {    
+            $h_seqs{$s_header} = $s_seq;
+            my $s_out_file = $n_id.".txt";
+            open(my $fh,">",$s_out_file) or die "CANT OPEN FILE $! $0";
+            print $fh ">".$s_header."\n";
+            print $fh $s_seq."\n";
+            close $fh;
+            $n_id = getID();
+        }              
+        $s_header = $_;
+        $s_header =~ s/^>//; # remove ">"
+        $s_header =~ s/\s+$//; # remove trailing whitespace
+        if($s_header =~ m/ (\D{1,3}\d{0,1}\*\S+) /){
+            $s_header = "HLA-".$1;
+        }
+        $s_seq = ""; # clear out old sequence
+    }else {    
+        s/\s+//g; # remove whitespace
+        $s_seq .= $_; # add sequence
+    }
+}
+
+if ($s_seq) { # handle last sequence
+    my $s_out_file = $n_id.".txt";
+    open(my $fh,">",$s_out_file) or die "CANT OPEN FILE $! $0";
+    print $fh ">".$s_header."\n";
+    print $fh $s_seq."\n";
+    close $fh;
+}
+
+
+sub getID{
+    my $id = int(rand(10000));
+    my $s_out_file = $id.".txt";
+    if(!-e $s_out_file){
+        return $id;
+    }else{
+        return getID();
+    }
+}
+
+
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+

GFE_Submission/bin/fasta.nf

@@ -0,0 +1,80 @@
+#!/usr/bin/env nextflow
+
+params.fasta         = ""
+params.output        = ""
+params.name          = ""
+outputDir            = file("${params.output}")
+
+// Extracting consensus sequences
+process extractConsensus{
+
+  tag{ expected }
+
+  input:
+    set file(expected) from file("${params.fasta}")
+
+  output:
+    set file('*.txt') into fastaFiles mode flatten
+
+  """
+    breakup-fasta < ${expected}
+  """
+}
+
+
+//Get GFE For each sequence
+process getGFE{
+  errorStrategy 'ignore'
+
+  tag{ fastafile }
+
+  input:
+    set file(fastafile) from fastaFiles
+
+  output:
+    set file {"*.txt"}  into gfeResults mode flatten
+
+  """
+    cat ${fastafile} | fasta2structure
+  """
+}
+
+gfeResults
+.collectFile() {  gfe ->
+       [ "${params.name}.txt", gfe.text ]
+   }
+.subscribe { file -> copyToFailedDir(file) }
+
+
+//Copy file to output directory
+def copyToFailedDir (file) { 
+  log.info "Copying ${file.name} into: $outputDir"
+  file.copyTo(outputDir)
+  def copiedFile = new File( "${params.output}/${file.name}" )
+  log.info copiedFile.name
+  if( !copiedFile.exists() ) {
+    log.info "Failed to copy file copiedFile.name ${file.name} into: $outputDir"
+  }else{
+    log.info "Copied $copiedFile ${file.name} into: $outputDir"
+  }
+}
+
+//Get subject id from fasta file
+def subjectId(Path path) {
+  def name      = path.getFileName().toString()
+  def subject   = name.split('_')
+  return subject[0]
+}
+
+//Get subject id from fasta file
+def blastSubjectId(Path path) {
+  def fileName  = path.getFileName().toString()
+  def subject   = fileName.split('.txt')
+  return subject[0]
+}
+
+
+
+
+
+