libgenome-model-tools-music-perl 0.04-3 / usr / share / perl5 / Genome / Model / Tools / Music / Pfam.pm

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package Genome::Model::Tools::Music::Pfam;

use warnings;
use strict;
use Genome;
use IO::File;
use IPC::Cmd qw/can_run/;

our $VERSION = $Genome::Model::Tools::Music::VERSION;

class Genome::Model::Tools::Music::Pfam {
    is => 'Genome::Model::Tools::Music::Base',
    has_input => [
        maf_file => {
            is => 'Text', is_input => 1,
            doc => "List of mutations using TCGA MAF specification v2.3",
        },
        output_file => {
            is => 'Text', is_output => 1,
            doc => "Output MAF file with an extra column that reports Pfam annotation domains",
        },
        reference_build => {
            is => 'Text', default => 'Build37',
            doc => "Options are 'Build36' or 'Build37'. This parameter ensures appropriate annotation of domains",
            valid_values => ['Build36', 'Build37'],
       },
    ],
    doc => "Add Pfam annotation to a MAF file",
};

sub help_synopsis {
    return <<EOS
 ... music pfam \\
        --maf-file myMAF.tsv \\
        --output-file myMAF.tsv.pfam
EOS
}

sub help_detail {
    return <<EOS
This command adds Pfam Domains to a column at the end of a MAF file.

This tool takes a MAF file, determines the location of each variant therein, and then uses a fast-lookup to retrieve all of the Pfam annotation domains that the variant crosses. A column is appended to the end of the input MAF file called "Pfam_Annotation_Domains" where the results are listed. "NA" is listed if no Pfam domains are found.
EOS
}

sub _doc_authors {
    return " Nathan D. Dees, Ph.D.";
}

sub _doc_credits {
    return <<EOS,
This tool uses tabix, by Heng Li.  See http://samtools.sourceforge.net/tabix.shtml.

This tool also depends on copies of data from the following databases, packaged in a form useable for quick analysis:

 * Pfam - http://pfam.sanger.ac.uk/
 * SMART - http://smart.embl-heidelberg.de/
 * SUPERFAMILY - http://supfam.cs.bris.ac.uk/SUPERFAMILY/
 * PatternScan - http://www.expasy.ch/prosite/
EOS
}

sub execute {

    #parse input arguments
    my $self = shift;
    my $maf_file = $self->maf_file;
    my $reference_build = $self->reference_build;
    my $output_file = $self->output_file;

    #parse the MAF file and output a new MAF with Pfam info appended
    my $maf_fh = IO::File->new( $maf_file ) or die "Couldn't open MAF file!\n";
    my $out_fh = IO::File->new( $output_file, ">" )or die "Couldn't open $output_file for writing!\n";
    while( my $line = $maf_fh->getline ) {

        chomp $line;
        my @cols = split( /\t/, $line );
        my ( $chr, $start, $stop ) = @cols[4..6];

        #print out any headers directly to the output file
        if( $line =~ m/^(#|Hugo_Symbol)/ ) {
            $out_fh->print( $line );
            $out_fh->print(( $line =~ m/^Hugo_Symbol/ ) ? "\tPfam_Annotation_Domains\n" : "\n" );
            next;
        }

        #construct a tabix command
        my $db_path = Genome::Sys->dbpath( 'pfam', 'latest' ) or die "Cannot find the pfam db path.";
        my $tabix = can_run( 'tabix' ) or die "Cannot find the tabix command. It can be obtained from http://sourceforge.net/projects/samtools/files/tabix";
        my $tabix_cmd = "$tabix";
        if( $reference_build eq 'Build36' ) {
            $tabix_cmd .= " $db_path/pfam.annotation.build36.gz $chr:$start-$stop - |";
        }
        elsif( $reference_build eq 'Build37' ) {
            $tabix_cmd .= " $db_path/pfam.annotation.build37.gz $chr:$start-$stop - |";
        }
        else {
            die "Please specify either 'Build36' or 'Build37' for the --reference-build parameter.";
        }

        #run tabix command
        my %domains;
        open( TABIX, $tabix_cmd ) or die "Cannot run 'tabix'. Please check it is in your PATH. It can be installed from the samtools project. $!";
        while( my $tabline = <TABIX> ) {
            chomp $tabline;
            my ( undef, undef, undef, $csv_domains ) = split( /\t/, $tabline );
            my @domains = split( /,/, $csv_domains );
            for my $domain ( @domains ) {
                $domains{$domain}++;
            }
        }
        close(TABIX);

        #print output to new file
        my $all_domains = join( ",", sort keys %domains );
        my $output_line = "$line\t";
        unless( $all_domains eq "" ) {
            $output_line .= "$all_domains\n";
        }
        else {
            $output_line .= "NA\n";
        }
        $out_fh->print( $output_line );
    }

    return( 1 );
}

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