Commit e58730a7 authored by Karyn Megy's avatar Karyn Megy
Browse files

New Xrefs parser for Aedes aegypti (CAP annotation)

parent 96d75e7d
package XrefParser::AedesCAPParser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
# Aedes CAP database dump - FASTA format
# >...
#
#
#
# Anopheles one:
# >ANXB10B|Annexin B10B
# MSWYYTPHPTVVPAEDFDASADANALRKAMKGFGTDEQAIIDILCARSNGQRQEIAEAFKRELGRDLIDDLKSELGGKFEDVILGLMLRPEAYLCKQLHKAMDGIGTDEKSLIEII
# CPQTNDQIRAIVDCYEEMYSRPLAEHLCSETSGSFRRLLTMIIVGSRDPQGTVDPELAVEQAKQLYDAGEGKLGTDEEVFYKILAHASFDQLEIVFEEYKSLSGRTIEQALKAELS
# GELYDALSAIVECVQMAPHFFAKRLHKAMDGVGTDDATLIRIIVSRSEIDLQNIKDEFEQMYNKTLVSAVRSETSGDYKRALCALIGNA
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files = shift;
my $release_file = shift;
my $verbose = shift;
my $file = @{$files}[0];
next if (/^File:/); # skip header
my @xrefs;
local $/ = "\n>";
my $file_io = $self->get_filehandle($file);
if ( !defined $file_io ) {
print STDERR "Could not open $file\n";
return 1;
}
while ( $_ = $file_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
# deconstruct header - just use first part
my ($accession, $symbol, $description, $chr, $start, $end) = split /\|/, $header;
if ($symbol eq "") { $symbol = "$accession" ; }
# make sequence into one long string
$sequence =~ s/\n//g;
# build the xref object and store it
$xref->{ACCESSION} = $accession;
$xref->{LABEL} = $symbol;
$xref->{DESCRIPTION} = $description;
$xref->{SEQUENCE} = $sequence;
$xref->{SOURCE_ID} = $source_id;
$xref->{SPECIES_ID} = $species_id;
$xref->{SEQUENCE_TYPE} = 'peptide';
$xref->{STATUS} = 'manual annotation';
push @xrefs, $xref;
}
$file_io->close();
XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
print scalar(@xrefs) . " Aedes CAP xrefs succesfully parsed\n" if($verbose);
return 0;
}
1;
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