Raw content of XrefParser::AnophelesSymbolParser package XrefParser::AnophelesSymbolParser; use strict; use File::Basename; use base qw( XrefParser::BaseParser ); # AnophelesSymbol database dump for anopheles - FASTA format # # >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, $description) = split /\|/, $header; # make sequence into one long string $sequence =~ s/\n//g; # build the xref object and store it $xref->{ACCESSION} = $accession; $xref->{LABEL} = $accession; $xref->{DESCRIPTION} = $description; $xref->{SEQUENCE} = $sequence; $xref->{SOURCE_ID} = $source_id; $xref->{SPECIES_ID} = $species_id; $xref->{SEQUENCE_TYPE} = 'peptide'; $xref->{STATUS} = 'experimental'; push @xrefs, $xref; } $file_io->close(); XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs); print scalar(@xrefs) . " AnophelesSymbol xrefs succesfully parsed\n" if($verbose); return 0; } 1;