From e58730a7dc8b66b268af922c5f9b7e744cc31f7a Mon Sep 17 00:00:00 2001
From: Karyn Megy <kmegy@sanger.ac.uk>
Date: Fri, 11 Dec 2009 13:00:08 +0000
Subject: [PATCH] New Xrefs parser for Aedes aegypti (CAP annotation)
---
.../xref_mapping/XrefParser/AedesCAPParser.pm | 82 +++++++++++++++++++
1 file changed, 82 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm b/misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm
new file mode 100644
index 0000000000..33e72cefbb
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm
@@ -0,0 +1,82 @@
+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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