From 54966aa4cb100cac0726b353d583d05c4b382696 Mon Sep 17 00:00:00 2001
From: Karyn Megy <kmegy@sanger.ac.uk>
Date: Wed, 5 Jul 2006 16:46:44 +0000
Subject: [PATCH] New parser for AedesGenBank xrefs
---
.../XrefParser/AedesGenBankParser.pm | 95 +++++++++++++++++++
1 file changed, 95 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
new file mode 100644
index 0000000000..5769b8da38
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
@@ -0,0 +1,95 @@
+package XrefParser::AedesGenBankParser;
+
+use strict;
+use File::Basename;
+
+use XrefParser::BaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+
+#Aedes GenBank protein - because not yet in UniProt
+#>EAT48991.1
+#MGKSKAHRIKGLTGPKMSLGDQITEGRVSKKPKAPKIRLRAEEEEFVDSRTTKKILQQAR
+#KQQAELNLLDDSFGPSLAESAAAASVGKRRHRLGDAASSDESDEEYREEADVDGQDFFDD
+#IKINEEDERALEMFQNKDGVKTRTLADLIMDKITEKQTEIQTQFSDTGSLKMEEIDPRVR
+
+sub run {
+
+ my ($self, $file, $source_id, $species_id) = @_;
+ my $cpt = 0 ;
+
+ next if (/^File:/); # skip header
+
+ my @xrefs;
+
+ local $/ = "\n>";
+
+ if(!open(FILE,"<".$file)){
+ print "Could not open $file\n";
+ return 1;
+ }
+ while (<FILE>) {
+
+ my $xref;
+
+ my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
+ #print "My header is -$header-\n" ;
+ #print "My sequence is -$sequence-\n" ;
+
+ if ($header eq "") {
+ $header = "Aedes_GenBank".$cpt ;
+ print STDERR "One sequence with a random name ... \n" ;
+ $cpt++ ;
+ }
+
+ # deconstruct header - just use first part
+ #my ($accession, $description) = split /\|/, $header; #if description
+ my $accession = $header; #if no description
+
+
+
+ # make sequence into one long string
+ $sequence =~ s/\n//g;
+
+ # build the xref object and store it
+ #print "ACCESSION & LABEL are $accession\n" ;
+ #print "SEQUENCE is $sequence\n" ;
+ #print "SOURCE_ID is $source_id\n" ;
+ #print "SPECIES_ID is $species_id\n" ;
+ #print "SEQUENCE_TYPE is peptide!\n";
+ #print "STATUS is experimental!\n" ;
+
+ $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;
+
+ }
+
+ close (FILE);
+
+ print scalar(@xrefs) . " AedesGenBank xrefs succesfully parsed\n";
+
+ XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
+
+ print "Done\n";
+ return 0;
+}
+
+
+sub new {
+
+ my $self = {};
+ bless $self, "XrefParser::AedesGenBankParser";
+ return $self;
+
+}
+
+1;
--
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