Raw content of XrefParser::JGI_Parser
<![CDATA[package XrefParser::JGI_Parser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
# JGI protein file with gene predictons - FASTA FORMAT
#
#
# This is the parser that provides most functionality, subclasses
# (JGI_ProteinParser) just set sequence type)
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];
my $source_name = $self->get_source_name_for_source_id ($source_id) ;
# the source name defines how to parse the header
# different formats for different sources (all have entries in external_db.txt and populate_metadata.sql )
#
#
# SOURCES : cint_jgi_v1 AND cint_aniseed_jgi_v1
# -------------------------------------------------
#
# filename : ciona.prot.fasta
# >ci0100130001
# MLPIVDFKQCRPSVEASDKEINETAKLLVDALSTVGFAYLKNCGIKKNCRRSQKHRG*MGGVRYLYYPPI
# RVNIPDDEVKRNSIRRSIGYFVFPDDDVVINQPLQFKGDADVPDPVKDPITALKYIQQKLSHTCQNT*
#
#
#
# SOURCES : cint_jgi_v2 && cint_aniseed_jgi_v2
# ------------------------------------------------
#
# filename : FM1.aa.fasta
# >jgi|Cioin2|201001|fgenesh3_pm.C_chr_01p000019
# MQQQQQDDLVVKLVLVGDGGVGKTTFVKRHLTGEFEKKYVATLGVEVHPIVFQTQRGRIRFNVWDTAGQE
# DEDDDL*
#
my @xrefs;
local $/ = "\n>";
my $file_io = $self->get_filehandle($file);
if ( !defined $file_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 is an error
}
while ( $_ = $file_io->getline() ) {
next if (/^File:/); # skip header
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
my @attr = split/\|/, $header ;
my $acession = $header ;
# split header in different ways according to source name :
my ( $version,$label ) ;
if ($source_name=~m/cint_jgi_v1/) {
# header format is >ci0100146277
# we want 146277
($acession = $header) =~s/\w{6}//;
$version = "JGI 1.0" ;
} elsif ($source_name=~m/cint_aniseed_jgi_v1/) {
# header format is >ci0100146277, we want this
$version = "JGI 1.0" ;
} elsif ($source_name=~m/cint_jgi_v2/) {
$acession = $attr[2] ;
$version = "JGI 2.0" ;
$label = $attr[3] ;
} elsif ($source_name=~m/cint_aniseed_jgi_v2/) {
my $aniseed_prefix = "ci0200" ;
$acession = $aniseed_prefix . $attr[2] ;
$version = "JGI 2.0" ;
}else {
print STDERR "WARNING : The source-name specified in the populate_metatable.sql file is\n" .
"WARNING : not matching the differnt cases specified in JGI_Parser.pm - plese\n" .
"WARNING : edit the parser \n" ;
return 1;
}
#print "ACCESSION $acession\n" ;
# make sequence into one long string
$sequence =~ s/\n//g;
# build the xref object and store it
$xref->{ACCESSION} = $acession;
$xref->{LABEL} = $acession;
$xref->{SEQUENCE} = $sequence;
$xref->{SOURCE_ID} = $source_id;
$xref->{SPECIES_ID} = $species_id;
$xref->{SEQUENCE_TYPE} = $self->get_sequence_type();
$xref->{STATUS} = 'experimental';
# pull cg_name from peptide files as well and create dependent xrefs
# if ($self->get_sequence_type() =~ /peptide/) {
# my ($cg_name) = $cg =~ /cg_name=(.*)/;
# my %dep;
# $dep{SOURCE_NAME} = 'JGI__Gene';
# $dep{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
# $dep{SOURCE_ID} = $celera_gene_source_id;
# $dep{ACCESSION} = $cg_name;
# push @{$xref->{DEPENDENT_XREFS}}, \%dep; # array of hashrefs
# }
#
push @xrefs, $xref;
}
$file_io->close();
print scalar(@xrefs) . " JGI_ xrefs succesfully parsed\n" if($verbose);
XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
return 0; # successful
}
sub new
{
my $proto = shift;
my $self = $proto->SUPER::new(@_);
return $self;
}
1;
]]>