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gpertea |
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#!/usr/bin/perl |
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use strict; |
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use Getopt::Std; |
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use LWP::Simple; |
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use FindBin;use lib $FindBin::Bin; |
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#use dbSession; |
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my $url='http://www.expasy.org/cgi-bin/lists?dbxref.txt'; |
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my $usage = qq/Usage: |
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dbxref2bcp.pl [-f <input_dbxref.txt>] |
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Parses the UniProt's dbxref.txt info preparing it for loading into geanno db, |
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table xrefdbs. The required data file is either given explicitely or |
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downloaded from the embedded url: |
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$url |
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/; |
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umask 0002; |
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getopts('f:') || die($usage."\n"); |
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my $file=$Getopt::Std::opt_f; |
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unless ($file) { |
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print STDERR "downloading file..\n"; |
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$file='dbxref_uniprot.txt'; |
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unlink($file); |
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die("Error: file $file already exists (couldn't remove!)\n") |
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if -f $file; |
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die "Error downloading with getstore()!\n" |
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if is_error(getstore($url, $file)); |
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die "Error: file $file is non-existent or zero size after retrieval!\n" |
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unless -s $file; |
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print STDERR "Download OK.\n"; |
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} |
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my @knowntags=('Abbrev', 'Name', 'Cat', 'LinkTp', 'Ref', 'Server', 'Db_URL', 'Note'); |
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# xrefdb name cat linktp linktp_info server db_url note |
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my %known; |
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@known{@knowntags}=(1) x scalar(@knowntags); |
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open(INF, $file) || die("Error opening file $file!\n"); |
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my ($curtag, $curval); |
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open(OUTF, '>xrefdbs.bcp') || die("Error creating file xrefdbs.bcp!\n"); |
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my %val; |
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while (<INF>) { |
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if (m/^$/) { |
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#end record |
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if ($curtag) { |
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storeCurVal(); |
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putValues(); |
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($curtag,$curval)=(undef,undef); |
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} |
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next; |
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} |
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if (m/^Abbrev:\s*(.+)/) { |
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($curtag, $curval)=('Abbrev',$1); |
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putValues(); |
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next; |
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} |
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next unless $curtag; |
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chomp; |
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if (m/^(\S+)\s*:(.+)/) { #new tag |
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my ($t, $v)=($1,$2); |
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die("Error: unrecognized tag $t at '$_'!\n") unless exists $known{$t} || $t eq 'AC'; |
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storeCurVal() unless $t eq 'AC'; |
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$curtag=$t; |
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$curval=$v; |
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if ($curtag eq 'LinkTp') { |
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if ($v=~m/^\s*(\w[\w ]+)\;\s+(\S.+)/) { |
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$curval=$1; |
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$val{$curtag}=$curval; |
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$curtag='linfo'; |
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$curval=$2; |
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} |
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} |
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} |
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elsif (m/^\s+(.+)/) { |
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my $vx=$1; |
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$vx=~s/^\s+//;$vx=~s/\s+$//; |
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$curval.=' '.$vx; |
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} |
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chomp; |
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} |
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storeCurVal() if ($curtag); |
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putValues(); |
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close(INF); |
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close(OUTF); |
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# map { print STDERR $_."\t".$known{$_}."\n" } @knowntags; |
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sub putValues { |
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return unless keys(%val); |
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my @vals = map { $val{$_} } @knowntags; |
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print OUTF join("\t",@vals)."\n"; |
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undef(%val); |
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} |
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sub storeCurVal { |
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$curval=~s/^\s+//; $curval=~s/\s+$//; |
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$val{$curtag}=$curval; |
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$known{$curtag}=length($curval) if $known{$curtag}<length($curval); |
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} |
