| 1 |
#!/usr/bin/perl |
| 2 |
use strict; |
| 3 |
use Getopt::Std; |
| 4 |
use LWP::Simple; |
| 5 |
use FindBin;use lib $FindBin::Bin; |
| 6 |
#use dbSession; |
| 7 |
my $url='http://www.expasy.org/cgi-bin/lists?dbxref.txt'; |
| 8 |
my $usage = qq/Usage: |
| 9 |
dbxref2bcp.pl [-f <input_dbxref.txt>] |
| 10 |
|
| 11 |
Parses the UniProt's dbxref.txt info preparing it for loading into geanno db, |
| 12 |
table xrefdbs. The required data file is either given explicitely or |
| 13 |
downloaded from the embedded url: |
| 14 |
$url |
| 15 |
/; |
| 16 |
|
| 17 |
umask 0002; |
| 18 |
getopts('f:') || die($usage."\n"); |
| 19 |
my $file=$Getopt::Std::opt_f; |
| 20 |
unless ($file) { |
| 21 |
print STDERR "downloading file..\n"; |
| 22 |
$file='dbxref_uniprot.txt'; |
| 23 |
unlink($file); |
| 24 |
die("Error: file $file already exists (couldn't remove!)\n") |
| 25 |
if -f $file; |
| 26 |
die "Error downloading with getstore()!\n" |
| 27 |
if is_error(getstore($url, $file)); |
| 28 |
die "Error: file $file is non-existent or zero size after retrieval!\n" |
| 29 |
unless -s $file; |
| 30 |
print STDERR "Download OK.\n"; |
| 31 |
} |
| 32 |
|
| 33 |
my @knowntags=('Abbrev', 'Name', 'Cat', 'LinkTp', 'Ref', 'Server', 'Db_URL', 'Note'); |
| 34 |
# xrefdb name cat linktp linktp_info server db_url note |
| 35 |
my %known; |
| 36 |
@known{@knowntags}=(1) x scalar(@knowntags); |
| 37 |
|
| 38 |
open(INF, $file) || die("Error opening file $file!\n"); |
| 39 |
|
| 40 |
my ($curtag, $curval); |
| 41 |
open(OUTF, '>xrefdbs.bcp') || die("Error creating file xrefdbs.bcp!\n"); |
| 42 |
|
| 43 |
my %val; |
| 44 |
while (<INF>) { |
| 45 |
if (m/^$/) { |
| 46 |
#end record |
| 47 |
if ($curtag) { |
| 48 |
storeCurVal(); |
| 49 |
putValues(); |
| 50 |
($curtag,$curval)=(undef,undef); |
| 51 |
} |
| 52 |
next; |
| 53 |
} |
| 54 |
if (m/^Abbrev:\s*(.+)/) { |
| 55 |
($curtag, $curval)=('Abbrev',$1); |
| 56 |
putValues(); |
| 57 |
next; |
| 58 |
} |
| 59 |
next unless $curtag; |
| 60 |
chomp; |
| 61 |
if (m/^(\S+)\s*:(.+)/) { #new tag |
| 62 |
my ($t, $v)=($1,$2); |
| 63 |
die("Error: unrecognized tag $t at '$_'!\n") unless exists $known{$t} || $t eq 'AC'; |
| 64 |
storeCurVal() unless $t eq 'AC'; |
| 65 |
$curtag=$t; |
| 66 |
$curval=$v; |
| 67 |
if ($curtag eq 'LinkTp') { |
| 68 |
if ($v=~m/^\s*(\w[\w ]+)\;\s+(\S.+)/) { |
| 69 |
$curval=$1; |
| 70 |
$val{$curtag}=$curval; |
| 71 |
$curtag='linfo'; |
| 72 |
$curval=$2; |
| 73 |
} |
| 74 |
} |
| 75 |
} |
| 76 |
elsif (m/^\s+(.+)/) { |
| 77 |
my $vx=$1; |
| 78 |
$vx=~s/^\s+//;$vx=~s/\s+$//; |
| 79 |
$curval.=' '.$vx; |
| 80 |
} |
| 81 |
chomp; |
| 82 |
} |
| 83 |
|
| 84 |
storeCurVal() if ($curtag); |
| 85 |
putValues(); |
| 86 |
|
| 87 |
close(INF); |
| 88 |
close(OUTF); |
| 89 |
|
| 90 |
# map { print STDERR $_."\t".$known{$_}."\n" } @knowntags; |
| 91 |
|
| 92 |
sub putValues { |
| 93 |
return unless keys(%val); |
| 94 |
my @vals = map { $val{$_} } @knowntags; |
| 95 |
print OUTF join("\t",@vals)."\n"; |
| 96 |
undef(%val); |
| 97 |
} |
| 98 |
|
| 99 |
sub storeCurVal { |
| 100 |
$curval=~s/^\s+//; $curval=~s/\s+$//; |
| 101 |
$val{$curtag}=$curval; |
| 102 |
$known{$curtag}=length($curval) if $known{$curtag}<length($curval); |
| 103 |
} |
