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Updated cdd2cog.pl to work with 2014 version of COG #5

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Updated cdd2cog.pl to work with 2014 version of COG #5

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16 changes: 9 additions & 7 deletions cdd2cog/cdd2cog.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -299,7 +299,7 @@ =head1 LICENSE
}
$Skip = $line[0];

my $pssm_id = $1 if $line[1] =~ /^CDD\:(\d+)/; # get PSSM-Id from the subject hit
my $pssm_id = $1 if $line[1] =~ /^gnl\|CDD\|(\d+)/; # get PSSM-Id from the subject hit
my $cog = $CDDid{$pssm_id}; # get the COG# according to the PSSM-Id as listed in 'cddid.tbl'
$Cog_Stats{$cog}++; # increment hit-number for specific COG

Expand Down Expand Up @@ -388,7 +388,7 @@ sub parse_cdd_cog {
while (<$fun_fh>) {
chomp;
$_ =~ s/^\s*|\s+$//g; # get rid of all leading and trailing whitespaces
if (/^\[(\w)\]\s*(.+)$/) {
if (/^(\w)\s*(.+)$/) {
$Fun{$1} = {'desc' => $2, 'count' => 0}; # anonymous hash in hash
# $1 = single-letter functional category, $2 = description of functional category
# count used to find functional categories not present in the query proteins for final overall assignment statistics
Expand All @@ -400,13 +400,15 @@ sub parse_cdd_cog {
open (my $whog_fh, "<", "$Whog_File");
print "Parsing COGs '$Whog_File' file ...\n"; # status message
while (<$whog_fh>) {
if (/^#/) { # skip header line
next;
}
chomp;
$_ =~ s/^\s*|\s+$//g; # get rid of all leading and trailing whitespaces
if (/^\[(\w+)\]\s*(COG\d{4})\s+(.+)$/) {
$Whog{$2} = {'function' => $1, 'desc' => $3}; # anonymous hash in hash
# $1 = single-letter functional categories, maximal five per COG (only COG5032 with five)
# $2 = COG#, $3 = COG protein description
}
my @line = split(/\t/, $_); # split tab-separated cognames
$Whog{$line[0]} = {'function' => $line[1], 'desc' => $line[2]}; # anonymous hash in hash
# $2 = single-letter functional categories, maximal five per COG (only COG5032 with five)
# $1 = COG#, $3 = COG protein description
}
close $whog_fh;

Expand Down