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Added output_file option to cdd2cog #12

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Added output_file option to cdd2cog #12

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6 changes: 6 additions & 0 deletions cdd2cog/cdd2cog.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -223,13 +223,15 @@ =head1 LICENSE

### Get the options with Getopt::Long
my $Rps_Report; # path to the rps-blast report/output
my $output_file; # file to write rps-blast report
my $CDDid_File; # path to the CDD 'cddid.tbl' file
my $Fun_File; # path to the COG 'fun' file
my $Whog_File; # path to the COG 'whog' file
my $Opt_All_Hits; # give all blast hits for a query, not just the best (lowest evalue)
my $VERSION = 0.1;
my ($Opt_Version, $Opt_Help);
GetOptions ('rps_report=s' => \$Rps_Report,
'output_file=s' => \$output_file,
'cddid=s' => \$CDDid_File,
'fun=s' => \$Fun_File,
'whog=s' => \$Whog_File,
Expand Down Expand Up @@ -277,6 +279,8 @@ =head1 LICENSE
my $Blast_Out = 'rps-blast_cog.txt'; # output file for COG assignments appended to RPS-BLAST results
open (my $Blast_Out_Fh, ">", "$Out_Dir"."$Blast_Out");
print $Blast_Out_Fh "query id\tsubject id\t% identity\talignment length\tmismatches\tgap opens\tq. start\tq. end\ts. start\ts. end\tevalue\tbit score\tCOG#\tfunctional categories\t\t\t\t\tCOG protein description\n"; # header for $Blast_Out
open(my $output_file_Fh, ">", $output_file) if(defined $output_file);
print $output_file_Fh "query id\tsubject id\t% identity\talignment length\tmismatches\tgap opens\tq. start\tq. end\ts. start\ts. end\tevalue\tbit score\tCOG#\tfunctional categories\t\t\t\t\tCOG protein description\n" if(defined $output_file); # header for $output_file

my $Locus_Cog = "protein-id_cog.txt"; # slimmed down $Blast_Out only including locus_tags, COGs, and functional categories
open (my $Locus_Cog_Fh, ">", "$Out_Dir"."$Locus_Cog");
Expand Down Expand Up @@ -314,10 +318,12 @@ =head1 LICENSE
print $Locus_Cog_Fh "$line[0]\t$cog\t$functions\n"; # locus_tag\tCOG\tfunctional categories
$functions .= "\t" x (5 - @functions); # add additional tabs for COGs with fewer than five functions (which is the maximum number)
print $Blast_Out_Fh "$_\t$cog\t$functions\t$Whog{$cog}->{'desc'}\n"; # $_ = RPS-BLAST line
print $output_file_Fh "$_\t$cog\t$functions\t$Whog{$cog}->{'desc'}\n" if(defined $output_file); # $_ = RPS-BLAST line
}

close $Rps_Report_Fh;
close $Blast_Out_Fh;
close $output_file_Fh if(defined $output_file);
close $Locus_Cog_Fh;


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