[Bioperl-l] Using Bio::SeqUtils->cat()

[Roy Chaudhuri]

Hi Trina,

That's probably how cat should work, but in fact the first sequence in 
the list is modified by concatenating on the other sequences. The 
function just returns 1 if it worked. So you need code like:

Bio::SeqUtils->cat(@seqs);
my $mergedseqs=$seqs[0];

You can blame the idiot who wrote that code for the slightly awkward 
interface (sorry). I think the module documentation is correct, but let 
us know if you think it should be clarified.

Cheers,
Roy.

On 06/06/2011 13:21, Trina McMahon wrote:
> Hello everyone,
>
> I am a complete (bio)perl neophyte and am struggling with what should
> be some very basic code.
>
> I am trying to write a simple script to merge a bunch of gbk
> sequences into one big sequence, while preserving the feature
> coordinates.  I was so proud of myself because I found this function
> in Bio::SeqUtils called cat().  But I can't figure out how the hell
> to make it work!!!
>
> I'm attaching the script that I wrote below.  Can you help me figure
> out what is wrong?  I did some troubleshooting and I am pretty sure
> it is the Bio::SeqUtils->cat() function that is the problem.  It
> seems like it should return a seq object but if you look at the
> original code in the documentation online I am not sure.
>
> thanks!! trina
>
> #!/usr/local/ActivePerl-5.10/bin/perl # #
>
> use strict; use warnings; use Bio::SeqIO; use Bio::SeqUtils; use
> Getopt::Long;
>
> # get command-line arguments, or die with a usage statement
>
> my $USAGE=<<USAGE;
>
> * catgb *
>
> concatenates multiple genbank records and adjusts feature coordinates
> in the final merged sequence
>
> catgb -i listofseqs.gbk -o mergedseqs.gbk
>
>
> USAGE
>
> my ($help,$infile,$outfile);
>
> GetOptions ( 'h|help'	   =>   \$help, 'i|infile=s'       =>
> \$infile, 'o|outfile=s'      =>  \$outfile, );
>
> ########################################################################
>
>  if ($help)      	{ die $USAGE; } if (!$infile)    { die "$USAGE\nNo
> input file! (-infile)\n"; } if (!$outfile)    { die "$USAGE\nNo
> output file! (-outfile)\n"; }
>
> my @seqs;
>
>
> my $seqin = Bio::SeqIO->new(-file =>  $infile, -format=>"genbank");
> my $seqout = Bio::SeqIO->new(-file=>  ">$outfile", -format =>
> "genbank");
>
>
> # create an array to hold the sequences from infile  while (my $seq =
> $seqin->next_seq) {  push (@seqs, $seq);
>
> }
>
> # concatenate the sequenes held in the array @seqs  my $mergedseqs =
> Bio::SeqUtils->cat(@seqs);
>
> # write the new merged sequence into the specified file
>
> $seqout->writeseq($mergedseqs);
>
> exit;
> -------------------------------------------------------------------------------------
>
>
Katherine (Trina) McMahon, Associate Professor
> Goddess of Funkosity Departments of Civil and Environmental
> Engineering and Bacteriology Environmental Chemistry and Technology
> Program Limnology and Marine Science Program Microbiology Doctoral
> Training Program
>
> **On sabbatical leave starting August 20, 2010**
>
> Mailing Address: 3204 Engineering Hall, 1415 Engineering Drive
> University of Wisconsin - Madison, Madison, WI  53706-1691
>
> Alternate Office:  5552 Microbial Sciences Building
>
> Phone: 608/890-2836     Fax: 608/262-9865 Email:
> tmcmahon at engr.wisc.edu McMahon Lab:
> http://www.engr.wisc.edu/cee/faculty/mcmahon_katherine.html North
> Temperate Lakes Microbial Observatory:
> http://microbes.limnology.wisc.edu/
>
> -------------------------------------------------------------------------------------
>
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