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Hi all,<br>
<br>
I've started to use bl2seq and am having a perplexing problem. I couldn't
find this being asked previously so guess it may be a mistake in my Perl
code, but if any one can see it then I'd be grateful.<br>
<br>
This is part of a script where two files are fetched and input into bl2seq...<br>
<br>
<font size="-1">for my $cluster_id (keys %list) {<br>
print ": $cluster_id : $list{$cluster_id}[0]\n";<br>
my $file1=$list{$cluster_id}[0];<br>
my $file2=$list{$cluster_id}[1];<br>
print "$file1:$file2\n";<br>
my $input1="$path2files/$file1.pep";<br>
my $input2="$path2files/$file2.pep";<br>
print "$input1:$input2\n";<br>
<br>
my $factory = Bio::Tools::Run::StandAloneBlast->new('outfile' =>
"$outdir/$cluster_id.out",'program'=>'blastp');<br>
my $bl2seq_report = $factory->bl2seq($input1, $input2);<br>
}</font><br>
<br>
<br>
I get the following error:<br>
<br>
------------- EXCEPTION -------------<br>
MSG: indiv_seq/Peptide/.pep not Seq Object or file name!<br>
STACK Bio::Tools::Run::StandAloneBlast::bl2seq /usr/local/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/StandAloneBlast.pm:539<br>
STACK toplevel /necator/jamesw/bin/bl2seq_nb.pl:36<br>
<br>
--------------------------------------<br>
<br>
<br>
When I ask to print out $cluster_id nothing is printed. However if I comment
out <font size="-1">my $bl2seq_report = $factory->bl2seq($input1, $input2);</font>
then $cluster_id is found! I am also able to run bl2seq as a system call
in the program with the desired results.<br>
<br>
I tried reading the files in as seq objects through SeqIO, but again I can
the error caused through the disappearence of $cluster_id!<br>
<br>
Anyone any ideas?<br>
<br>
J<br>
<br>
<br>
<pre class="moz-signature" cols="$mailwrapcol">--
Nematode Bioinformatics
Blaxter Nematode Genomics Group
Institute of Cell, Animal and Population Biology
Ashworth Labs
University of Edinburgh
King's Buildings
Edinburgh
EH9 3JT
UK
0131 650 7403
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