Beefy Boxes and Bandwidth Generously Provided by pair Networks
go ahead... be a heretic
 
PerlMonks  

Re^2: mitoprot bioperl code help

by cburger (Acolyte)
on Mar 21, 2012 at 03:31 UTC ( #960712=note: print w/ replies, xml ) Need Help??


in reply to Re: mitoprot bioperl code help
in thread mitoprot bioperl code help

Thanks all for the help, I got it to run on the test file. I'm trying now to get it reading through a whole fasta file. But it stops after the first sequence and doesn't go through the whole file. Any idea why?

#!/usr/bin/perl-w use strict; use Bio::Tools::Analysis::Protein::Mitoprot; use Bio::PrimarySeq; use Bio::SeqIO; my $inputstream = Bio::SeqIO->new(-file => "myseq2.fa",-format => 'Fa +sta'); while (my $seqobj = $inputstream->next_seq){ # print the sequence print ">"; print $seqobj->id,"\n"; my $seq= $seqobj-> seq; my $id= $seqobj->id; my $seq = new Bio::PrimarySeq(-seq=>$seq, -primary_id=>$id); my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new(-seq +=> $seq); # sequence must be >!5aa long and start with an M. $mitoprot->run(); die "Could not get a result" unless $mitoprot->status =~ /^COMPLETED +/; print $mitoprot->result; # print raw prediction to STDOUT my $rawdata = my $analysis_object->result; print "rawdata: $rawdata\n"; ## .................................................... } # close while

here is the output I get with error message :

>SPAC212.11.1 Input sequence length : 1887 aa VALUES OF COMPUTED PARAMETERS Net charge of query sequence : -14 Analysed region : 5 Number of basic residues in targeting sequence : 0 Number of acidic residues in targeting sequence : 0 Cleavage site : not predictable Cleaved sequence : HYDROPHOBIC SCALE USED GES KD GVH1 ECS H17 : 1.776 1.635 0.456 0.701 MesoH : -0.097 0.599 -0.205 0.261 MuHd_075 : 8.891 2.722 0.982 0.422 MuHd_095 : 40.686 26.860 12.359 9.439 MuHd_100 : 45.583 25.681 12.613 9.543 MuHd_105 : 45.113 22.080 11.556 8.739 Hmax_075 : 1.867 9.625 -1.365 2.660 Hmax_095 : 15.800 20.400 3.835 6.380 Hmax_100 : 16.000 20.300 3.835 6.190 Hmax_105 : 15.600 15.600 2.796 5.250 PROBABILITY of export to mitochondria: 0.5284 Can't call method "result" on an undefined value at test.pl line 36, < +GEN0> line 1.

Thanks!!


Comment on Re^2: mitoprot bioperl code help
Select or Download Code
Re^3: mitoprot bioperl code help
by molecules (Monk) on Mar 21, 2012 at 15:50 UTC
    Try removing these lines and seeing if it works:
    my $rawdata = my $analysis_object->result; print "rawdata: $rawdata\n";

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://960712]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others making s'mores by the fire in the courtyard of the Monastery: (6)
As of 2014-11-26 07:02 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    My preferred Perl binaries come from:














    Results (163 votes), past polls