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Bio::SeqIO module in for loop

P: 5
Hi friends ...

Actually i am a beginner in perl i am using Bio::seqIO module for genbank file in a for loop, if the condition is below or equal to 10 (ten) the result is proper .. but when its crosses the limit 10 its not working properly its taking previous files sequence and next files limits to splice...

there is any limitations in that module ?

please help me friends

regards and thanks
siva
Oct 29 '08 #1
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5 Replies


nithinpes
Expert 100+
P: 410
Hi friends ...

Actually i am a beginner in perl i am using Bio::seqIO module for genbank file in a for loop, if the condition is below or equal to 10 (ten) the result is proper .. but when its crosses the limit 10 its not working properly its taking previous files sequence and next files limits to splice...

there is any limitations in that module ?

please help me friends

regards and thanks
siva
Probably you may have to undefine certain variables after looping in your script. But, can't predict anything without seeing your code. Post your code.
Oct 29 '08 #2

P: 5
Probably you may have to undefine certain variables after looping in your script. But, can't predict anything without seeing your code. Post your code.
hi ...

sorry i can't show fill part of my code ,but my code looks like below one ...
Expand|Select|Wrap|Line Numbers
  1. for($i=1;$i<=$no;$++)
  2. {
  3. my $filename = $session[$i].".txt";
  4.         my $seqobj = Bio::SeqIO->new( -format => 'GenBank',-file => $filename);
  5.         my $seq=$seqobj->next_seq();
  6. ....
  7.  
  8. etc...
  9. }
  10.  
thank you..
Oct 30 '08 #3

KevinADC
Expert 2.5K+
P: 4,059
You might get better help with BioPerl specific questions from the BioPerl mailing list:

http://www.bioperl.org/wiki/Mailing_lists
Oct 30 '08 #4

P: 5
You might get better help with BioPerl specific questions from the BioPerl mailing list:

http://www.bioperl.org/wiki/Mailing_lists
Thank you nithin
nithinpes ..

Thanks for your responce towords my doubt i am trying the url which you have mentioned here ....
Oct 31 '08 #5

nithinpes
Expert 100+
P: 410
Thanks for your responce towords my doubt i am trying the url which you have mentioned here ....
The URL was not mentioned by me :)
Oct 31 '08 #6

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