The HOWTO link is here now: https://bioperl.org/howtos/SeqIO_HOWTO.html
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bjwiley23 •
Bioperl Seqio Reset (Next_Seq())
Hi all I am writing a script that gets a sequence from several hundred files containing genes from several database fasta files. I am reusing these database fasta files in a loop so it does not get reindexed.
However my code only works with 1 iteration.
The condition in the while loop "my $seq = $file->next_seq()" is not met after the first iteration and I am assuming that I may need to reset it. Does anyone know how I can go about this?
Thanks
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Urbanspr1Nter •
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Urbanspr1Nter •
1 answer
You can add a line at the end of the loop so the the file handle seeks back to the start:
seek($file->_fh, 0, 0);
Or use the methods like $file->first_seq (which resets the file pointer to 0) followed by a series of $file->next_seq.
A better way, depending on the size of the file, may be to read the sequences into an array, see the examples here: http://www.bioperl.org/wiki/HOWTO:SeqIO
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why not delete the filehandle and create a new one?
Need to see more of the code to answer this properly.
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