[Bioperl-l] use Bio::SeqIO to read Fasta sequence from pipe, or @ARGV, like "while (<>) {....}"

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Sun Jul 13 00:53:21 UTC 2014

> Thanks for your quick replay and advice. I have tried your method. But it
> complains that
> ------------------------------------
> [linhy at bioinfo1 Script]$ less try.fa | perl ./fastaLen.pl
> Name "main::DATA" used only once: possible typo at ./fastaLen.pl line
> 42.
> Use of uninitialized value in print at ./fastaLen.pl line 49.
> ------------------------------------

I don't think you mean to use the "less" command. Try one of these:

% cat try.fa | perl ./fastaLen.pl


% perl ./fastaLen.pl < try.fa

--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA
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