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Re^2: simple perl script to trim a FASTA file

by erix (Parson)
on Apr 09, 2010 at 15:52 UTC ( #833851=note: print w/replies, xml ) Need Help??


in reply to Re: simple perl script to trim a FASTA file
in thread simple perl script to trim a FASTA file

You should indeed not edit the sequence files.

The previous answers (by almut and BrowserUK) just use __DATA__ because that makes it easy to show as compact example. And to use the examples they'll need a little editing.

For instance, in almut's script, replace the line:

while( <DATA> ) {
with
while( <> ) {

and invoke the script as:

perl almuts_answer.pl sequences.fa > sequences_cleaned.fa

Replacing <DATA> with <> means it will not read the __DATA__ section of the program-file itself, but instead read from STDIN (aka standard input).

hth

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