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> ) {

[download]
with 
while( <> ) {

[download]

and invoke the script as: 

perl almuts_answer.pl sequences.fa > sequences_cleaned.fa

[download]

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

In reply to Re^2: simple perl script to trim a FASTA file by erix
in thread simple perl script to trim a FASTA file by RabidMortal

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