Re: simple perl script to trim a FASTA file

Thank you thank you.

So far, I have not been able to get either script to run. I keep getting a missing semicolon error--I am not sure what that means but that seems like something I can figure out on my own.

What I cannot figure out is if there an easy way I can get these scripts to run on a specified FASTA file? Again, my files are very very large (gigabytes) and I'd prefer not to edit them manually...

Again, I really appreciate the help.

Comment on Re: simple perl script to trim a FASTA file

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Re^2: simple perl script to trim a FASTA file by erix (Prior) on Apr 09, 2010 at 15:52 UTC
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	[reply] [d/l] [select]

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Re^2: simple perl script to trim a FASTA file
by erix (Prior) on Apr 09, 2010 at 15:52 UTC

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]

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

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