piping to fastacmd (bioinformatics)

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Hi there, The stand-alone BLAST in windows can't yet support the -i flag allowing retrieval of multiple sequences through fastacmd. I am trying to get around this with a simple script that looks through the accession numbers I want to retrieve and stores these as $id. I then use:

system 'fastacmd -d mydatabase -s $id >output.txt
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This runs each time $id gets replaced with a new sequence number.

However this doesnt work - it can't find $id in my database as it doesnt seem to be replacing $id with what is actually stored in $id !

any ideas ?
Thanks,
basm100

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Re: piping to fastacmd (bioinformatics) by Abigail-II (Bishop) on Nov 14, 2002 at 17:15 UTC
That's because you are using single quotes in your string. Use double quotes to get the required interpolation. Abigail	[reply]
Re: piping to fastacmd (bioinformatics) by Zaxo (Archbishop) on Nov 14, 2002 at 17:15 UTC
Use double quotes or qq() to get $id to interpolate its value. Probably a pasto, but you don't close quotes or end the statement with a semicolon. After Compline, Zaxo	[reply]
Re: piping to fastacmd (bioinformatics) by tommyw (Hermit) on Nov 14, 2002 at 17:17 UTC
Use `"` instead of `'`. Variables don't get replaced (interpolate) inside single quotes. -- Tommy Too stupid to live. Too stubborn to die.	[reply] [d/l] [select]