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Old 07-19-2013, 03:01 AM   #1
aw90
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Location: England

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Default Question: Searching FASTA file for specific IDs

Hi all,

Apologies if this is answered elsewhere, I've searched for it but can't find!

I have a list of UniProt IDs (e.g., Q95T64 Q8INK6 Q9GNK5) and want to search through them all (n=~450) to see if they exist in a fasta file of a species, outputting two lists, one list of the IDs that do appear in the species fasta, and one list of those that do not!

Grep perhaps?

Many thanks

Andy

EDIT: The list of IDs are contained within a .txt file, return seperated
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Old 07-19-2013, 03:14 AM   #2
rhinoceros
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Default

Something like:

grep '>' species.fasta | grep -f idFile.txt > HeaderLinesThatMatch.txt
grep '>' species.fasta | grep -v -f idFile.txt > HeaderLinesThatDoNotMatch.txt

Might work, might not. I'm too lazy to check how the second command behaves..

Last edited by rhinoceros; 07-19-2013 at 03:18 AM.
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