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Re: Need Help with Maybe a Regex Issue

by Kenosis (Priest)
on Feb 27, 2014 at 00:13 UTC ( #1076325=note: print w/replies, xml ) Need Help??


in reply to Need Help with Maybe a Regex Issue

It's evident that you're attempting to search a GenBank file. What, specifically, are you trying to find in that file, i.e., in which GenBank field?

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Re^2: Need Help with Maybe a Regex Issue
by sharkbait (Initiate) on Feb 27, 2014 at 15:07 UTC

    Thanks for the reply! I have a list (technically a spreadsheet that I made a list) of bacterial genes from an RNASeq sequencing run. I've isolated a sublist of strings that correspond to gene names that I am interested in investigating further, but I need to get information on them from the GenBank file, nothing too elaborate, basically Gene Name, GeneBank ID or GeneID, and a brief description. Initially I set up a simple script to type in the name to search (see the commented out STDIN section), which matched the pattern to the string in the GeneBank file-I just copied and pasted the lines I needed-but when I realized there were way too many for this to be feasible, I tried the current approach of inputing the list of genes from the RNASeq run as search patterns to match.

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