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Change sequence names in fasta file

 
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# 1  
Old 02-27-2013
Change sequence names in fasta file
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:

Code:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC
>rps12_5end_(reverse_strand)
ATGAGAATCAATCCTACTACTTCTGGTTCTGAAGTTTCCGCGGTTG


to look like this:

Code:
>accD
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC
>rps12_5end
ATGAGAATCAATCCTACTACTTCTGGTTCTGAAGTTTCCGCGGTTG


Any help would be appreciated!
Moderator's Comments:
Mod Comment
Please use code tags when posting data and code samples!
Last edited by vgersh99; 02-27-2013 at 05:40 PM.. Reason: code tags, please!
# 2  
Old 02-27-2013
are you sure about the last mod? do you really want to have >rps12_5end?
something to start with:
Code:
sed '/>/s/[:_].*//' myFile

# 3  
Old 02-28-2013
I do want to have
Code:
>rps12_5end

The sequence names have to match a set of prescribed names for me to upload them to a particular database.

---------- Post updated 02-28-13 at 10:06 AM ---------- Previous update was 02-27-13 at 06:39 PM ----------

Thanks a million. It worked perfectly.
 
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