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Trimming sequences based on specific pattern

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# 1  
Old 06-23-2010
Trimming sequences based on specific pattern
My files look like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTACGCCCCGGGGC
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTACCCGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTAGATTTTCTGGGGCCCCGGGG
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTATAGCTGGATTTTCTGGGACGCCCCGGGGTGC
And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted.
Quote:
AGCCCTA
The expected result should look like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTA
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTA
Thus, all the sequences would end with AGCCCTA but whatever is to the left of that particular pattern and the identifiers (>GHXCZCC01AJ8CJ) should be kept intact.
Thanks in advance
# 2  
Old 06-23-2010
Hi Xterra, try this:
Code:
sed 's/\(.*AGCCCTA\).*/\1/' infile

This User Gave Thanks to Scrutinizer For This Post:
Xterra
# 3  
Old 06-23-2010
Fantastic!!!!
It works like a charm!
Thanks once again!
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