07-01-2010
Trimming sequences based on Reference
My file looks something like this
Quote:
>GHL8OVD01BNNCA Freq 4
TTGATGTGCCCGTGGGTTTCCCGTCAACACCGG-------------------------------
>GHL8OVD01CMQVT Freq 15
TTGATGTCGTGGGTTTCCCGTCAACACCGGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>Reference1 Freq 1
TTGATGTGCCAGTTTCCCGTCTAGCAGCACTACCAGGACCTTCGCCCA----------------
>GHL8OVD01CMQVW Freq 11
TTGATGTGTCCCGTCGACACCGGCAAATAGCAGCAGCACTACCAGGACCTTCGCCCA-------
>GHL8OVD01A45V3 Freq 9
TTGATTCCCGTCGACACCGGCAAATAGCAGCAGCACTACAGGACCTTCGCCCA-----------
>GHL8OVD01B9PRR Freq 1
TTGATGTGCCAGCTTTCGCGTCGACACCGGCAAATAGTAGCAGCGCTACCAGGACCTTCGCCCA
>GHL8OVD01BL8BD Freq 1
TTGATGAGTACTTCCCCCGGTGACGTGGGTCAGCACTACCAGGACCTTCGCCCA----------
>GHL8OVD01AV2U9 Freq 17
TTGATGTGCCAGCTTTCGCGTCGACACCGGCAAATAGTAGCAGCGCTA----------------
Wnat I need is to look for the Reference sequence (">Reference1") and based on the length of that sequence trim all the entries in that file. So, the rersulting file will contain all sequences with the same length, like this
Quote:
>GHL8OVD01BNNCA Freq 4
TTGATGTGCCCGTGGGTTTCCCGTCAACACCGG---------------
>GHL8OVD01CMQVT Freq 15
TTGATGTCGTGGGTTTCCCGTCAACACCGGCAAATAGTAGCAGCACTA
>Reference1 Freq 1
TTGATGTGCCAGTTTCCCGTCTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01CMQVW Freq 11
TTGATGTGTCCCGTCGACACCGGCAAATAGCAGCAGCACTACCAGGAC
>GHL8OVD01A45V3 Freq 9
TTGATTCCCGTCGACACCGGCAAATAGCAGCAGCACTACAGGACCTTC
>GHL8OVD01B9PRR Freq 1
TTGATGTGCCAGCTTTCGCGTCGACACCGGCAAATAGTAGCAGCGCTA
>GHL8OVD01BL8BD Freq 1
TTGATGAGTACTTCCCCCGGTGACGTGGGTCAGCACTACCAGGACCTT
>GHL8OVD01AV2U9 Freq 17
TTGATGTGCCAGCTTTCGCGTCGACACCGGCAAATAGTAGCAGCGCTA
Thus, all sequences will keep their identifier intact (">Identifier") and have the same length. In case of being shorter than the Reference sequence, then the dashes ("-") will be consider as characters to make the length up.
Any help will be very much appreciated.
Last edited by Xterra; 07-01-2010 at 01:04 AM..
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