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Trimming sequences based on Reference

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# 1  
Old 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..
# 2  
Old 07-01-2010
Hi

Code:
awk 'NR==FNR{if($0 ~ /Reference1/){getline; gsub("-","");x=length;}next;}{print substr($0,1,x);}' file file

Guru.
This User Gave Thanks to guruprasadpr For This Post:
Xterra
# 3  
Old 07-01-2010
Guru
The output file is empty. Am I using your code in the right way?
Code:
$ awk 'NR==FNR{if($0 ~ /Reference1/){getline; gsub("-","");x=length;}next;}{print substr($0,1,x);}' Input > Output

# 4  
Old 07-01-2010
Hi xterra

Not like this. if you want to redirect the output to a file,

Code:
awk 'NR==FNR{if($0 ~ /Reference1/){getline; gsub("-","");x=length;}next;}{print substr($0,1,x);}' Input Input > Output

Guru.
This User Gave Thanks to guruprasadpr For This Post:
Xterra
# 5  
Old 07-01-2010
My bad!
Thanks alot! It worked like a charm!
# 6  
Old 07-01-2010
guruprasadpr's code can't help you for this request:

In case of being shorter than the Reference sequence, then the dashes ("-") will be consider as characters to make the length up.

Here is my update.
Code:
awk -F ""  'NR==FNR{if ($0~/Reference1/){getline; gsub("-","");x=length;}next;}
     {if ($0~/^>/) {print $0} else { {for (i=1;i<=x;i++) printf ($i=="")?"-":$i};printf "\n"}}' urfile urfile

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