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Full Discussion: Extract the part of sequences from a file
Top Forums Shell Programming and Scripting Extract the part of sequences from a file Post 302881041 by rahim42 on Thursday 26th of December 2013 09:07:43 AM
Old 12-26-2013
Thank you for your answer. I corrected the code. But the first character of each sequence is not printing. I got the output like this
Code:
>P02649:3-23
LWAALLVTFLAGCQAKVEQA
>P02649:130-162
GRLVQYRGEVQAMLGQSTEELRVRLASHLRKL
>P17427:25-27
KE

My desired output is

Code:
>P02649:3-23
VLWAALLVTFLAGCQAKVEQA
>P02649:130-162
CGRLVQYRGEVQAMLGQSTEELRVRLASHLRKL
>P17427:25-27
SKE

---------- Post updated at 09:04 AM ---------- Previous update was at 09:00 AM ----------

Quote:
Originally Posted by Akshay Hegde
An Awk approch :

Code:
$ cat input.fasta
>P02649
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY
QAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMG
SRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEK
VQAAVGTSAAPVPSDNH
>P17427
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA

Code:
$ cat ids.txt
P02649  3   23
P02649  130 162
P17427  25  27

Code:
$ awk '{print $0,length($0)}' input.fasta
>P02649 7
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT 60
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA 60
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY 60
QAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMG 60
SRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEK 60
VQAAVGTSAAPVPSDNH 17
>P17427 7
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC 60
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL 60
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP 60
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA 60

Code:
$ awk 'FNR==NR{A[FNR]=$1 FS $2 FS $3;next}{x=$1;for(i in A){split(A[i],S);if(x == ">"S[1]){print x":"S[2]"-"S[3];getline;print substr($0,S[2],S[3]-S[2])}} }' ids.txt input.fasta

Code:
>P02649:3-23
VLWAALLVTFLAGCQAKVEQ
>P02649:130-162

>P17427:25-27
SK

---------- Post updated at 09:07 AM ---------- Previous update was at 09:04 AM ----------

Dear Hedge,

Thanks for your answer. But your output is different from my desired output.
 

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