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Extract the part of sequences from a file

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# 8  
Old 12-26-2013
This is easily done with the package bedtools with FastaFromBed function

https://code.google.com/p/bedtools/

Code:
# cat input1.fasta
>P02649
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY
QAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMG
SRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEK
VQAAVGTSAAPVPSDNH
>P17427
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
# cat pos1.bed
P02649  3       23
P02649  130     162
P17427  25      27

# ./bin/bedtools-2.17.0/bin/fastaFromBed -fi input1.fasta -bed pos1.bed -fo out1.fasta
# cat out1.fasta
>P02649:3-23
LWAALLVTFLAGCQAKVEQA
>P02649:130-162
GRLVQYRGEVQAMLGQSTEELRVRLASHLRKL
>P17427:25-27
KE


make sure you adjust for the 0 and 1-based coordinate system
Last edited by newbie83; 12-26-2013 at 12:53 PM..
These 2 Users Gave Thanks to newbie83 For This Post:
rahim42 Yoda
# 9  
Old 12-27-2013
As simply as:
Code:
s= int(line[1])-1

In your original script.
This User Gave Thanks to Klashxx For This Post:
rahim42
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