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


# cat input1.fasta
# 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

make sure you adjust for the 0 and 1-based coordinate system

Last edited by newbie83; 12-26-2013 at 12:53 PM..
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# 9  
Old 12-27-2013
As simply as:
s= int(line[1])-1

In your original script.
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