Question: genome sequence look up tool
0
gravatar for evcon
4 months ago by
evcon0
evcon0 wrote:

Is there a tool to look up genomic sequences? Something in python would be most helpful. For example something like this:

>>>getseq('chr1'.'100500','100505')
AACTGC
sequence genome • 171 views
ADD COMMENTlink modified 4 months ago by h.mon21k • written 4 months ago by evcon0

search this site for "samtools faidx" and the related python libraries (pyfaidx)

ADD REPLYlink written 4 months ago by Pierre Lindenbaum115k

Thanks! This is perfect! Knew this had to exist already.

ADD REPLYlink written 4 months ago by evcon0
1
gravatar for h.mon
4 months ago by
h.mon21k
Brazil
h.mon21k wrote:

BioPython and pyfaidx in python, samtools on the command-line

ADD COMMENTlink written 4 months ago by h.mon21k
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