samtools faidx foo.fa chromosome:pos1-pos2
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written
by
Devon Ryan
And if you need to do it in a script or use Windows
pip install --user pyfaidx
faidx foo.fa chr:pos1-pos2
It prints the sequence to the screen. It just has to build an index the first time you use it.
Yes, an unfortunate behavior of samtools is that you must invoke faidx once to generate the index, then again to fetch sequence. This is something I did not emulate with pyfaidx.
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written
by
Matt Shirley
This must have already gotten fixed, since the version of samtools I have (granted, I track the github repo) will create the index (if needed) and then load it in a single go.
You might be right, or I might be remembering incorrectly :)
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