pygr not finding chr9

Getting back an error in seqdb in pygr

no key 'chr9' in database <SequenceFileDB '/local/resources/hg18/karyotypic/hg18.fa'>

While it worked fine for chr15, what is the error mean, that it can't find the chromosome in the assembly? Thanks!

python pygr

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updated 4.9 years ago by Ram

• written 12.2 years ago by alex

print all keys and see what is going on print db.keys()

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written 12.2 years ago by Istvan Albert

So I believe this was due to a corrupt assembly file (i.e. hg18.fa). I rebuilt it and it worked.

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updated 6.6 years ago by Ram

• written 12.2 years ago by alex

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