global name 'maketrans' is not defined

BradnerLab / pipeline

bradner lab computation pipeline scripts

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global name 'maketrans' is not defined #50

Closed fburdet closed 9 years ago

fburdet commented 9 years ago

Hello,

When running python bamToGFF.py -e 200 -r -m 1 -b myBam.bam -i myGFF.gff -o myOutput.gff I get a

[1;31mNameError[0m: global name 'maketrans' is not defined

Can you please check?

jdimatteo commented 9 years ago

@fburdet this should be fixed now -- can you do a git pull and verify?

jdimatteo commented 9 years ago

@bradnerComputation / Charles: does Bradner Lab still use bamToGFF.py ? Do you instead always use bamliquidator_batch.py --match_bamToGFF? It seems like this maketrans error has been there since ae86f8a in May 2014. I fixed the error since it was trivial (see 0467ae9).

Charles, can you please advise @fburdet if bamToGFF.py should no longer be used?

charlesylin commented 9 years ago

Hi @fburdet bamToGFF.py is deprecated and is no longer being used by our lab. I would recommend installing bamliquidator instead:

https://github.com/BradnerLab/pipeline/wiki/bamliquidator