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Please help me with pyfasta

Hi all,

I have a basic question. I am trying to use pyfasta 0.5.2 for splitting a large fasta file. I successfully install pyfasta via python setup.py install --user. But, when I try to run the program with pyfasta split, it gives me an error that command not found. There is a directory called "pyfasta" within pyfasta-0.5.2 directory, it contain three files named, fasta.py, __init__.py, records.py, and split_fasta.py. I'm totally confused how to run the program. Could you please help me for solve this issue?

Thank you

fasta pyfasta
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updated by Ram Ram • written by seta seta

Is ~/.local/bin in your PATH? That's where the executables will get installed.

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written by Devon Ryan Devon Ryan

I think you need to re-run as a super user (sudo) because its not in path, but its installed or add it to path manually. You will also require setuptool for it to run properly.

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written by Sukhi Singh Sukhi Singh

@seta Hi are you able to run the split - header in pyfasta I am unable to run it can you give the usage for it im able to run other split options but not - header I want the usage in windows

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written by lakshmi.bioinformatics • lakshmi.bioinformatics

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

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written by WouterDeCoster WouterDeCoster

1 answer

Note the --user option. It's quite likely that ~/.local/bin just isn't in the PATH.

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written by Devon Ryan Devon Ryan

Thank you very much, Devon. I added ~/.local/bin to the PATH and the problem was solved.

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written by seta seta

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