Question: Please help me with pyfasta
0
gravatar for seta
3.4 years ago by
seta1.2k
Sweden
seta1.2k wrote:

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 direcotry, it contain three files named, fasta.py __init__.py records.py split_fasta.py. I'm totally confused how to run the program. Could you please help me for solve this issue?

Thank you

fasta file pyfasta splitting • 2.9k views
ADD COMMENTlink modified 2.3 years ago by lakshmi.bioinformatics20 • written 3.4 years ago by seta1.2k

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

ADD REPLYlink written 3.4 years ago by Devon Ryan91k

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.

ADD REPLYlink written 3.4 years ago by Sukhdeep Singh9.8k

@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

ADD REPLYlink written 2.3 years ago by lakshmi.bioinformatics20

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.

ADD REPLYlink written 2.3 years ago by WouterDeCoster40k
2
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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

ADD COMMENTlink written 3.4 years ago by Devon Ryan91k
1

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

ADD REPLYlink written 3.4 years ago by seta1.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1622 users visited in the last hour