Q. BioPython: CodeML FileNotFoundError: [WinError 2]

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5.2 years ago

mtbreeze • 0

I'm trying to run codeml in Biopython, following by Biopython cookbook. But it doesn't work with an FileNotFoundError: [WinError 2]. I found ctl file does not contain file's full path, like

seqfile = seq2.phy  
outfile = result.out  
treefile = template.tree

Files are on 'C:/Users/admin/Desktop'.

I set seqfile, outfile, treefile path with absolute path

''C:/Users/admin/Desktop/seq2.phy', 'C:/Users/admin/Desktop/result.out', 'C:/Users/admin/Desktop/template.tree'.

With fixed ctl file, cmd mode codeml run (not Biopython) works!

Now, I wonder why Biopython's codeml doesnt get file PATH. about four years ago, someone get same problem with me, but I cant get any clue to solve this problem. [solved] BioPython: CodeML FileNotFoundError: [WinError 2]

paml biopython • 1.3k views

ADD COMMENT • link updated 12 months ago by Hend • 0 • written 5.2 years ago by mtbreeze • 0

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Hi,

It seems like a long time since you've asked that question! I am having the same problem now, and I was wondering if you found a way around to fix it.

Cheers, Hend

ADD REPLY • link 12 months ago by Hend • 0

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