Problems with primary_transcript.py

[mbarkdull]

Hi!

I'm encountering two issues with primary_transcript.py. One, the command given in the OrthoFinder tutorials to run the script gives the path to the script incorrectly:
for f in *fa ; do python ~/orthofinder-tutorial/OrthoFinder/tools/primary_transcript.py $f ; done
where it should be:
for f in *fa ; do python ~/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py $f ; done
This might save other folks some frustration in trying to figure out why the script can't be found.

Second, when I do run the primary_transcript.py script on my dowloaded proteomes, I get this whole series of errors:

Traceback (most recent call last):
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 147, in <module>
    main(args)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 143, in main
    CreatePrimaryTranscriptsFile(fn, dout)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 63, in CreatePrimaryTranscriptsFile
    if not line.startswith(">"): continue
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
Traceback (most recent call last):
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 147, in <module>
    main(args)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 143, in main
    CreatePrimaryTranscriptsFile(fn, dout)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 63, in CreatePrimaryTranscriptsFile
    if not line.startswith(">"): continue
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
Traceback (most recent call last):
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 147, in <module>
    main(args)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 143, in main
    CreatePrimaryTranscriptsFile(fn, dout)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 63, in CreatePrimaryTranscriptsFile
    if not line.startswith(">"): continue
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
Traceback (most recent call last):
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 147, in <module>
    main(args)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 143, in main
    CreatePrimaryTranscriptsFile(fn, dout)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 63, in CreatePrimaryTranscriptsFile
    if not line.startswith(">"): continue
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
Traceback (most recent call last):
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 147, in <module>
    main(args)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 143, in main
    CreatePrimaryTranscriptsFile(fn, dout)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 63, in CreatePrimaryTranscriptsFile
    if not line.startswith(">"): continue
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
Traceback (most recent call last):
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 147, in <module>
    main(args)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 143, in main
    CreatePrimaryTranscriptsFile(fn, dout)
  File "/Users/meganbarkdull/orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py", line 63, in CreatePrimaryTranscriptsFile
    if not line.startswith(">"): continue
TypeError: startswith first arg must be bytes or a tuple of bytes, not str

It seems that there is an error in the script such that it is not reading the .fasta files correctly, but I don't know enough to locate and fix the problem.

Thanks so much for the help!

[davidemms]

Hi

Thanks for letting me know about this, I've updated the primary_transcript.py script to make it compatible with python3 so that should resolve those problems.

I've also updated the tutorial so that it refers to "orthofinder_tutorial", which now makes it consistent with the previous tutorial etc.

All the best
David

[mbarkdull]

Thank you so much! I really appreciate it.