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fakeQuals.py

PBJelly Tickets
Afif Elghraoui
2017-07-27
2017-07-27

  • Afif Elghraoui

    Afif Elghraoui - 2017-07-27

    One of our users ran into an error with fakeQuals.py:

    $ fakeQuals.py --help
Traceback (most recent call last):
  File "/usr/local/apps/pbsuite/15.8.24/bin/fakeQuals.py", line 4, in <module>
    from FileHandlers import FastaFile
ImportError: No module named FileHandlers

    It looks like the import statement is off. The following change fixes it.

    --- /usr/local/apps/pbsuite/15.8.24/bin/fakeQuals.py~   2017-07-21 18:27:28.697420000 -0400
+++ /usr/local/apps/pbsuite/15.8.24/bin/fakeQuals.py    2017-07-27 11:22:01.864624000 -0400
@@ -1,7 +1,7 @@
 #!/usr/bin/env pbsuite-python-wrapper
 import sys
 from optparse import OptionParser
-from FileHandlers import FastaFile
+from pbsuite.utils.FileHandlers import FastaFile

 USAGE = """USAGE: %prog <input.fasta> <output.qual> [--options]
 Creates fake quality information for fasta files that do not have associated \

    By the way, it'd be nice if user-facing scripts didn't expose the implementation language.

    And my shebang line is different because I had to use a wrapper for python in order to prevent PYTHONPATH from breaking python3 programs that a user might want to use in the same session.

     

    • Afif Elghraoui

      Afif Elghraoui - 2017-07-27

      looks like this file was supposed to be a symlink. I guess mine got converted to a regular file somehow.

       

  • Adam English

    Adam English - 2017-09-12
     

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