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fhcrc / seqmagick

An imagemagick-like frontend to Biopython SeqIO
http://seqmagick.readthedocs.org
GNU General Public License v3.0
112 stars 22 forks source link

- is not recognized as stdin/stdout in seqmagick convert #11

Closed habnabit closed 13 years ago

cmccoy commented 13 years ago

This breaks mogrify:

rhino4 gag  ᐅ seqmagick mogrify --sort length-desc tosort.fasta
Traceback (most recent call last):
  File "/mnt/orca/home/phs_grp/matsengrp/local/bin/seqmagick", line 7, in <module>
    sys.exit(cli.main(sys.argv[1:]))
  File "/mnt/orca/home/phs_grp/matsengrp/python-local/lib/python2.7/site-packages/seqmagick/scripts/cli.py", line 29, in main
    return action(arguments)
  File "/mnt/orca/home/phs_grp/matsengrp/python-local/lib/python2.7/site-packages/seqmagick/subcommands/mogrify.py", line 36, in action
    convert.transform_file(input_file, temp_name, arguments)
  File "/mnt/orca/home/phs_grp/matsengrp/python-local/lib/python2.7/site-packages/seqmagick/subcommands/convert.py", line 193, in transform_file
    file_ext = os.path.splitext(source_file.name)[1]
AttributeError: 'str' object has no attribute 'name'
habnabit commented 13 years ago

Whoops, one moment...

habnabit commented 13 years ago

How is it now? I updated matsengrp's seqmagick.

cmccoy commented 13 years ago

Looks great, thanks!

habnabit commented 13 years ago

Closed by c9cd65647d0d0c5cd5ed7ee0e97fcedb3499a416.