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sff_extract error



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  • sff_extract error


    sorry I am new in this I tried to convert sff file to fasta and fastq files. Firstly I installed python 2.7.6 then biopython 1.65 and finally seq_crumbs 0.1.9 and i tried sff_extract but there is a problem :

    ]# sff_extract IXXLJHH01.sff
    Traceback (most recent call last):
    File "/usr/bin/sff_extract", line 25, in <module>
    from crumbs.seqio import write_seqs
    File "/usr/lib/python2.6/site-packages/crumbs/seqio.py", line 35, in <module>
    from crumbs.utils.file_formats import get_format, peek_chunk_from_file
    File "/usr/lib/python2.6/site-packages/crumbs/utils/file_formats.py", line 22, in <module>
    from crumbs.settings import get_setting
    File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 133, in <module>
    _settings = _Settings()
    File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 114, in __init__
    File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 119, in load_settings
    for key, val in globals().viewitems():
    AttributeError: 'dict' object has no attribute 'viewitems'

    What should I do for this?

  • #2
    Does seq_crumbs require python 2.7.x? Looks like your software got installed in python2.6.


    • #3
      Yes, you are right. However, I installed 2.7.6 how can i change it do you have any idea?


      • #4
        Use one of the options here to see if you can set your default python version to 2.7. You may be able to use crumbs installed in 2.6 but the other thing to try would be to re-do the biopython/crumbs install so they would install under 2.7.x.


        • #5
          Thank you!


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