ValueError: Provide the genome with the enzyme or specify enzyme=...

Issue #30 new
Anonymous created an issue

how to fix that errow, have tried evertyhing that I can.

Comments (9)

  1. Ray Z.

    Thanks for the suggestions, but I still don't know how to fix it, could you provide more details please?

    The 1st script runs fine, but gets error when running the 2nd and 3rd scripts, see the logs for the last parts.

    In a recent update by default we're not saving sequences!!!
    use parse_sams(save_seqs=True) to save sequences
    /usr/local/lib/python2.7/dist-packages/hiclib-0.0.0-py2.7.egg/hiclib/mapping.py:726: RuntimeWarning: Since 14-01-20 we're not saving sequences by default
    INFO:hiclib.mapping:Parse the second side of the reads from sams/sample7_2.bam
    INFO:hiclib.mapping:Parsing SAM files with basename sams/sample7_2.bam, # of reads: 27600966
    In a recent update by default we're not saving sequences!!!
    use parse_sams(save_seqs=True) to save sequences
    For faster computations, please compile binarySearch!!! It is in the main folder of the library
    Traceback (most recent call last):
      File "03_mergeDatasets.py", line 15, in <module>
        TR = HiCdataset("bla", genome=genomeDb, inMemory=True,)   # inMemory, as files are probably small (less than hundreds mililon reads)
      File "build/bdist.linux-x86_64/egg/hiclib/fragmentHiC.py", line 197, in __init__
    ValueError: Provide the genome with the enzyme or specify enzyme=...
    For faster computations, please compile binarySearch!!! It is in the main folder of the library
    Traceback (most recent call last):
      File "033_saveHeatmaps.py", line 20, in <module>
        TR = HiCdataset("bla", genome=genomeDb, inMemory=True,)   # inMemory, as data are small (<1e8 reads) 
      File "build/bdist.linux-x86_64/egg/hiclib/fragmentHiC.py", line 197, in __init__
    ValueError: Provide the genome with the enzyme or specify enzyme=...
    
  2. Ray Z.

    Should I put it below this line?

    genomeDb = genome.Genome('../data/BS79', chrmFileTemplate="%s.fa", readChrms=[])
    

    To make it like this?

    genomeDb = genome.Genome('../data/BS79', chrmFileTemplate="%s.fa", readChrms=[])
    genome_db.setEnzyme('HindIII')
    
  3. Ray Z.

    It's working with the following code.

    genomeDb.setEnzyme('HindIII')
    

    I also found that, my orignal scripts work good on the older version of hiclib build, the one I have tested was built on 2014-12-12, why it won't work on the most recent version?

    Thank you so much for helping.

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