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  • Making bam files in Pysam

    I have made a script that should generate bam files with the help of Pysam. But the problem is that that code does not work.

    The mistake in the code is somewhere in the following code:
    =============================================

    inputSamFile = pysam.Samfile(inputBamFile, "rb")
    outputSamFile = pysam.Samfile(outputBamFile, "wb", template=inputSamFile)
    ============================================

    When I run this code, the following error message is generated:
    ===============================================

    [martijn@animal provisional]$ python DPBamFileMaker.py TCGA-A6-2672-10A-01W-0833-10_SOLiD.bam man.bam
    Traceback (most recent call last):
    File "DPBamFileMaker.py", line 117, in <module>
    main(sys.argv)
    File "DPBamFileMaker.py", line 114, in main
    convertInputBamFileToOutputBamFileWithOnlyDPs(inputBamFile, outputBamFile)
    File "DPBamFileMaker.py", line 49, in convertInputBamFileToOutputBamFileWithOnlyDPs
    outputSamFile = pysam.Samfile(outputBamFile, "wb", template=inputSamFile)
    File "csamtools.pyx", line 463, in csamtools.Samfile.__cinit__ (pysam/csamtools.c:4758)
    File "csamtools.pyx", line 609, in csamtools.Samfile._open (pysam/csamtools.c:6330)
    IOError: could not open file `man.bam`
    ==================================================

    I don't understan this error.

    What am I doing wrong in this code? Can anyone tell me?

  • #2
    Do you have write permissions it this directory?

    Comment

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