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  • HTSeq - how do I cimport it for Cython?

    TL;DR
    How do I `cimport HTSeq` in Cython module?

    --- Details ---
    I am trying to use HTSeq to read BAM files that are quite large but it takes days to process them in pure Python. Therefore I decided to use Cython and cythonize reading BAM file part.
    Here is example code:
    Code:
    import HTSeq
    
    bam_file = '.../test.bam'
    bam = HTSeq.BAM_Reader(bam_file)
    for aln in bam:
        # process alignment
    Now I am trying to replace `import HTSeq` with `cimport HTSeq` but the Cython can not find `HTSeq.pxd` file. I found that the header file is actually `src/HTSeq/_HTSeq.pxd`(full link: https://github.com/simon-anders/htse...Seq/_HTSeq.pxd )
    as also described here: http://htseq.readthedocs.io/en/master/contrib.html
    So, the file starts with underscore and is in the htseq repo but `pip install` does not copy it to any of Includes directories. Therefore, I copied it manually to the root directory of my package so that `setup.py` can see it. Then I added `cimport _HTSeq as HTSeq` to my `*.pyx` file and it got compiled to an `*.so` file but when I ran the app it throws error:
    Code:
    ImportError: No module named _HTSeq
    My system: macOS 10.13.3 High Sierra; Python 2.7.14 (will port the code to 3.6 later); HTSeq 0.6.0;

    Any suggestion about solving this problem OR speeding up reading BAM files is appreciated. (One more trick I want to try next is to extract chromosome info from BAM header file and run them in parallel using multiprocessing/cython_nogil/openMPI or something; still don't know what will work best with Cython.)

    Thanks!
    Last edited by Proteos; 03-26-2018, 01:28 PM.

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