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Old 03-26-2018, 11:12 AM   #1
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Location: USA

Join Date: Dec 2011
Posts: 6
Unhappy HTSeq - how do I cimport it for Cython?

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:
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: )
as also described here:
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 `` 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:
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.)


Last edited by Proteos; 03-26-2018 at 01:28 PM.
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bam, bam_reader, cython, cythonize, htseq

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