Help with sorting sam files in python!

[mavadhani]

Hello All!

I am new to coding. I have written a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess module to call bowtie2 in order to index the genome and align the unpaired short reads to the genome.My script generates a sam file which needs to be sorted before running the cuffdiff module. The linux sort command works perfectly on my mac, however, in spite of installing the Unxupdates on my windows at work, I am unable to make my script work. I am hoping for some help/advice here to sort my sam file in python. Here is the script I tried.

#!/usr/bin/env python2.7

import os, sys

inputFile = open(‘Outputfile1.txt’, 'r')

lineList = inputFile.readlines()

for line in sorted(lineList):

print(line.rstrip());

With this script, the stdout is written to the screen. But this recognizes only the text file. Sam files are not recognized.

Any help is much appreciated.

Thanks in advance.
-M

[wdecoster]

No, that's really not how you should sort a sam file. You should either have a look at samtools sort or pysam (python module).

I don't think doing this in plain python is a good idea, there are better alternatives such as bash loops, gnu-parallel, snakemake.

[mavadhani]

Hi wdecoster,

Thanks for your response. Samtools sort function does not work on the windows terminal with either sam or bam files. But the samtools view function converts sam to bam format successfully. Also, the latest version of pysam for windows is not running on my machine. I will try snakemake.

Thanks again,
-M

[GenoMax]

Samtools sort function does not work on the windows terminal with either sam or bam files.

Is that reference to "ubuntu bash on windows 10" or something else?

[mavadhani]

Thanks GenoMax. Samtools sort sorts only bam files on the windows 10 terminal. With the sam file input, it gives the following error: samtools.exe has stopped working.

Also, does pysam work on windows? From what I saw, there is no pysam version for windows yet.

Thanks again,
-M

[GenoMax]

AFAIK the linux version of samtools works with ubuntu bash terminal in windows 10. Are you not using that (I see a reference to samtools.exe)?

[mavadhani]

That is what I am using. samtools view works fine. The sort function works only on bam input, not on the sam input.

I downloaded unix utilities from
http://gnuwin32.sourceforge.net/packages/coreutils.htm.

Now the linux sort works on windows.

Thanks again.
-M