Hello,
I am currently using a python package methylpy, which uses samtools as a
dependency. When calling samtools in the package script I'm getting a
binary output in my terminal window. When viewing the package code I see
two different methods of calling samtools, one that is active and one that
is inactive. I was wondering if the code that is active is somehow wrong
and I should be using the inactive code when calling samtools, and was
hoping that you would be able to point me in the right direction.
Active python code:
subprocess.check_call(shlex.split(path_to_samtools+"samtools sort
"+path_to_files+sample+"_processed_reads_"+str(current_library)+"_no_clonal.bam
-o
"+path_to_files+sample+"_processed_reads_"+str(current_library)+"_no_clonal.bam"))
Inactive python Code:
#subprocess.check_call(shlex.split(path_to_samtools+"samtools sort
"+path_to_files+sample+"_processed_reads_"+str(current_library)+"_no_clonal.bam
"+path_to_files+sample+"_processed_reads_"+str(current_library)+"_no_clonal"))
Also, when run with a file (CG-16C-N_S18_L004_R1_001) it seems to be saying
my input is the same as my output (see below). This was all done with the
active code.
/usr/local/intel64/broadwell/gcc/samtools-0.1.19/bin//samtools sort
CG-16C-N_S18_L004_R1_001_processed_reads_libA_no_clonal.bam -o
CG-16C-N_S18_L004_R1_001_processed_reads_libA_no_clonal.bam
Any advice on the matter would be greatly appreciated. Thank you very much
for your time.
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