I am writing a script to sort a file based on a specific column. I tried calling the 'sort' Linux command for this. The code I am using is:
from subprocess import
path_store = /homes/varshith/maf
input = path_store
field = "-k2"
store_output_in_new_file = ">"
new_path = path_store + "_sort.bed"
sorting = Popen(["sort", field, input, append, new_path], stdout=PIPE)
But this doesn't work properly. Thanks in advance for helping.
Use communicate to get the output:
from subprocess import PIPE,Popen
sorting = Popen(["sort", field, output, append, new_path], stdout=PIPE)
out, err = sorting.communicate()
print out
Or just use check_output for python >= 2.7:
sorting = check_output(["sort", field, output, append, new_path])
If you want to just write the sorted contents you can redirect stdout to a file object:
output = "path/to/parentfile"
cmd = "sort -k2 {}".format(output)
with open(new_file,"w") as f:
sorting = Popen(cmd.split(),stdout=f)
> not the file, one sec I will editFirst of all, I hope that output and new_path are actually strings (I assume so, but it's not clear from what you posted). But assuming all of that is sorted out:
sorting = Popen(...)
sorting_output = sorting.communicate()[0]
That should store the contents of the subprocess's standard output to sorting_output.
To emulate the shell command:
$ sort -k2 /homes/varshith/maf > /homes/varshith/maf_sort.bed
i.e., to sort /homes/varshith/maf file by the 2nd column and to store the sorted output to /homes/varshith/maf_sort.bed file in Python:
#!/usr/bin/env python
from subprocess import check_call
field = '-k2'
input_path = '/homes/varshith/maf'
output_path = input_path + '_sort.bed'
with open(output_path, 'wb', 0) as output_file:
check_call(["sort", field, input_path], stdout=output_file)
It overwrites the output file. To append to the file instead, use ab mode instead of wb.
