Create an indexed tabix file from a Pandas dataframe via subprocess

pandas_df_to_tabix_via_subprocess.py

#!/usr/bin/env python

'''
Create an indexed tabix file from a Pandas dataframe 
via temporary intermediate file and subprocess
''' 

import os
import io
import pandas as pd
import tempfile
import subprocess

ds = io.StringIO('''chr1	842320	842327
chr1	842328	842330
chr1	842328	842330
chr1	855426	855427
chr1	855739	855740''')

df = pd.read_csv(ds, delimiter='\t', header=None)

with tempfile.NamedTemporaryFile() as temp_fh:
    df.to_csv(temp_fh, sep='\t', header=False, index=False)
    out_bgz_fn = "test_pd_subprocess.bed.gz"
    with open(out_bgz_fn, 'wb') as out_bgz_fh:
        res = subprocess.call(['bgzip', '-c', temp_fh.name], stdout=out_bgz_fh)
        if res != 0 or os.stat(out_bgz_fn).st_size == 0:
            raise Exception("Error: Could not create bgzip archive")
    out_index_fn = "{}.tbi".format(out_bgz_fn)
    if not os.path.exists(out_index_fn):
        subprocess.call(['tabix', out_bgz_fn, '-p', 'bed'])
        if not os.path.exists(out_index_fn) or os.stat(out_index_fn).st_size == 0:
            raise Exception("Error: Could not create index of bgzip archive")