/
elprep_io_wrapper.py
executable file
·123 lines (113 loc) · 5.86 KB
/
elprep_io_wrapper.py
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#!/usr/bin/env python
import sys
import subprocess
import os
import multiprocessing
# utilities
def member(el,l):
i = iter(l)
for val in i:
if val == el:
rest = list(i)
return [el] + rest
def flg_option(opt, cmdl):
val = member(opt, cmdl)
return [opt] if val else []
def cmd_option(opt, cmdl):
val = member(opt, cmdl)
return [opt,val[1]] if val else []
def remove_flg_option(cmd_l, name):
nl = []
i = iter(cmd_l)
val = next(i, None)
while(val):
if not(val == name):
nl = nl + [val]
val = next(i, None)
return nl
def remove_cmd_option(cmd_l, name):
"removes a command with its option value from a list of commands"
nl = []
i = iter(cmd_l)
val = next(i, None)
while(val):
if not(val == name):
nl = nl + [val]
val = next(i, None)
else:
next(i, None)
val = next(i, None)
return nl
def cmd_wrap_input (cmd_list, file_in, file_out, cmd_opts):
input = os.path.basename(file_in)
input_prefix, input_extension = os.path.splitext(input)
nr_of_threads_opt = cmd_option("--nr-of-threads", cmd_opts)
nr_of_threads = str(nr_of_threads_opt[1]) if nr_of_threads_opt else str(multiprocessing.cpu_count())
if (input_extension == ".bam" or input_extension == ".cram"):
p1 = subprocess.Popen(["samtools", "view", "-h", "-@", nr_of_threads, file_in], bufsize=-1, stdout=subprocess.PIPE)
p2 = subprocess.Popen(cmd_list + ["/dev/stdin", file_out] + cmd_opts, bufsize=-1, stdin=p1.stdout)
p2.communicate()
if p2.returncode != 0: raise SystemExit, p2.returncode
else:
ret = subprocess.call(cmd_list + [file_in, file_out] + cmd_opts)
if ret != 0: raise SystemExit, ret
def cmd_wrap_output (cmd_list, file_in, file_out, cmd_opts):
output = os.path.basename(file_out)
output_prefix, output_extension = os.path.splitext(output)
nr_of_threads_opt = cmd_option("--nr-of-threads", cmd_opts)
nr_of_threads = str(nr_of_threads_opt[1]) if nr_of_threads_opt else str(multiprocessing.cpu_count())
if (output_extension == ".bam" or output_extension == ".cram"):
p1 = subprocess.Popen(cmd_list + [file_in, "/dev/stdout"] + cmd_opts, bufsize=-1, stdout=subprocess.PIPE)
p2 = subprocess.Popen(["samtools", "view", "-bS", "-@", nr_of_threads, "-o", file_out, "-"], bufsize=-1, stdin=p1.stdout)
p2.communicate()
if p2.returncode != 0: raise SystemExit, p2.returncode
else:
ret = subprocess.call(cmd_list + [file_in, file_out] + cmd_opts)
if ret != 0: raise SystemExit, ret
def cmd_wrap_io(cmd_list, file_in, file_out, cmd_opts):
input = os.path.basename(file_in)
output = os.path.basename(file_out)
output_prefix, output_extension = os.path.splitext(output)
input_prefix, input_extension = os.path.splitext(input)
nr_of_threads_opt = cmd_option("--nr-of-threads", cmd_opts)
nr_of_threads = str(nr_of_threads_opt[1]) if nr_of_threads_opt else str(multiprocessing.cpu_count())
if (input_extension == ".bam" or input_extension == ".cram"):
p1 = subprocess.Popen(["samtools", "view", "-h", "-@", nr_of_threads, file_in], bufsize=-1, stdout=subprocess.PIPE)
if (output_extension == ".bam"):
p2 = subprocess.Popen(cmd_list + ["/dev/stdin", "/dev/stdout"] + cmd_opts, bufsize=-1, stdin=p1.stdout, stdout=subprocess.PIPE)
p3 = subprocess.Popen(["samtools", "view", "-bS", "-@", nr_of_threads, "-o", file_out, "-"], bufsize=-1, stdin=p2.stdout)
p3.communicate()
if p3.returncode != 0: raise SystemExit, p3.returncode
elif (output_extension == ".cram"):
reference_t_opt = cmd_option("--reference-t", cmd_opts)
reference_bigT_opt = cmd_option("--reference-T", cmd_opts)
if not(reference_t_opt) and not(reference_bigT_opt): return "Converting to .cram. Need to pass reference-t or reference-T"
opt_to_delete = "--reference-t" if reference_t_opt else "--reference-T"
p2 = subprocess.Popen(cmd_list + ["/dev/stdin", "/dev/stdout"] + remove_cmd_option(cmd_opts, opt_to_delete), bufsize=-1, stdin=p1.stdout, stdout=subprocess.PIPE)
t_opt = ["-t", reference_t_opt[1]] if reference_t_opt else ["-T", reference_bigT_opt[1]]
p3 = subprocess.Popen(["samtools", "view", "-C", "-@", nr_of_threads] + t_opt + ["-o", file_out, "-"], bufsize=-1, stdin=p2.stdout)
p3.communicate()
if p3.returncode != 0: raise SystemExit, p3.returncode
else: # output_extension == ".sam"
p2 = subprocess.Popen(cmd_list + ["/dev/stdin", file_out] + cmd_opts, bufsize=-1, stdin=p1.stdout)
p2.communicate()
if p2.returncode != 0: raise SystemExit, p2.returncode
else: # input_extension == ".sam"
if (output_extension == ".bam"):
p1 = subprocess.Popen(cmd_list + [file_in, "/dev/stdout"] + cmd_opts, bufsize=-1, stdout=subprocess.PIPE)
p2 = subprocess.Popen(["samtools", "view", "-bS", "-@", nr_of_threads, "-o", file_out, "-"], bufsize=-1, stdin=p1.stdout)
p2.communicate()
if p2.returncode != 0: raise SystemExit, p2.returncode
elif (output_extension == ".cram"):
reference_t_opt = cmd_option("--reference-t", cmd_opts)
reference_bigT_opt = cmd_option("--reference-T", cmd_opts)
if not(reference_t_opt) and not(reference_bigT_opt): return "Converting to .cram. Need to pass reference-t or reference-T"
opt_to_delete = "--reference-t" if reference_t_opt else "--reference-T"
p1 = subprocess.Popen(cmd_list + [file_in, "/dev/stdout"] + remove_cmd_option(cmd_opts, opt_to_delete), bufsize=-1, stdout=subprocess.PIPE)
t_opt = ["-t", reference_t_opt[1]] if reference_t_opt else ["-T", reference_bigT_opt[1]]
p2 = subprocess.Popen(["samtools", "view", "-C", "-@", nr_of_threads] + t_opt + ["-o", file_out, "-"], bufsize=-1, stdin=p1.stdout)
p2.communicate()
if p2.returncode != 0: raise SystemExit, p2.returncode
else: # output_extension == ".sam"
ret = subprocess.call(cmd_list + [file_in, file_out] + cmd_opts)
if ret != 0: raise SystemExit, ret