comparison tools/protein_analysis/wolf_psort.py @ 19:f3ecd80850e2 draft

v0.2.9 Python style improvements

18:eb6ac44d4b8e

normally use Python's multiprocessing library in this situation but it requires
at least Python 2.6 and at the time of writing Galaxy still supports Python 2.4.
"""
import sys
import os
from seq_analysis_utils import sys_exit, split_fasta, run_jobs, thread_count

FASTA_CHUNK = 500
exe = "runWolfPsortSummary"

"""

os.chdir("/opt/WoLFPSORT_package_v0.2/bin")
args = ["./runWolfPsortSummary"] + sys.argv[1:]
return_code = subprocess.call(args)
os.chdir(saved_dir)
sys.exit(return_code)
"""

if len(sys.argv) != 5:
    sys_exit("Require four arguments, organism, threads, input protein FASTA file & output tabular file")

organism = sys.argv[1]
if organism not in ["animal", "plant", "fungi"]:
    sys_exit("Organism argument %s is not one of animal, plant, fungi" % organism)

num_threads = thread_count(sys.argv[2], default=4)
fasta_file = sys.argv[3]
tabular_file = sys.argv[4]

def clean_tabular(raw_handle, out_handle):
    """Clean up WoLF PSORT output to make it tabular."""
    for line in raw_handle:
        if not line or line.startswith("#"):
            continue
        name, data = line.rstrip("\r\n").split(None,1)
        for rank, comp_data in enumerate(data.split(",")):
            comp, score = comp_data.split()
            out_handle.write("%s\t%s\t%s\t%i\n" \
                             % (name, comp, score, rank+1))

fasta_files = split_fasta(fasta_file, tabular_file, n=FASTA_CHUNK)
temp_files = [f+".out" for f in fasta_files]
assert len(fasta_files) == len(temp_files)
jobs = ["%s %s < %s > %s" % (exe, organism, fasta, temp)
        for (fasta, temp) in zip(fasta_files, temp_files)]
assert len(fasta_files) == len(temp_files) == len(jobs)

def clean_up(file_list):
    for f in file_list:
        if os.path.isfile(f):
            os.remove(f)

if len(jobs) > 1 and num_threads > 1:
    #A small "info" message for Galaxy to show the user.
    print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
results = run_jobs(jobs, num_threads)
assert len(fasta_files) == len(temp_files) == len(jobs)
for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
    error_level = results[cmd]

    except IOError:
        output = ""
    if error_level or output.lower().startswith("error running"):
        clean_up(fasta_files)
        clean_up(temp_files)
        sys_exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
                 error_level)
del results

out_handle = open(tabular_file, "w")
out_handle.write("#ID\tCompartment\tScore\tRank\n")

19:f3ecd80850e2

normally use Python's multiprocessing library in this situation but it requires
at least Python 2.6 and at the time of writing Galaxy still supports Python 2.4.
"""
import sys
import os
from seq_analysis_utils import split_fasta, run_jobs, thread_count

FASTA_CHUNK = 500
exe = "runWolfPsortSummary"

"""

os.chdir("/opt/WoLFPSORT_package_v0.2/bin")
args = ["./runWolfPsortSummary"] + sys.argv[1:]
return_code = subprocess.call(args)
os.chdir(saved_dir)
sys.exit(return_code)

For more details on this workaround, see:
https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-December/023386.html
"""

if len(sys.argv) != 5:
    sys.exit("Require four arguments, organism, threads, input protein FASTA file & output tabular file")

organism = sys.argv[1]
if organism not in ["animal", "plant", "fungi"]:
    sys.exit("Organism argument %s is not one of animal, plant, fungi" % organism)

num_threads = thread_count(sys.argv[2], default=4)
fasta_file = sys.argv[3]
tabular_file = sys.argv[4]


def clean_tabular(raw_handle, out_handle):
    """Clean up WoLF PSORT output to make it tabular."""
    for line in raw_handle:
        if not line or line.startswith("#"):
            continue
        name, data = line.rstrip("\r\n").split(None, 1)
        for rank, comp_data in enumerate(data.split(",")):
            comp, score = comp_data.split()
            out_handle.write("%s\t%s\t%s\t%i\n"
                             % (name, comp, score, rank + 1))

fasta_files = split_fasta(fasta_file, tabular_file, n=FASTA_CHUNK)
temp_files = [f + ".out" for f in fasta_files]
assert len(fasta_files) == len(temp_files)
jobs = ["%s %s < %s > %s" % (exe, organism, fasta, temp)
        for (fasta, temp) in zip(fasta_files, temp_files)]
assert len(fasta_files) == len(temp_files) == len(jobs)


def clean_up(file_list):
    for f in file_list:
        if os.path.isfile(f):
            os.remove(f)

if len(jobs) > 1 and num_threads > 1:
    # A small "info" message for Galaxy to show the user.
    print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
results = run_jobs(jobs, num_threads)
assert len(fasta_files) == len(temp_files) == len(jobs)
for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
    error_level = results[cmd]

    except IOError:
        output = ""
    if error_level or output.lower().startswith("error running"):
        clean_up(fasta_files)
        clean_up(temp_files)
        sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
                 error_level)
del results

out_handle = open(tabular_file, "w")
out_handle.write("#ID\tCompartment\tScore\tRank\n")