comparison tools/protein_analysis/wolf_psort.py @ 9:e52220a9ddad draft

Uploaded v0.1.2 Use the new <stdio> settings in the XML wrappers to catch errors. Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).

8:976a5f2833cd

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 stop_err, split_fasta, run_jobs

FASTA_CHUNK = 500
exe = "runWolfPsortSummary"

"""
Note: I had trouble getting runWolfPsortSummary on the path (via a link, other
than by including all of /opt/WoLFPSORT_package_v0.2/bin , so used a wrapper
python script called runWolfPsortSummary as follows:

#!/usr/bin/env python
#Wrapper script to call WoLF PSORT from its own directory.

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

try:
   num_threads = int(sys.argv[2])
except:
   num_threads = 0
if num_threads < 1:
   stop_err("Threads argument %s is not a positive integer" % sys.argv[2])

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:

9:e52220a9ddad

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 stop_err, split_fasta, run_jobs, thread_count

FASTA_CHUNK = 500
exe = "runWolfPsortSummary"

"""
Note: I had trouble getting runWolfPsortSummary on the path (via a link), other
than by including all of /opt/WoLFPSORT_package_v0.2/bin , so used a wrapper
python script called runWolfPsortSummary as follows:

#!/usr/bin/env python
#Wrapper script to call WoLF PSORT from its own directory.

organism = sys.argv[1]
if organism not in ["animal", "plant", "fungi"]:
   stop_err("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: