comparison tools/protein_analysis/tmhmm2.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

when there is no output from tmhmm2, and raise an error.
"""
import sys
import os
import tempfile
from seq_analysis_utils import stop_err, split_fasta, run_jobs

FASTA_CHUNK = 500

if len(sys.argv) != 4:
   stop_err("Require three arguments, number of threads (int), input protein FASTA file & output tabular file")
try:
   num_threads = int(sys.argv[1])
except:
   num_threads = 1 #Default, e.g. used "$NSLOTS" and environment variable not defined
if num_threads < 1:
   stop_err("Threads argument %s is not a positive integer" % sys.argv[1])
fasta_file = sys.argv[2]
tabular_file = sys.argv[3]

tmp_dir = tempfile.mkdtemp()

9:e52220a9ddad

when there is no output from tmhmm2, and raise an error.
"""
import sys
import os
import tempfile
from seq_analysis_utils import stop_err, split_fasta, run_jobs, thread_count

FASTA_CHUNK = 500

if len(sys.argv) != 4:
   stop_err("Require three arguments, number of threads (int), input protein FASTA file & output tabular file")

num_threads = thread_count(sys.argv[1], default=4)
fasta_file = sys.argv[2]
tabular_file = sys.argv[3]

tmp_dir = tempfile.mkdtemp()