comparison tools/protein_analysis/signalp3.py @ 26:20139cb4c844 draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty

25:41a42022f815

the predictors which gives a cleavage site). *WORK IN PROGRESS*
"""
import sys
import os
import tempfile
from seq_analysis_utils import stop_err, split_fasta, fasta_iterator
from seq_analysis_utils import run_jobs, thread_count

FASTA_CHUNK = 500
MAX_LEN = 6000 #Found by trial and error

if len(sys.argv) not in  [6,8]:
    stop_err("Require five (or 7) arguments, organism, truncate, threads, "
             "input protein FASTA file & output tabular file (plus "
             "optionally cut method and GFF3 output file). "
             "Got %i arguments." % (len(sys.argv)-1))

organism = sys.argv[1]
if organism not in ["euk", "gram+", "gram-"]:
    stop_err("Organism argument %s is not one of euk, gram+ or gram-" % organism)

try:
    truncate = int(sys.argv[2])
except:
    truncate = 0
if truncate < 0:
    stop_err("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])

num_threads = thread_count(sys.argv[3], default=4)
fasta_file = sys.argv[4]
tabular_file = sys.argv[5]

if len(sys.argv) == 8:
    cut_method = sys.argv[6]
    if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]:
        stop_err("Invalid cut method %r" % cut_method)
    gff3_file = sys.argv[7]
else:
    cut_method = None
    gff3_file = None

        output = open(temp).readline()
    except IOError:
        output = "(no output)"
    if error_level or output.lower().startswith("error running"):
        clean_up(fasta_files + temp_files)
        stop_err("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")
fields = ["ID"]

26:20139cb4c844

the predictors which gives a cleavage site). *WORK IN PROGRESS*
"""
import sys
import os
import tempfile
from seq_analysis_utils import sys_exit, split_fasta, fasta_iterator
from seq_analysis_utils import run_jobs, thread_count

FASTA_CHUNK = 500
MAX_LEN = 6000 #Found by trial and error

if len(sys.argv) not in  [6,8]:
    sys_exit("Require five (or 7) arguments, organism, truncate, threads, "
             "input protein FASTA file & output tabular file (plus "
             "optionally cut method and GFF3 output file). "
             "Got %i arguments." % (len(sys.argv)-1))

organism = sys.argv[1]
if organism not in ["euk", "gram+", "gram-"]:
    sys_exit("Organism argument %s is not one of euk, gram+ or gram-" % organism)

try:
    truncate = int(sys.argv[2])
except:
    truncate = 0
if truncate < 0:
    sys_exit("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])

num_threads = thread_count(sys.argv[3], default=4)
fasta_file = sys.argv[4]
tabular_file = sys.argv[5]

if len(sys.argv) == 8:
    cut_method = sys.argv[6]
    if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]:
        sys_exit("Invalid cut method %r" % cut_method)
    gff3_file = sys.argv[7]
else:
    cut_method = None
    gff3_file = None

        output = open(temp).readline()
    except IOError:
        output = "(no output)"
    if error_level or output.lower().startswith("error running"):
        clean_up(fasta_files + 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")
fields = ["ID"]