def main():
options = mainUsage()
script = options.run
checkDoRun(script)
try:
# Read organism common name and related fasta sequence file
list_file = options.list
util.checkFile(list_file)
for line in open(list_file, "r"):
if line[0] == '!':
continue
if line.count('||') < 1:
continue
# ! common_name||sequence_file
common_name, input_file = util.splitLine(line)
util.checkFile(input_file)
# Run command
cmd = 'python -c "from genepy.annotators.%s import doRun; doRun()" -o %s -i %s' % (script, common_name, input_file)
if util.isLsf():
job_name = "%s.%s" % (common_name, ANNOTATOR_EXTENSION[script])
util.submitJob(job_name, cmd, ANNOTATOR_QUEUE[script])
else:
util.runProcess(cmd)
except Exception, e:
log.error(e)
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
# ropy import
import ropy
# genepy import
import util
from setup import connectionFactory, logger
### ---------------------------------------------------------------------------
### GENEPY constants
### ---------------------------------------------------------------------------
# platform
IS_LSF = util.isLsf()
bsub_dir = "bsub"
# software
soft_lists = ['fasta35', 'pfscan']
# data
mygenome_dir = "mygenome"
mygenome_fastafile_allcds = "mygenome_allcds.faa"
refgenomes_dir = "refgenomes"
# results
fasta_dir = "results_fasta"
reciprocalfasta_dir = "results_reciprocalfasta"
refgenomes_extractedseq_dir = "refgenomes_extractedseq"
hamap_dir = "results_hamap"
### ---------------------------------------------------------------------------