def main():
usage = "usage: %prog [Options]"
parser = OptionParser(usage=usage)
parser.add_option("-f", "--file", metavar="FILE", help="Fasta FILE to analyse", action="store", type="string", dest="file")
(options, args) = parser.parse_args()
if not (options.file):
parser.print_help()
sys.exit()
infoseq(options.file)
infoseq_file = open("%s.infoseq" % options.file, 'r').readlines()
total_nb_residues = 0
number_of_sequences = 0
stat_list = []
for line in infoseq_file:
line = line.strip()
number_of_sequences = number_of_sequences + 1
total_nb_residues = total_nb_residues + int(line)
stat_list.append(int(line))
average_length = total_nb_residues / number_of_sequences
stat_list.sort()
smallest = stat_list[0]
largest = stat_list[-1]
stats_file = open("%s.stats" % options.file, 'w')
# tab delimited output
stats_file.write("#seq\t#bases\tsmallest\tlargest\tavg\tN50_size\tN50_#seq\n")
stats_file.write("%s\t%s\t%s\t%s\t%s\t" % (number_of_sequences, total_nb_residues, smallest, largest, average_length))
# N50
stat_list.reverse()
n50_sum = 0
n50_size = 0
n50_number_of_sequences = 0
for x in stat_list:
n50_sum = n50_sum + x
n50_number_of_sequences = n50_number_of_sequences + 1
n50_size = x
if (n50_sum > (total_nb_residues / 2)):
stats_file.write("%s\t%s\n" % (n50_size, n50_number_of_sequences))
break
# clean tmp file
util.rmFile("%s.infoseq" % options.file)
log.info("Results in %s.stats" % options.file)
def doRun():
usage = "usage: %prog [Options]"
parser = OptionParser(usage=usage)
parser.add_option("-o", metavar="NAME", help="organism common name", action="store", type="string", dest="name")
parser.add_option(
"-i",
metavar="FILE",
help="input organism sequence file in FASTA format",
action="store",
type="string",
dest="input",
)
(options, args) = parser.parse_args()
try:
common_name = options.name
input_file = checkValidInput(options.input, common_name)
output_file = "%s.prodigal" % common_name
# Print info
log.info("Running prodigal on %s\n" % common_name)
log.info("Getting sequence from %s\n" % input_file)
# Run prodigal
softname = "prodigal"
util.checkSoft(softname)
cmd = "%s < %s > %s" % (softname, input_file, output_file)
util.runProcess(cmd)
# Run the conversion only if successful
if os.path.exists(output_file):
# Convert output results into a feature table EMBL file.
tab_file = convertToTab(output_file, common_name)
# Tidy up
util.rmFile(common_name + ".fna")
util.rmFile(output_file)
log.info("%s is the final feature table Prodigal predictions\n" % tab_file)
else:
log.info("%s file does not exists\n" % output_file)
except Exception, e:
log.error(e)
raise e
def doRun():
usage = "usage: %prog [Options]"
parser = OptionParser(usage=usage)
parser.add_option("-o", metavar="NAME", help="organism common name", action="store", type="string", dest="name")
parser.add_option("-i", metavar="FILE", help="input organism sequence file in FASTA format", action="store", type="string", dest="input")
(options, args) = parser.parse_args()
try:
common_name = options.name
input_file = checkValidInput(options.input, common_name)
# Print info
log.info("Running Glimmer3 on %s\n" % common_name)
log.info("Getting sequence from %s\n" % input_file)
# Run glimmer3 iterated
script = "/software/pathogen/external/applications/glimmer/glimmer/scripts/g3-iterated.csh"
util.checkFile(script)
cmd = "%s %s %s" % (script, input_file, common_name)
util.runProcess(cmd)
# Run the conversion only if g3 successful
g3_predict_file = "%s.predict" % common_name
if os.path.exists(g3_predict_file):
# Convert output results into a feature table EMBL file.
g3_tab = convertToTab(g3_predict_file, common_name)
# Tidy up
util.rmFile(common_name + ".longorfs")
util.rmFile(common_name + ".train")
util.rmFile(common_name + ".icm")
util.rmFile(common_name + ".run1.detail")
util.rmFile(common_name + ".run1.predict")
util.rmFile(common_name + ".coords")
util.rmFile(common_name + ".upstream")
util.rmFile(common_name + ".motif")
util.rmFile(common_name + ".detail")
util.rmFile(g3_predict_file)
log.info("%s is the final feature table Glimmer3 predictions\n" % g3_tab)
else:
log.info("%s file does not exists\n" % g3_predict_file)
except Exception, e:
log.error(e)
raise e