def readGenomesFromFile(multi_files_fname, genome_dir, genome_dicts, column_index=1, load_fxn=biofile.firstField, species=None, outstream=None):
if outstream is None:
outstream = util.OutStreams()
# Format for
species_map = {}
for line in file(multi_files_fname,'r').readlines():
if line[0] != '#' and not line.strip() == '': # skip comments and blank lines
flds = line.strip().split()
#print flds, column_index
species_map[flds[0]] = flds[column_index]
if species is None:
species = species_map.keys()
else:
assert set(species).intersection(set(species_map.keys())) == set(species), "Not all specified species found in mapping file"
for spec in species:
genome_file = os.path.join(os.path.expanduser(genome_dir), species_map[spec])
if not os.path.isfile(genome_file):
outstream.write("# Cannot find file %s\n" % genome_file)
genome = biofile.readFASTADict(genome_file, load_fxn)
genome_dicts[spec] = genome
outstream.write("# species=%s, genome file=%s has %d entries, example ID=%s\n" % (spec, genome_file, len(genome.keys()), genome.keys()[0]))
return species_map
# Required arguments
parser.add_argument(dest="orthodb_id", type=str, help="OrthoDB ID")
# Optional arguments
parser.add_argument("-o",
"--out",
dest="out_fname",
default=None,
help="output filename")
parser.add_argument("--fasta-out",
dest="fasta_out_fname",
default=None,
help="output FASTA filename")
#parser.add_argument("-o", "--out-dir", dest="out_dir", default='', help="output file directory")
options = parser.parse_args()
info_outs = util.OutStreams()
#data_outs = util.OutStreams()
fasta_outs = util.OutStreams()
# Start up output
if not options.out_fname is None:
outf = file(options.out_fname, 'w')
info_outs.addStream(outf)
else:
# By default, write to stdout
info_outs.addStream(sys.stdout)
if not options.fasta_out_fname is None:
outf = file(options.fasta_out_fname, 'w')
fasta_outs.addStream(outf)
else:
# By default, write to stdout
pos = n-1
return pval_list[pos]
if __name__=='__main__':
parser = argparse.ArgumentParser(description="Compute P-values for entropy")
# Required arguments
parser.add_argument(dest="in_fname", help="input filename")
parser.add_argument(dest="in_distribution_fname_pattern", help="input distribution filename pattern")
# Optional arguments
parser.add_argument("-a", "--adjust", dest="adjust", action='store_true', default=False, help="adjust P-values")
parser.add_argument("-l", "--lower", dest="min_window_size", default=5, help="minimum window size")
parser.add_argument("-u", "--upper", dest="max_window_size", default=300, help="maximum window size")
parser.add_argument("-o", "--out", dest="out_fname", default=None, help="output filename")
options = parser.parse_args()
info_outs = util.OutStreams(sys.stdout)
data_outs = util.OutStreams()
# Start up output
if not options.out_fname is None:
outf = file(options.out_fname,'w')
data_outs.addStream(outf)
else:
# By default, write to stdout
data_outs.addStream(sys.stdout)
# Write out parameters
data_outs.write("# Run started {}\n".format(util.timestamp(timeformat="%a %b %d %H:%M:%S %Y")))
data_outs.write("# Parameters:\n")
optdict = vars(options)
for (k,v) in optdict.items():
help="random-number generator seed")
parser.add_argument("-p",
"--optimize",
dest="optimize",
action="store_true",
default=False,
help="optimize the codons?")
options = parser.parse_args()
# Fetch sequence
seq = options.sequence
random.seed(options.seed)
# Start up output
info_outs = util.OutStreams([sys.stdout])
data_outs = util.OutStreams()
multi_outs = util.OutStreams([info_outs, data_outs])
if not options.out_fname is None:
outf = file(options.out_fname, 'w')
data_outs.addStream(outf)
else:
data_outs.addStream(sys.stdout)
# Read sequences from a FASTA file?
fname = os.path.expanduser(seq)
if os.path.isfile(fname):
(headers, seq_list) = biofile.readFASTA(fname)
seqs = zip(headers, seq_list)
info_outs.write("# Read {0:d} sequences from {1}\n".format(
len(seqs), fname))
action="store_true",
default=False,
help="generate short species IDs (e.g. S.cerevisiae) for each sequence?"
)
parser.add_argument("-o",
"--out",
dest="out_fname",
default=None,
help="output filename")
parser.add_argument("--fasta-out",
dest="fasta_out_fname",
default=None,
help="FASTA output filename")
options = parser.parse_args()
info_outs = util.OutStreams(sys.stdout)
data_outs = util.OutStreams()
# Start up output
if not options.out_fname is None:
outf = open(options.out_fname, 'w')
data_outs.addStream(outf)
else:
# By default, write to stdout
data_outs.addStream(sys.stdout)
# Write out parameters
data_outs.write("# Run started {}\n".format(util.timestamp()))
data_outs.write("# Command: {}\n".format(' '.join(sys.argv)))
data_outs.write("# Parameters:\n")
optdict = vars(options)
if prot_align[i] == '-':
out_align += "-"
else:
out_align += prot[j]
j += 1
return out_align
if __name__=='__main__':
parser = argparse.ArgumentParser(description="Muscle alignment")
parser.add_argument("in_fname", help="input filename")
parser.add_argument("-p", "--path", dest="muscle_path", default=const_default_muscle_exepath, help="path to Muscle binary")
parser.add_argument("-t", "--translate", dest="translate", action="store_true", default=False, help="translate the input sequences?")
parser.add_argument("-o", "--out", dest="out_fname", default=None, help="output filename")
options = parser.parse_args()
outs = util.OutStreams()
if not options.out_fname is None:
fname = os.path.expanduser(options.out_fname)
#print fname
outf = open(fname,'w')
outs.addStream(outf)
else:
outs.addStream(sys.stdout)
(headers, seqs) = biofile.readFASTA(open(options.in_fname,'r'))
seqs_to_align = seqs
if options.translate:
seqs_to_align = [translate.translate(s) for s in seqs]
alseqs = alignSequences(seqs_to_align, exepath=options.muscle_path)
#print alseqs
if options.translate:
dest="normalize_ratio_by_orf",
default=None,
help="ORF to use for normalization across runs")
parser.add_argument(
"--ratio-sig",
dest="ratio_significance_field",
default="ratio_hl_normalized",
help="field to use for ratio significance calculations")
parser.add_argument("--abundance",
dest="abundance_field",
default="intensity",
help="field to use for abundance calculations")
options = parser.parse_args()
# Set up some output
info_outs = util.OutStreams(sys.stdout)
orf_dict = None
if not options.database_fname is None:
orf_dict = biofile.readFASTADict(options.database_fname)
evidences = []
if not options.in_fname is None:
#print "# Loading..."
# Read more experiments from master file
inf = file(os.path.expanduser(options.in_fname), 'r')
dlr = util.DelimitedLineReader(inf, header=True)
while not dlr.atEnd():
flds = dlr.nextDict()
if os.path.isfile(os.path.expanduser(flds['filename'])):
ed = mq.EvidenceDescriptor()
action='store_true',
default=False,
help="execute debugging code?")
parser.add_argument("-o",
"--out",
dest="out_fname",
default=None,
help="output filename")
parser.add_argument("--isolate-out",
dest="isolate_out_fname",
default=None,
help="output filename")
options = parser.parse_args()
info_outs = util.OutStreams(sys.stdout)
data_outs = util.OutStreams()
isolate_outs = util.OutStreams()
params_outs = util.OutStreams([data_outs])
motif_outs = None
# Start up output
if not options.out_fname is None:
outf = file(options.out_fname, 'w')
data_outs.addStream(outf)
else:
# By default, write to stdout
if options.isolate_out_fname is None:
data_outs.addStream(sys.stdout)
if not options.isolate_out_fname is None:
isolate_outf = file(options.isolate_out_fname, 'w')
# Optional arguments
parser.add_argument(
"--resolution-ml",
dest="resolution_ml",
default=0.005,
help=
"output resolution, in mL: average output over elution-volume ranges no larger than this number"
)
parser.add_argument("-o",
"--out",
dest="out_fname",
default=None,
help="output filename")
options = parser.parse_args()
info_outs = util.OutStreams(sys.stdout)
data_outs = util.OutStreams()
# Start up output
if not options.out_fname is None:
outf = open(options.out_fname, 'w')
data_outs.addStream(outf)
else:
# By default, write to stdout
data_outs.addStream(sys.stdout)
# Create the instance using default options
if os.path.isdir(options.in_fname):
basedir = options.in_fname
for in_fname in os.listdir(options.in_fname):
full_fname = os.path.join(basedir, in_fname)
