def main(argv=None):
"""
Main function called once at the end of this module. Configures and parses command line arguments, parses input
files and generates output files.
"""
# Parse command line arguments
import argparse
parser = ap.PrintUsageParser(description=__doc__)
optional = parser._action_groups.pop()
required = parser.add_argument_group('required arguments')
parser._action_groups.append(optional) # added this line
required.add_argument(
'--input',
required=True,
type=argparse.FileType('r'),
help='A multi-frame contact-file generated by dynamic_contact.py')
required.add_argument('--output',
required=False,
type=str,
help='The json file to write flare to')
optional.add_argument(
'--itypes',
required=False,
default=["all"],
type=str,
nargs='*',
help=
'Interaction types to include (comma separated list) [default: all]')
optional.add_argument('--flarelabels',
required=False,
default=None,
type=argparse.FileType('r'),
help='Flare-label file')
args = parser.parse_args(argv)
if args.output:
print("Parsing contact types %s from %s" %
(str(args.itypes), args.input.name))
# Read contacts and generate graph
itypes = parse_itypes(args.itypes)
contacts, num_frames = parse_contacts(args.input, itypes)
labels, colors = parse_residuelabels(args.flarelabels)
graph = create_flare(contacts, labels,
colors) # create_graph(contacts, labels)
args.input.close()
if args.flarelabels is not None:
args.flarelabels.close()
# Write output
if args.output:
write_json(graph, args.output)
print("Done. Wrote flare-json to %s" % args.output)
else:
write_json(graph, sys.stdout)
def main(argv=None):
# Parse arguments
parser = ap.PrintUsageParser(__doc__)
parser.add_argument("--input_contacts",
type=argparse.FileType('r'),
required=True,
metavar="FILE",
help="Path to contact file")
parser.add_argument("--clusters",
type=int,
required=False,
nargs="+",
default=[2, 5, 10],
metavar="INT",
help="Number of clusters [default: 2 5 10]")
parser.add_argument("--tab_output",
type=str,
required=False,
metavar="FILE",
help="Path to TICC output file (tab-separated time/cluster indicators)")
parser.add_argument("--frequency_output",
type=str,
required=False,
metavar="FILE",
help="Prefix to TICC output files (one res-frequency file for each cluster)")
parser.add_argument("--beta",
type=int,
required=False,
nargs="+",
default=[10, 50, 100],
metavar="INT",
help="Beta parameter [default: 10 50 100]")
parser.add_argument("--max_dimension",
type=int,
required=False,
default=50,
metavar="INT",
help="Max number of dimensions [default: 50]")
args = parser.parse_args(argv)
# Check output format and call corresponding function(s)
if all(a is None for a in [args.tab_output, args.frequency_output]):
parser.error("--tab_output or --frequency_output must be specified")
print("Reading atomic contacts from " + args.input_contacts.name)
atomic_contacts, num_frames = parse_contacts(args.input_contacts)
args.input_contacts.close()
print("Converting atomic contacts to residue contacts")
residue_contacts = res_contacts(atomic_contacts)
print("Performing dimensionality reduction")
time_matrix = featurize_contacts(residue_contacts, args.max_dimension)
print("Running TICC (clustered time-segmentation)")
segmentation = run_ticc(time_matrix, cluster_number=args.clusters, beta=args.beta)
if args.tab_output is not None:
print("Writing time-segments to " + args.tab_output)
with open(args.tab_output, "w") as f:
f.writelines(map(lambda l: str(int(l)) + "\n", segmentation[0][0]))
if args.frequency_output is not None:
k = segmentation[0][2][2]
for c in range(k):
cluster_frames = set([frame for frame, cluster in enumerate(segmentation[0][0]) if cluster == c])
cluster_contacts = [contact for contact in residue_contacts if contact[0] in cluster_frames]
num_frames = len(cluster_frames)
counts = gen_counts(cluster_contacts)
total_frames, frequencies = gen_frequencies([(num_frames, counts)])
fname = "%s_resfreq_cluster%03d.tsv" % (args.frequency_output, c)
print("Writing frequency-flare to " + fname)
with open(fname, "w") as output_file:
output_file.write('#\ttotal_frames:%d\tinteraction_types:all\n' % total_frames)
output_file.write('#\tColumns:\tresidue_1,\tresidue_2\tframe_count\tcontact_frequency\n')
for (res1, res2), (count, frequency) in frequencies.items():
output_file.write('\t'.join([res1, res2, "%.3f" % frequency]) + "\n")
def main(argv=None):
# Parse command line arguments
parser = ap.PrintUsageParser(description=__doc__)
parser.add_argument('--input_frequencies',
type=argparse.FileType('r'),
required=True,
nargs='+',
help="Paths to one or more residue frequency files")
parser.add_argument(
'--frequency_cutoff',
type=float,
required=False,
default=0.6,
help=
"Only interactions occurring at least this frequently will be plotted (default: 0.6)"
)
parser.add_argument(
'--column_headers',
type=str,
required=False,
nargs='+',
help=
"Header column labels. If nothing is specified, the input_frequencies filenames are used"
)
parser.add_argument(
'--cluster_columns',
type=bool,
required=False,
default=False,
help="Perform hierarchical clustering on the columns (default: False)")
parser.add_argument(
'--table_output',
type=str,
required=False,
default=None,
help=
"If specified, the tab-separated frequency table will be written to this file"
)
parser.add_argument(
'--plot_output',
type=str,
required=False,
default=None,
help=
"If specified, the heatmap will be written to this file (supports svg and png formats)"
)
parser.add_argument(
'--flare_output',
type=str,
required=False,
default=None,
help="If specified, a compare-flare will be written to this json-file")
parser.add_argument(
'--pymol_output',
type=str,
required=False,
default=None,
help=
"If specified, a distance-selection will be written to this pml-file")
args = parser.parse_args(argv)
freq_table = parse_frequencyfiles(args.input_frequencies,
args.frequency_cutoff)
# Determine column headers and exit on error
column_headers = [f.name for f in args.input_frequencies
] if args.column_headers is None else args.column_headers
if len(column_headers) != len(args.input_frequencies):
parser.error(
"--column_header arguments must match length of --input_frequencies"
)
# Check output format and call corresponding function(s)
if all(a is None for a in [
args.table_output, args.flare_output, args.plot_output,
args.pymol_output
]):
parser.error(
"--table_output, --flare_output, or --plot_output must be specified"
)
if args.table_output is not None:
write_frequencytable(freq_table, column_headers, args.table_output)
print("Wrote frequency table to " + args.table_output)
if args.flare_output is not None:
compare_flare = compose_frequencytable(freq_table, column_headers,
args.frequency_cutoff)
write_json(compare_flare, args.flare_output)
print("Wrote multi flare to " + args.flare_output)
if args.plot_output is not None:
plot_frequencies(freq_table, column_headers, args.plot_output,
args.cluster_columns)
print("Wrote fingerprint heatmap to " + args.plot_output)
if args.pymol_output is not None:
compare_flare = compose_frequencytable(freq_table, column_headers,
args.frequency_cutoff)
write_pymol_distances(compare_flare, args.pymol_output)
print("Wrote pymol file to " + args.pymol_output)
for f in args.input_frequencies:
f.close()
def main(argv=None):
"""
Main function called once at the end of this module. Configures and parses command line arguments, parses input
files and generates output files.
"""
# Set up command line arguments
import argparse
# parser = ap.ArgumentParser(description=__doc__, formatter_class=ap.RawTextHelpFormatter)
parser = ap.PrintUsageParser(description=__doc__)
optional = parser._action_groups.pop()
required = parser.add_argument_group('required arguments')
parser._action_groups.append(optional) # added this line
required.add_argument(
'--input_contacts',
required=True,
nargs='+',
type=argparse.FileType('r'),
help='A multi-frame contact-file generated by dynamic_contact.py')
required.add_argument(
'--interactions',
required=True,
type=str,
nargs='+',
help='Interaction patterns, each a space-separated pair of regexes')
optional.add_argument(
'--trace_output',
required=False,
type=str,
help='An image file to write the trace-plot to (png and svg supported)'
)
optional.add_argument(
'--jaccard_output',
required=False,
type=str,
help=
'An image file to write the Jaccard-matrix to (png and svg supported)')
optional.add_argument(
'--correlation_output',
required=False,
type=str,
help=
'An image file to write the Jaccard-matrix to (png and svg supported)')
optional.add_argument(
'--labels',
required=False,
type=str,
nargs='+',
help=
'Interaction pattern labels. If not specified, the regexes will be used'
)
args = parser.parse_args(argv)
if args.trace_output is None and args.jaccard_output is None and args.correlation_output is None:
parser.error("--trace_output or --jaccard_output must be specified")
# Process arguments
itypes = parse_itypes(['all'])
print("Reading contacts")
contact_lists = [
parse_contacts(contact_file, itypes)[0]
for contact_file in args.input_contacts
]
print("Parsing interaction patterns")
interaction_patterns = parse_interaction_patterns(args.interactions,
contact_lists)
labels = parse_labels(args.labels, args.input_contacts,
interaction_patterns)
# Filter contacts and generate trace
print("Filtering interactions")
contact_frames = filter_contacts(contact_lists, interaction_patterns)
if args.trace_output is not None:
write_trace(contact_frames, labels, args.trace_output)
if args.jaccard_output is not None:
write_jaccard(contact_frames, labels, args.jaccard_output)
if args.correlation_output is not None:
write_correlation(contact_frames, labels, args.correlation_output)