def main():
parser = argparse.ArgumentParser(
description="Update predictors min, max and count")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
cmd.add_selected_predictors_args()
args, logger = cmd.parse_args("pred-update")
db = cmd.open_db()
try:
predictors = cmd.get_selected_predictors(default_all=True)
logger.info("Updating predictors ...")
start_time = datetime.now()
db.update_predictors(predictors)
db.commit()
logger.info("Finished. elapsed={}".format(datetime.now() - start_time))
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="Generate datasets needed to evaluate performance from Cosmic mutations")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("data_path", metavar="PATH",
help="The CosmicMutantExport tsv file")
parser.add_argument("cgc_path", metavar="PATH",
help="The list of CGC genes")
parser.add_argument("tdrivers_path", metavar="PATH",
help="The list of TD drivers")
parser.add_argument("pdrivers_path", metavar="PATH",
help="The list of PD drivers")
parser.add_argument("-o", dest="prefix", metavar="PREFIX",
help="Output prefix.")
args, logger = cmd.parse_args("perf-cosmic")
fanns_db = cmd.open_db()
try:
snvs = extract_snvs(fanns_db, args.data_path, logger=logger)
create_datasets(snvs, args.cgc_path, args.tdrivers_path, args.pdrivers_path, args.prefix)
except:
cmd.handle_error()
return 0
def main():
parser = argparse.ArgumentParser(
description="Remove annotations")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("id", metavar="ID", nargs="+",
help="Annotation identifier.")
args, logger = cmd.parse_args("ann-rm")
db = cmd.open_db()
try:
if "*" in args.id:
logger.info("Removing all the annotations ...")
for ann in db.maps():
logger.info(" {} {} ...".format(ann["id"], ann["name"]))
db.remove_map(ann["id"])
else:
for ann_id in args.id:
logger.info("Removing annotation {} ...".format(ann_id))
db.remove_map(ann_id)
db.commit()
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="Create a functional scores database")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("predictors", metavar="PREDICTORS", nargs="*",
help="Predictor identifiers")
args, logger = cmd.parse_args("create")
db = cmd.create_db()
try:
for predictor_id in args.predictors:
logger.info("Adding predictor {} ...".format(predictor_id))
db.add_predictor(predictor_id, FannsDb.SOURCE_PREDICTOR_TYPE)
db.set_initialized()
db.commit()
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="Manipulate database indices")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("ops", metavar="OPERATIONS", nargs="+", choices=["drop", "create"],
help="The operations to perform on the indices.")
args, logger = cmd.parse_args("index")
db = cmd.open_db()
try:
start_time = datetime.now()
for op in args.ops:
if op == "drop":
logger.info("Dropping indices ...")
db.drop_indices()
elif op == "create":
logger.info("Creating indices ...")
db.create_indices()
elapsed_time = datetime.now() - start_time
logger.info("Done. Elapsed time: {}".format(elapsed_time))
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="List predictors")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("--json", dest="to_json", action="store_true", default=False,
help="Print the results in json format")
args, log = cmd.parse_args("pred-list")
db = cmd.open_db()
try:
if args.to_json:
d = {}
for pred in db.predictors():
d[pred["id"]] = dict([(k,pred[k]) for k in ["type", "source", "min", "max", "count"]])
import json
print json.dumps(d, indent=True)
else:
print "\t".join(["ID", "TYPE", "SOURCE", "MIN", "MAX", "COUNT"])
for pred in db.predictors():
print "\t".join([str(pred[k]) for k in ["id", "type", "source", "min", "max", "count"]])
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(description="Add annotations")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("id", metavar="ID", help="Annotation identifier.")
parser.add_argument("name", metavar="NAME", help="Annotation name.")
parser.add_argument(
"type", metavar="TYPE", choices=["transcript", "protein"], help="Annotation type: transcript, protein"
)
parser.add_argument("path", metavar="PATH", help="Annotation items")
parser.add_argument(
"--priority",
dest="priority",
default=0,
help="Priority for translating input annotations. 0 means not considered for translation. Default 0.",
)
parser.add_argument(
"--header",
dest="header",
action="store_true",
default=False,
help="Specify that the annotation items file have a header.",
)
args, logger = cmd.parse_args("ann-add")
db = cmd.open_db()
try:
logger.info("Creating annotation {} ...".format(args.name))
db.add_map(args.id, args.name, args.type, args.priority)
logger.info("Loading items ...")
with tsv.open(args.path) as f:
for source, value in tsv.lines(f, (str, str), header=args.header):
if len(source) > 0 and len(value) > 0:
db.add_map_item(args.id, source, value)
db.commit()
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="Export SNV's")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("dest_path", metavar="DEST",
help="The destination file. Use - for standard output.")
args, log = cmd.parse_args("export-snvs")
db = cmd.open_db()
logger.info("Exporting SNV's ...")
total_count = 0
total_start_time = time.time()
try:
progress = RatedProgress(logger, name="SNVs")
rows_count = 0
with tsv.open(args.dest_path, "w") as f:
for snv in db.snvs():
rows_count += 1
tsv.write_line(f, snv["chr"], snv["start"], snv["start"], snv["strand"], "{}>{}".format(snv["ref"], snv["alt"]), "S")
progress.update()
log.info("Finished. Total rows = {}, elapsed_time = {}".format(rows_count, progress.elapsed_time))
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="List annotations")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
args, logger = cmd.parse_args("ann-list")
db = cmd.open_db()
try:
print "\t".join(["ID", "NAME", "TYPE", "PRIORITY"])
for ann in db.maps():
print "\t".join([str(ann[k]) for k in ["id", "name", "type", "priority"]])
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(description="Map score values")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
cmd.add_transform_args()
parser.add_argument(
"--skip-empty-scores",
dest="skip_empty_scores",
action="store_true",
default=False,
help="Skip transformation for empty scores",
)
args, logger = cmd.parse_args("scores-transform")
db = cmd.open_db()
try:
transforms = cmd.get_transforms()
predictors = transforms.keys()
logger.info("Transforming scores ...")
progress = RatedProgress(logger, name="SNVs")
rows_count = updated_count = 0
for row in db.query_scores(predictors=predictors):
rows_count += 1
scores = row["scores"]
upd_scores = {}
for predictor in transforms:
score = scores[predictor]
if args.skip_empty_scores and score is None:
continue
prev_score = score
for name, func in transforms[predictor]:
try:
score = func(score)
except:
raise Exception("Error transforming the {} score {} with {}".format(predictor, score, name))
if prev_score != score:
upd_scores[predictor] = score
if len(upd_scores) > 0:
db.update_scores(row["id"], upd_scores)
updated_count += 1
progress.update()
progress.log_totals()
logger.info("Commit ...")
db.commit()
logger.info(
"Finished. Total rows = {}, updated rows = {}, elapsed time = {}".format(
rows_count, updated_count, progress.elapsed_time
)
)
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(description="Calculate Baseline Tolerance statistics per gene")
cmd = DefaultCommandHelper(parser)
parser.add_argument("tree_path", metavar="TREE_PATH", help="The groups descendant tree")
parser.add_argument("root_group", metavar="ROOT_GROUP", help="Tree root group")
parser.add_argument("group_genes_path", metavar="GROUP_FEATS_PATH", help="Map between groups and features")
parser.add_argument("stats_path", metavar="STATS_PATH", help="Partial gene statistics")
parser.add_argument("out_path", metavar="OUTPUT_PATH", help="Output gene statistics")
parser.add_argument(
"-c",
"--count-threshold",
dest="count_threshold",
metavar="N",
default=DEFAULT_COUNT_THRESHOLD,
help="Minimum number of features per group",
)
parser.add_argument(
"--stdev-threshold",
dest="stdev_threshold",
metavar="V",
default=DEFAULT_STDEV_THRESHOLD,
help="Skip feature statistics with a standard deviation less than V (it will be calculated at the level of groups)",
)
args, logger = cmd.parse_args("blt-groups")
logger.info("Loading groups tree ...")
group_children = defaultdict(set)
with tsv.open(args.tree_path) as f:
for group, children in tsv.lines(f, (str, lambda v: set(v.split(",")))):
group_children[group] |= children
logger.info("Loading mappings between groups and features ...")
group_genes = defaultdict(set)
with tsv.open(args.group_genes_path) as f:
for group, genes in tsv.lines(f, (str, lambda v: set(v.split(",")))):
group_genes[group] |= genes
logger.info("Loading partial statistics ...")
partial_stats = {}
with tsv.open(args.stats_path) as f:
predictors = f.readline().rstrip("\n").split("\t")[1:]
num_predictors = len(predictors)
for line in f:
fields = line.rstrip("\n").split("\t")
gene = fields[0]
gene_stats = [[float(v) if i > 0 else int(v) for i, v in enumerate(ss.split("/"))] for ss in fields[1:]]
partial_stats[gene] = gene_stats
logger.info(" Predictors: {}".format(", ".join(predictors)))
logger.info(" Features: {}".format(len(partial_stats.keys())))
logger.info("Calculating features ...")
stats = {}
feat_count = 0
feat_partial_count = [0] * num_predictors
for feature, feat_partial_stats in partial_stats.items():
feat_with_stats = False
feat_stats = [None] * (num_predictors + 1)
for i in range(num_predictors):
s0, s1, s2 = feat_partial_stats[i]
if s0 == 0.0:
continue
if s0 < args.count_threshold:
continue
x = (s0 * s2 - s1 * s1) / (s0 * (s0 - 1))
if x < -1e-12:
continue
mean = s1 / s0
std = math.sqrt(abs(x))
if std < args.stdev_threshold:
continue
feat_stats[i] = (int(s0), mean, std)
feat_partial_count[i] += 1
feat_with_stats = True
if feat_with_stats:
feat_count += 1
stats[feature] = feat_stats
# print feature, "\t".join(["/".join([str(v) for v in feat_stats[i] or []]) for i in range(num_predictors)])
logger.info(
" {} ({}) features out of {} calculated directly from partial statistics".format(
feat_count, "/".join(map(str, feat_partial_count)), len(partial_stats)
)
)
logger.info("Calculating groups ...")
calculate_group(
logger, args.root_group, args.count_threshold, group_children, group_genes, partial_stats, num_predictors, stats
)
logger.info(" {} features calculated in total".format(len(stats)))
with tsv.open(args.out_path, "w") as of:
tsv.write_line(of, "GENE", "GROUP", *predictors)
for gene in sorted(stats.keys()):
gene_stats = stats[gene]
sb = [gene]
stats_group = gene_stats[num_predictors]
if stats_group is not None:
sb += [stats_group]
else:
sb += ["|" + ("-" * num_predictors)]
for i in range(num_predictors):
if gene_stats[i] is not None:
sb += ["/".join([str(v) for v in gene_stats[i]])]
else:
sb += ["-/-/-"]
tsv.write_line(of, *sb)
return 0
def main():
parser = argparse.ArgumentParser(
description="Fetch Condel scores")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("muts_path", metavar="SNVS_PATH",
help="SNV's to check. Use - for standard input.")
parser.add_argument("out_path", metavar="OUTPUT_PATH",
help="The results path. Use - for standard output.")
cmd.add_selected_predictors_args()
cmd.add_selected_annotations_args()
cmd.add_selected_columns_args()
args, logger = cmd.parse_args("fetch")
db = cmd.open_db()
predictors = cmd.get_selected_predictors()
annotations = cmd.get_selected_annotations()
columns = cmd.get_selected_columns()
logger.info("Reading {} ...".format(args.muts_path if args.muts_path != "-" else "from standard input"))
try:
progress = RatedProgress(logger, name="SNVs")
with tsv.open(args.muts_path) as f:
with tsv.open(args.out_path, "w") as wf:
tsv.write_line(wf, "ID", *[c.upper() for c in columns] + [a.upper() for a in annotations] + predictors)
hit = fail = 0
mut = DnaAndProtMutationParser()
for line_num, line in enumerate(f, start=1):
line = line.rstrip(" \n\r")
if len(line) == 0 or line.startswith("#"):
continue
try:
mut.parse(line)
except PrematureEnd:
logger.error("Missing fields at line {}".format(line_num))
fail += 1
continue
except UnexpectedToken as ex:
logger.error("Unexpected field '{}' at line {}".format(ex.args[0], line_num))
fail += 1
continue
exists = False
for row in query_mutation(logger, db, mut, annotations, predictors):
exists = True
ann = row["annotations"]
scores = row["scores"]
tsv.write_line(wf, mut.identifier,
*[row[c] for c in columns]
+ [ann[a] for a in annotations]
+ [scores[p] for p in predictors])
"""
if logger.isEnabledFor(logging.DEBUG):
logger.debug(" --> {} {} {} {} {} {} {} {} {} {}".format(
row["chr"], row["start"], row["ref"], row["alt"], row["transcript"],
row["protein"], row["aa_pos"], row["aa_ref"], row["aa_alt"],
mut.identifier or "*"))
"""
progress.update()
if exists:
hit += 1
else:
fail += 1
progress.log_totals()
logger.info("Finished. total={}, hits={}, fails={}, elapsed={}".format(hit + fail, hit, fail, progress.elapsed_time))
except:
return cmd.handle_error()
finally:
db.close()
def main():
parser = argparse.ArgumentParser(
description="Update scores in the database")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("source_path", metavar="SOURCE",
help="The source file. Use - for standard input.")
cmd.add_selected_predictors_args()
parser.add_argument("--update-predictors", dest="update_predictors", action="store_true", default=False,
help="Update of the predictors.")
parser.add_argument("--ignore-errors", dest="ignore_errors", action="store_true", default=False,
help="When errors on the input file, report them but continue processing the input.")
args, logger = cmd.parse_args("update")
db = cmd.open_db()
predictors = cmd.get_selected_predictors(check_missing=False)
try:
progress = RatedProgress(logger, name="SNVs")
total_lines = 0
logger.info("Reading {} ...".format(args.source_path if args.source_path != "-" else "from standard input"))
with tsv.open(args.source_path) as f:
# Parse header
hdr_line = f.readline()
hdr = dict([(name, index) for index, name in enumerate(hdr_line.rstrip("\n").split("\t"))])
db_predictors = set([p["id"] for p in db.predictors()])
if len(predictors) == 0:
predictors = [name for name in hdr if name in db_predictors]
if len(predictors) == 0:
raise Exception("Any input file header match the available predictors in the database. Please specify them using -p.")
logger.info("Predictors: {}".format(", ".join(predictors)))
for predictor in filter(lambda p: p not in db_predictors, predictors):
logger.info("Creating predictor {} ...".format(predictor))
db.add_predictor(predictor, FannsDb.SOURCE_PREDICTOR_TYPE)
use_genome_coords = len(set(hdr.keys()) & set(GENOME_COORD_COLUMNS)) > 0
use_protein_coords = len(set(hdr.keys()) & set(PROTEIN_COORD_COLUMNS)) > 0
if not use_genome_coords and not use_protein_coords:
raise Exception("No coordinate columns found. "
"Use {} for genomic coordinates or {} for protein coordinates.".format(
GENOME_COORD_COLUMNS, PROTEIN_COORD_COLUMNS))
elif use_genome_coords and use_protein_coords:
logger.warn("Both, genomic and protein coordinates columns found. Using genomic coordinates by default")
if use_genome_coords:
coord_column_names = [n for n in hdr if n in set(GENOME_COORD_COLUMNS)]
coord_column_types = [GENOME_COORD_COLUMN_TYPE[n] for n in coord_column_names]
#get_rows = db.get_transcripts_by_dna
elif use_protein_coords:
coord_column_names = [n for n in hdr if n in set(PROTEIN_COORD_COLUMNS)]
coord_column_types = [PROTEIN_COORD_COLUMN_TYPE[n] for n in coord_column_names]
#get_rows = db.get_transcripts_by_protein
coord_column_indices = [hdr[n] for n in coord_column_names]
score_indices = [hdr[n] for n in predictors]
max_column_index = max(coord_column_indices + score_indices)
for line_num, line in enumerate(f, start=2):
fields = line.rstrip("\n").split("\t")
if len(fields) < max_column_index:
log.error("Missing columns for line {}: {}".format(line_num, " ".join(fields)))
if not args.ignore_errors:
raise
try:
coords = dict([(name.lower(), type_cast(fields[index])) for name, type_cast, index in zip(
coord_column_names, coord_column_types, coord_column_indices)])
scores = dict([(p, score_value(fields[i])) for p, i in zip(predictors, score_indices)])
except Exception as ex:
logger.error("{} at line {}: {}".format(str(ex), line_num, " ".join(fields)))
if not args.ignore_errors:
raise
try:
for row in db.query_scores(fields=[], **coords):
db.update_scores(row["id"], scores)
except Exception as ex:
logger.error("Error updating SNV at line {}: {}".format(line_num, str(ex)))
logger.error("SNV: {}".format(", ".join(["{}={}".format(k, v) for k, v in coords.items()])))
if not args.ignore_errors:
raise
progress.update()
progress.log_totals()
logger.info("Finalizing database ...")
if args.update_predictors:
logger.info("Updating predictors ...")
db.update_predictors()
logger.info("Committing ...")
db.commit()
logger.info("Finished successfully. Elapsed time: {}".format(progress.elapsed_time))
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="Filter for the longest transcript")
cmd = DefaultCommandHelper(parser)
parser.add_argument("len_path", metavar="PATH",
help="The tsv containing the transcripts length")
parser.add_argument("data_path", metavar="PATH",
help="The data file")
parser.add_argument("out_path", metavar="PATH",
help="Output file. Use - for standard output.")
parser.add_argument("-k", "--key", dest="key", metavar="KEY", default="PROTEIN,AA_POS,AA_REF,AA_ALT",
help="List of columns that conforms the key. Default: PROTEIN,AA_POS,AA_REF,AA_ALT")
args, logger = cmd.parse_args("filter-transcript")
try:
logger.info("Loading transcripts length ...")
trslen = defaultdict(int)
with tsv.open(args.len_path) as f:
for name, length in tsv.rows(f):
trslen[name] = length
logger.info("Filtering {} ...".format(os.path.basename(args.data_path)))
total_count = filter_count = 0
progress = RatedProgress(logger, name="mutations")
key_columns = args.key.split(",")
with tsv.open(args.data_path, "r") as df, tsv.open(args.out_path, "w") as of:
hdr_line = df.readline()
of.write(hdr_line)
_, hdr = tsv.header_from_line(hdr_line)
key_indices = [hdr[name] for name in key_columns]
trs_index = hdr["TRANSCRIPT"]
last_key = None
longest = (0, "")
for line in df:
total_count += 1
fields = line.rstrip("\n").split("\t")
key = tuple([fields[index] for index in key_indices])
trs = fields[trs_index]
tl = trslen[trs]
if last_key != key:
if last_key is not None:
of.write(longest[1])
filter_count += 1
longest = (tl, line)
last_key = key
elif tl > longest[0]:
longest = (tl, line)
progress.update()
filter_count += 1
of.write(longest[1])
progress.log_totals()
logger.info("Finished. in={}, out={}, filtered={}, elapsed={}".format(
total_count, filter_count, total_count - filter_count, progress.elapsed_time))
except:
cmd.handle_error()
return 0
def main():
parser = argparse.ArgumentParser(
description="Export Scores")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("dest_path", metavar="OUTPUT_PATH",
help="The output file. Use - for standard output.")
cmd.add_selected_predictors_args()
cmd.add_selected_annotations_args()
cmd.add_selected_columns_args()
parser.add_argument("--json", dest="to_json", action="store_true", default=False,
help="Export the results in json format")
parser.add_argument("--sample", dest="sample", type=int, metavar="PCT",
help="Export a random sample of PCT %%")
parser.add_argument("--start", dest="start", type=int, metavar="N",
help="Start to export from the SNV number N")
parser.add_argument("--limit", dest="limit", type=int, metavar="N",
help="Limit the number of SNVs to export to N")
args, logger = cmd.parse_args("export")
db = cmd.open_db()
predictors = cmd.get_selected_predictors()
annotations = cmd.get_selected_annotations()
columns = cmd.get_selected_columns()
logger.info("Exporting ...")
random.seed(time.time())
total_count = 0
total_start_time = time.time()
try:
progress = RatedProgress(logger, name="SNVs")
to_json = args.to_json
sample = args.sample
start = args.start or 0
limit = args.limit
doc = None
last_pos = None
rows_count = 0
snvs_count = 0
with tsv.open(args.dest_path, "w") as f:
if not to_json:
tsv.write_line(f, *[c.upper() for c in columns] + [a.upper() for a in annotations] + predictors)
for row in db.query_scores(predictors=predictors, maps=annotations):
if not to_json:
if start > 0:
start -= 1
continue
if sample is not None and random.randint(1, 100) > sample:
continue
pos = (row["chr"], row["strand"], row["start"], row["ref"], row["alt"])
if last_pos != pos:
if to_json:
if start > 0:
start -= 1
continue
if limit is not None and snvs_count >= limit:
if doc is not None:
json.dump(doc, f)
f.write("\n")
break
snvs_count += 1
rows_count += 1
ann = row["annotations"]
scores = row["scores"]
if to_json:
tdoc = dict([(k,row[k]) for k in ["transcript", "protein", "aa_pos", "aa_ref", "aa_alt"]] +
[(k,scores[k]) for k in predictors])
if pos != last_pos:
if doc is not None:
if sample is None or random.randint(1, 100) <= sample:
json.dump(doc, f)
f.write("\n")
else:
snvs_count -= 1
doc = dict([(k, row[k]) for k in ["chr", "strand", "start", "ref", "alt"]] +
[("transcripts", [tdoc])])
else:
doc["transcripts"] += [tdoc]
else:
tsv.write_line(f,
*[row[c] for c in columns]
+ [ann[a] for a in annotations]
+ [scores[p] for p in predictors])
progress.update()
last_pos = pos
if not to_json and limit is not None and rows_count >= limit:
break
progress.log_totals()
logger.info("Finished. Total rows = {}, SNVs = {}, elapsed_time = {}".format(rows_count, snvs_count, progress.elapsed_time))
except:
return cmd.handle_error()
finally:
db.close()
return 0
def main():
parser = argparse.ArgumentParser(
description="Generate datasets needed to evaluate performance from Cosmic mutations")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("data_path", metavar="PATH",
help="The CosmicMutantExport tsv file")
parser.add_argument("cgc_path", metavar="PATH",
help="The list of CGC genes")
parser.add_argument("drivers_path", metavar="PATH",
help="The list of CHASM drivers (drivers.tmps)")
parser.add_argument("-o", dest="prefix", metavar="PREFIX",
help="Output prefix.")
args, logger = cmd.parse_args("perf-cosmic")
prefix = args.prefix or "cosmic-"
fanns_db = cmd.open_db()
try:
snvs = dict()
logger.info("Counting the number of samples per mutation ...")
with tsv.open(args.data_path, "r") as df:
columns = [
#"Genome-wide screen",
"Mutation Description",
"Mutation CDS",
"Mutation AA",
"Mutation GRCh37 genome position",
"Mutation GRCh37 strand",
"Accession Number",
"ID_sample"]
total_rows = queried_rows = 0
for fields in tsv.rows(df, columns=columns, header=True):
total_rows += 1
#wide_screen, mut_desc, mut_cds, mut_aa, mut_pos, mut_strand, acc, sample_id = fields
mut_desc, mut_cds, mut_aa, mut_pos, mut_strand, acc, sample_id = fields
wide_screen = "y"
if wide_screen != "y" or mut_desc != "Substitution - Missense":
continue
queried_rows += 1
for row in get_transcripts(fanns_db, mut_cds, mut_aa, mut_pos, mut_strand, acc, logger):
k = tuple([row[k] for k in ["protein", "aa_pos", "aa_ref", "aa_alt"]])
if k not in snvs:
symbol = row["xrefs"]["symbol"]
snvs[k] = dict(
transcript=row["transcript"],
symbol=symbol,
samples=set([sample_id]))
else:
snvs[k]["samples"].add(sample_id)
logger.info("Total: total_rows={}, queried_rows={}, protein_changes={}".format(total_rows, queried_rows, len(snvs)))
logger.info("Loading CGC genes ...")
cgc_genes = set()
with open(args.cgc_path, "r") as f:
for line in f:
cgc_genes.add(line.rstrip("\n"))
logger.info("Loading CHASM drivers ...")
drivers = set()
with open(args.drivers_path, "r") as f:
for line in f:
drivers.add(line.rstrip("\n").split("\t")[0])
logger.info("Creating datasets ...")
progress = RatedProgress(logger, name="mutations")
with Dataset(prefix + "1") as rec1,\
Dataset(prefix + "2") as rec2,\
Dataset(prefix + "4") as rec4,\
Dataset(prefix + "CGC") as cgc,\
Dataset(prefix + "noCGC") as nocgc,\
Dataset(prefix + "D") as drv,\
Dataset(prefix + "O") as nodrv:
for (protein, aa_pos, aa_ref, aa_alt), snv in snvs.items():
num_samples = len(snv["samples"])
line = "\t".join([str(v) for v in [protein, aa_pos, aa_ref, aa_alt]])
if num_samples == 1:
rec1.write(line)
if num_samples >= 2:
rec2.write(line)
if num_samples >= 4:
rec4.write(line)
symbol = snv["symbol"]
if symbol is not None and ((isinstance(symbol, basestring) and symbol in cgc_genes) or len(set(symbol) & cgc_genes) > 0):
cgc.write(line)
elif num_samples == 1:
nocgc.write(line)
if snv["transcript"] in drivers:
drv.write(line)
elif num_samples == 1:
nodrv.write(line)
progress.update()
progress.log_totals()
logger.info("Datasets: {}".format(", ".join(["{}={}".format(os.path.basename(d.name), d.size) for d in [
rec1, rec2, rec4, cgc, nocgc, drv, nodrv]])))
except:
cmd.handle_error()
return 0
def main():
parser = argparse.ArgumentParser(
description="Export dbNSFP scores")
cmd = DefaultCommandHelper(parser)
parser.add_argument("source_path", metavar="SOURCE",
help="The original zip file")
parser.add_argument("ensp_map_path", metavar="MAP",
help="The mapping between Ensembl protein id's and Ensembl transcript id's and Uniprot id's")
parser.add_argument("uniprot_map_path", metavar="MAP",
help="The mapping between Ensembl protein id's and Uniprot id's")
parser.add_argument("-o", "--output", dest="out_path", metavar="OUT_PATH",
help="The output file")
parser.add_argument("--temp", dest="temp_path", metavar="TEMP_PATH",
help="A temporary path for zip extraction")
parser.add_argument("--chr", dest="chr", metavar="CHROMOSOMES",
help="Chromosomes to include: list separated by commas.")
parser.add_argument("--skip-empty-scores", dest="skip_empty_scores", action="store_true", default=False,
help="Skip SNV's where all the scores are empty")
args, logger = cmd.parse_args("dbnsfp-export")
if args.out_path is None:
basename = os.path.basename(args.source_path)
prefix = os.path.splitext(basename)[0]
args.out_path = "{}.tsv.gz".format(prefix)
logger.info("Loading maps ...")
uniprot_map = {}
trs_map = {}
with tsv.open(args.ensp_map_path) as f:
for ensp, enst in tsv.lines(f, (str, str)):
if len(enst) > 0:
trs_map[enst] = ensp
with tsv.open(args.uniprot_map_path) as f:
for ensp, uniprot_id in tsv.lines(f, (str, str)):
if len(uniprot_id) > 0:
uniprot_map[uniprot_id] = ensp
logger.info("Opening {} ...".format(args.source_path))
chromosomes = None
if args.chr is not None:
chromosomes = [c.strip().upper() for c in args.chr.split(",") if len(c.strip()) > 0]
logger.info("Selected chromosomes: {}".format(", ".join(chromosomes)))
chromosomes = set(chromosomes)
name_pattern = re.compile(r"dbNSFP.+_variant.chr(.+)")
COLUMNS = [
"#chr", "pos(1-coor)", "ref", "alt", "cds_strand",
"genename", "Uniprot_id", "Uniprot_aapos", "aaref", "aaalt",
"Ensembl_geneid", "Ensembl_transcriptid", "aapos",
"SIFT_score",
"Polyphen2_HVAR_score",
"MutationAssessor_score",
"FATHMM_score",
"MutationTaster_score",
# "GERP_RS",
"GERP++_RS",
# "PhyloP_score"
"phyloP"
]
tmp_prefix = args.temp_path or tempfile.gettempdir()
if not os.path.exists(tmp_prefix):
os.makedirs(tmp_prefix)
if tmp_prefix[-1] != "/":
tmp_prefix += "/"
extract_path = tempfile.mkdtemp(prefix=tmp_prefix)
try:
logger.info("Output: {}".format(args.out_path if args.out_path != "-" else "standard output"))
total_start_time = time.time()
total_lines = 0
with ZipFile(args.source_path, "r") as zf,\
tsv.open(args.out_path, "w") as of: #,\
#tsv.open(args.noprot_path, "w") as npf:
tsv.write_line(of, "CHR", "STRAND", "START", "REF", "ALT", "TRANSCRIPT",
"PROTEIN", "AA_POS", "AA_REF", "AA_ALT",
"SIFT", "PPH2", "MA", "FATHMM", "MT", "GERPRS", "PHYLOP")
#tsv.write_line(npf, "#CHR", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO")
entries = []
for entry in zf.infolist():
m = name_pattern.match(entry.filename)
if not m:
continue
chr = m.group(1)
index = CHR_INDEX[chr] if chr in CHR_INDEX else 99
if chromosomes is not None and chr not in chromosomes:
logger.debug("Skipping chromosome {} ...".format(chr))
continue
entries += [(index, chr, entry)]
for index, chr, entry in sorted(entries, key=lambda x: x[0]):
logger.info("Reading chromosome {} ...".format(chr))
zf.extract(entry, extract_path)
fpath = os.path.join(extract_path, entry.filename)
with open(fpath) as f:
# Parse header
hdr_line = f.readline()
hdr = {}
for index, name in enumerate(hdr_line.rstrip("\n").split("\t")):
hdr[name] = index
columns = [hdr[name] if name in hdr else None for name in COLUMNS]
read = set()
start_time = time.time()
partial_start_time = start_time
for line_num, line in enumerate(f, start=2):
fields = line.rstrip("\n").split("\t")
try:
fields = [fields[i] if i is not None and i < len(fields) else None for i in columns]
(chr, start, ref, alt, strand,
symbol, uniprot, uniprot_aapos, aa_ref, aa_alt,
gene, transcript, aapos,
sift, pph2, ma, fathmm,
mt, gerprs, phylop) = fields
start = safe_int(start)
ref = ref.upper() if ref is not None else None
alt = alt.upper() if alt is not None else None
aa_ref = aa_ref.upper() if aa_ref is not None else None
aa_alt = aa_alt.upper() if aa_alt is not None else None
sift = safe_float(sift)
ma = safe_float(ma)
fathmm = safe_float(fathmm)
mt = safe_float(mt)
gerprs = safe_float(gerprs)
phylop = safe_float(phylop)
if start is None or ref is None or alt is None:
logger.warn("None value for pos or ref or alt at line {}: {}".format(line_num, fields))
continue
elif ref not in BASE_INDEX or alt not in BASE_INDEX:
logger.warn("Unknown ref or alt at line {}: {}".format(line_num, fields))
continue
elif len(ref) != 1 or len(alt) != 1:
logger.warn("Length != 1 for ref or alt len at line {}: {}".format(line_num, fields))
continue
#elif aa_ref not in AA_INDEX or aa_alt not in AA_INDEX:
# logger.warn("Unknown aa_ref or aa_alt at line {}: {}".format(line_num, fields))
# continue
elif transcript is None or aapos is None or uniprot is None or uniprot_aapos is None:
logger.warn("None value for transcript or aapos or uniprot or uniprot_aapos at line {}: {}".format(line_num, fields))
continue
if aa_ref not in AA_INDEX:
aa_ref = None
if aa_alt not in AA_INDEX:
aa_alt = None
trs_values = transcript.split(";")
aapos_values = [safe_int(v) for v in aapos.split(";")]
l = len(trs_values) - len(aapos_values)
if l > 0:
aapos_values += [aapos_values[-1]] * l
uniprot_values = uniprot.split(";")
uniprot_aapos_values = [safe_int(v) for v in uniprot_aapos.split(";")]
l = len(uniprot_values) - len(uniprot_aapos_values)
if l > 0:
uniprot_aapos_values += [uniprot_aapos_values[-1]] * l
pph2_values = [safe_float(v) for v in pph2.split(";")] if pph2 is not None else [None]
l = len(uniprot_values) - len(pph2_values)
if l > 0:
pph2_values += [pph2_values[-1]] * l
uniprot_index = {}
for i, id in enumerate(uniprot_values):
if uniprot_aapos_values[i] is not None:
uniprot_index[uniprot_aapos_values[i]] = i
for i, trs in enumerate(trs_values):
pos = aapos_values[i]
if pos < 0:
pos = None
if pos is not None and pos in uniprot_index:
j = uniprot_index[pos]
uniprot_value = uniprot_values[j]
pph2_value = pph2_values[j]
else:
uniprot_value = pph2_value = None
if trs in trs_map:
prot_id = trs_map[trs]
elif uniprot_value in uniprot_map:
prot_id = uniprot_map[uniprot_value]
else:
logger.warn("Couldn't map neither protein {} or transcript {} at line {}: {}".format(uniprot_value, trs, line_num, "|".join([str(v) for v in fields])))
continue
#if pos < 0:
# logger.warn("Negative protein position at line {}: {}".format(line_num, pos))
# continue
#elif ...
if pph2_value is not None and (pph2_value < 0.0 or pph2_value > 1.0):
logger.warn("PPH2 score {} out of range at line {}: {}".format(pph2_value, line_num, fields))
continue
if aa_alt == "X": # fix stop codons having a sift score
sift = None
if args.skip_empty_scores and sift is None and pph2_value is None and ma is None \
and mt is None and gerprs is None and phylop is None:
continue
#log.info((chr, strand, start, ref, alt, aapos_values[i], aa_ref, aa_alt, trs, sift, pph2_value, ma))
if pos is None or aa_ref is None or aa_alt is None:
pass #tsv.write_line(npf, chr, start, ".", ref, alt, ".", "PASS",
# "dbNSFP={}|{}|{}|{}|{}|{}".format(trs, prot_id,
# sift or "", pph2_value or "", ma or "", fathmm or ""))
else:
tsv.write_line(of, chr, strand, start, ref, alt, trs,
prot_id, pos, aa_ref, aa_alt,
sift, pph2_value, ma, fathmm,
mt, gerprs, phylop)
except KeyboardInterrupt:
raise
except:
logger.warn("Malformed line {}: {}".format(line_num, "|".join([str(v) for v in fields])))
raise #continue
partial_time = time.time() - partial_start_time
if partial_time >= 5.0:
partial_start_time = time.time()
elapsed_time = time.time() - start_time
logger.debug(" {} lines, {:.1f} lines/second".format(hsize(line_num-1), (line_num-1) / float(elapsed_time)))
total_lines += line_num
logger.info(" > {} lines, {:.1f} lines/second".format(hsize(line_num), line_num / float(time.time() - start_time)))
logger.info(" >> {} lines, {:.1f} lines/second".format(hsize(total_lines), total_lines / float(time.time() - total_start_time)))
os.remove(fpath)
total_elapsed_time = timedelta(seconds=time.time() - total_start_time)
logger.info("Finished successfully. Elapsed time: {}".format(total_elapsed_time))
except:
return cmd.handle_error()
finally:
shutil.rmtree(extract_path)
return 0
def main():
parser = argparse.ArgumentParser(
description="Calculate Baseline Tolerance statistics")
cmd = DefaultCommandHelper(parser)
parser.add_argument("tree_path", metavar="TREE_PATH",
help="The groups descendant tree")
parser.add_argument("root_group", metavar="ROOT_GROUP",
help="Tree root group")
parser.add_argument("group_genes_path", metavar="GROUP_FEATS_PATH",
help="Map between groups and features")
parser.add_argument("stats_path", metavar="STATS_PATH",
help="Partial feature statistics")
parser.add_argument("out_path", metavar="OUTPUT_PATH",
help="Output feature statistics")
parser.add_argument("--tsv", dest="tsv_path", metavar="PATH",
help="Store baseline tolerance in tsv format too.")
parser.add_argument("-c", "--count-threshold", dest="count_threshold", metavar="N", default=DEFAULT_COUNT_THRESHOLD,
help="Minimum number of features per group")
parser.add_argument("--stdev-threshold", dest="stdev_threshold", metavar="V", default=DEFAULT_STDEV_THRESHOLD,
help="Skip feature statistics with a standard deviation less than V (it will be calculated at the level of groups)")
args, logger = cmd.parse_args("blt-groups")
logger.info("Loading groups tree ...")
tree = Tree()
with tsv.open(args.tree_path) as f:
for group, children in tsv.lines(f, (str, lambda v: set(v.split(",")))):
tree.add_node(group, children)
logger.info(" Nodes: {}".format(tree.node_count))
logger.info("Loading mappings between groups and features ...")
all_groups = set()
all_features = set()
with tsv.open(args.group_genes_path) as f:
for group, features in tsv.lines(f, (str, lambda v: set(v.split(",")))):
tree.add_node(group, features)
all_groups.add(group)
all_features.update(features)
logger.info(" Nodes: {}".format(tree.node_count))
logger.info(" Groups: {}".format(len(all_groups)))
logger.info(" Features: {}".format(len(all_features)))
logger.info("Loading partial statistics ...")
with tsv.open(args.stats_path) as f:
predictors = f.readline().rstrip("\n").split("\t")[1:]
num_predictors = len(predictors)
num_features = 0
for line in f:
try:
fields = line.rstrip("\n").split("\t")
feature = fields[0]
node = tree.get_or_create_node(feature)
for p, ss in zip(predictors, fields[1:]):
try:
s0, s1, s2 = [float(v) if i > 0 else int(v) for i, v in enumerate(ss.split("/"))]
node.set_pblt(p, PartialBLT(s0, s1, s2, sources=set([feature])))
except:
import traceback
traceback.print_exc()
logger.warn("Failed to parse partial baseline tolerance"
" for {}/{} from {}".format(feature, p, ss))
exit(-1)
continue
num_features += 1
except:
logger.warn("Failed to parse partial baseline tolerance"
" for {} from {}".format(feature, line))
continue
logger.info(" Nodes: {}".format(tree.node_count))
logger.info(" Features: {}".format(num_features))
logger.info(" Predictors: {}".format(", ".join(predictors)))
logger.info("Calculating baseline tolerance ...")
for predictor in predictors:
logger.info("For {} ...".format(predictor))
calculate_blt(
parent=None, node=tree.get_or_create_node(args.root_group), predictor=predictor,
count_threshold=args.count_threshold, stdev_threshold=args.stdev_threshold, logger=logger)
# TODO log summary info
logger.info("Writing results into {} ...".format(os.path.basename(args.out_path)))
if args.tsv_path is not None:
with tsv.open(args.tsv_path, "w") as of:
tsv.write_line(of, "FEATURE", *predictors)
for feature in all_features:
sb = [feature]
node = tree.get_node(feature)
predictors_with_blt = 0
for predictor in predictors:
blt = node.get_blt(predictor)
if blt is None or blt.n < args.count_threshold:
sb += ["/".join(["-"] * 5)]
continue
predictors_with_blt += 1
sb += ["/".join(map(str, [blt.from_node, blt.scope, blt.n, blt.mean, blt.stdev]))]
if predictors_with_blt > 0:
tsv.write_line(of, *sb)
with tsv.open(args.out_path, "w") as of:
tree_blt = {}
for node_name, node in tree.nodes.items():
predictors_blt = {}
for predictor in predictors:
pred_blt = node.get_blt(predictor)
if pred_blt is None or pred_blt.n < args.count_threshold:
continue
predictors_blt[predictor] = dict(
from_node=pred_blt.from_node, scope=pred_blt.scope,
N=pred_blt.n, mean=pred_blt.mean, stdev=pred_blt.stdev)
if len(predictors_blt) > 0:
tree_blt[node.name] = predictors_blt
doc = dict(
created=str(datetime.now()),
predictors=predictors,
count_threshold=args.count_threshold,
stdev_threshold=args.stdev_threshold,
tree=None, # tree relations
features=list(all_features),
pblt=None, # TODO
blt=tree_blt
)
json.dump(doc, of, indent=True)
return 0
