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#!/usr/bin/env python
#
# Part of: https://github.com/mateidavid/fast5
#
# (c) 2017: Matei David, Ontario Institute for Cancer Research
# MIT License
#
import argparse
import datetime
import dateutil.parser
import logging
import math
import os
import sys
import fast5
import signal
signal.signal(signal.SIGPIPE, signal.SIG_DFL)
def add_fast5(fn, rel_dn, args):
logger.info("adding fast5 fn=" + fn + " rel_dn=" + rel_dn)
return [fn]
def add_dir(dn, args):
l = list()
logger.info("processing dir dn=" + dn)
for t in os.walk(dn):
rel_dn = os.path.relpath(t[0], dn)
for rel_fn in t[2]:
fn = os.path.join(t[0], rel_fn)
if fast5.File.is_valid_file(fn):
l += add_fast5(fn, rel_dn, args)
if not args.recurse:
break
return l
def add_fofn(fn, args):
l = list()
logger.info("processing fofn fn=" + fn)
if fn != "-":
f = open(fn)
else:
f = sys.stdin
for p in f:
p = p.strip()
if fast5.File.is_valid_file(p):
l += add_fast5(p, "", args)
else:
logger.warning("fofn line not a fast5 file: " + p)
if fn != "-":
f.close()
return l
def add_paths(pl, args):
l = list()
if len(pl) == 0:
pl.append("-")
for p in pl:
if os.path.isdir(p):
l += add_dir(p, args)
elif fast5.File.is_valid_file(p):
l += add_fast5(p, "", args)
else:
l += add_fofn(p, args)
return l
def stat_file(ifn, args):
d = dict()
try:
f = fast5.File(ifn)
# cid params
d["cid"] = f.get_channel_id_params()
d["tid"] = f.get_tracking_id_params()
# raw samples
d["rs_rn_l"] = f.get_raw_samples_read_name_list()
d["rs"] = dict()
for rn in d["rs_rn_l"]:
d["rs"][rn] = dict()
d["rs"][rn]["params"] = f.get_raw_samples_params(rn)
d["rs"][rn]["packed"] = not f.have_raw_samples_unpack(rn)
# basecall groups
d["bc_gr_l"] = f.get_basecall_group_list()
d["bc"] = dict()
d["bc_desc"] = dict()
d["bc_summary"] = dict()
for gr in d["bc_gr_l"]:
d["bc"][gr] = dict()
d["bc"][gr]["desc"] = f.get_basecall_group_description(gr)
d["bc"][gr]["summary"] = f.get_basecall_summary(gr)
d["bc"][gr]["start"] = dict()
d["bc"][gr]["length"] = dict()
d["bc"][gr]["count"] = dict()
d["bc"][gr]["packed_fastq"] = dict()
d["bc"][gr]["packed_events"] = dict()
for st in [0, 1, 2]:
d["bc"][gr]["packed_fastq"][st] = not f.have_basecall_fastq_unpack(st, gr)
if st < 2:
if d["bc"][gr]["desc"]["have_events"][st]:
d["bc"][gr]["packed_events"][st] = not f.have_basecall_events_unpack(st, gr)
ev_params = f.get_basecall_events_params(st, gr)
d["bc"][gr]["start"][st] = ev_params["start_time"]
d["bc"][gr]["length"][st] = ev_params["duration"]
if d["bc"][gr]["start"][st] < 1e-3:
d["bc"][gr]["start"][st] = float('nan')
if d["bc"][gr]["length"][st] < 1e-3:
d["bc"][gr]["length"][st] = float('nan')
if False:
e = f.get_basecall_events(st, gr)
d["bc"][gr]["start"][st] = e[0]["start"]
d["bc"][gr]["length"][st] = e[-1]["start"] + e[-1]["length"] - e[0]["start"]
d["bc"][gr]["count"][st] = len(e)
else:
d["bc"][gr]["packed_alignment"] = not f.have_basecall_alignment_unpack(gr)
# eventdetection groups
d["ed_gr_l"] = f.get_eventdetection_group_list()
d["ed"] = dict()
for gr in d["ed_gr_l"]:
d["ed"][gr] = dict()
d["ed"][gr]["rn_l"] = f.get_eventdetection_read_name_list(gr)
d["ed"][gr]["rn"] = dict()
for rn in d["ed"][gr]["rn_l"]:
d["ed"][gr]["rn"][rn] = dict()
d["ed"][gr]["rn"][rn]["packed"] = not f.have_eventdetection_events_unpack(gr, rn)
except RuntimeError as e:
d = dict()
return d
def as_time(v, r):
if math.isnan(v):
return 'nan'
x = float(v)/r
m, s = divmod(x, 60)
h, m = divmod(m, 60)
return "%d:%02d:%02d.%03d" % (h, m, s, (x * 1000) % 1000)
def print_path(p, v, args):
if type(v) == list:
print(args.delim[1].join(str(e) for e in p) + args.delim[0] + args.delim[1].join(str(e) for e in v))
else:
print(args.delim[1].join(str(e) for e in p) + args.delim[0] + str(v))
def list_file(ifn, include_fn, args):
d = stat_file(ifn, args)
if include_fn:
print_path(["file"], ifn, args)
if "cid" not in d:
return
# tid
for k in ["device_id", "asic_id", "flow_cell_id", "exp_script_purpose"]:
if k not in d["tid"]:
continue
print_path(["tid", k], d["tid"][k], args)
if "exp_start_time" in d["tid"]:
if 'T' in d["tid"]["exp_start_time"]:
exp_start_time = dateutil.parser.parse(d["tid"]["exp_start_time"])
else:
exp_start_time = datetime.datetime.fromtimestamp(int(d["tid"]["exp_start_time"]))
print_path(["tid", "exp_start_date"], exp_start_time.date().isoformat(), args)
print_path(["tid", "exp_start_time"], exp_start_time.time().isoformat(), args)
# cid
for k in ["channel_number", "sampling_rate"]:
if k not in d["cid"]:
continue
print_path(["cid", k], d["cid"][k], args)
sampling_rate = d["cid"]["sampling_rate"]
# rs
for rn in d["rs_rn_l"]:
print_path(["rs", rn, "packed"], int(d["rs"][rn]["packed"]), args)
print_path(["rs", rn, "read_number"], d["rs"][rn]["params"]["read_number"], args)
print_path(["rs", rn, "read_id"], d["rs"][rn]["params"]["read_id"], args)
print_path(["rs", rn, "start"], as_time(d["rs"][rn]["params"]["start_time"], sampling_rate), args)
print_path(["rs", rn, "length"], as_time(d["rs"][rn]["params"]["duration"], sampling_rate), args)
# bc
for gr in d["bc_gr_l"]:
print_path(["bc", gr, "id"], d["bc"][gr]["desc"]["name"] + ":" + d["bc"][gr]["desc"]["version"], args)
for st in [0, 1, 2]:
if not d["bc"][gr]["desc"]["have_subgroup"][st]:
continue
# fastq
fq_len = 0
print_path(["bc", gr, st, "fastq", "packed"], int(d["bc"][gr]["packed_fastq"][st]), args)
if d["bc"][gr]["desc"]["have_fastq"][st]:
for k in ["sequence_length", "mean_qscore"]:
fk = ["basecall_1d_template", "basecall_1d_complement", "basecall_2d"][st] + "/" + k
if fk not in d["bc"][gr]["summary"]:
continue
print_path(["bc", gr, st, "fastq", k], d["bc"][gr]["summary"][fk], args)
if k == "sequence_length":
fq_len = d["bc"][gr]["summary"][fk]
if st < 2:
# events
if d["bc"][gr]["desc"]["have_events"][st]:
print_path(["bc", gr, st, "events", "packed"], int(d["bc"][gr]["packed_events"][st]), args)
for k in ["start", "length"]:
print_path(["bc", gr, st, "events", k], as_time(float(d["bc"][gr][k][st]), 1.0), args)
if st in d["bc"][gr]["count"]:
print_path(["bc", gr, st, "events", "count"], d["bc"][gr]["count"][st], args)
print_path(["bc", gr, st, "bps"], "%.2f" % (float(fq_len) / d["bc"][gr]["length"][st]), args)
# model
print_path(["bc", gr, st, "model"], int(d["bc"][gr]["desc"]["have_model"][st]), args)
else:
print_path(["bc", gr, st, "alignment", "packed"], int(d["bc"][gr]["packed_alignment"]), args)
if d["bc"][gr]["desc"]["have_subgroup"][2]:
print_path(["bc", gr, "bc_1d_gr"], d["bc"][gr]["desc"]["bc_1d_gr"], args)
if d["bc"][gr]["desc"]["have_subgroup"][0] or d["bc"][gr]["desc"]["have_subgroup"][1]:
print_path(["bc", gr, "ed_gr"], d["bc"][gr]["desc"]["ed_gr"], args)
# ed
for gr in d["ed_gr_l"]:
for rn in d["ed"][gr]["rn_l"]:
print_path(["ed", gr, rn, "packed"], int(d["ed"][gr]["rn"][rn]["packed"]), args)
if __name__ == "__main__":
description = """
Summarize contents of ONT fast5 files.
"""
parser = argparse.ArgumentParser(description=description, epilog="")
parser.add_argument("--log-level", default="warning",
help="log level")
#
parser.add_argument("--delim", default="\t/",
help="Delimiters list; first char used between path and value, second char used between path elements.")
parser.add_argument("-R", "--recurse", action="store_true",
help="Recurse in input directories.")
#
parser.add_argument("inputs", nargs="*", default=[], action="append",
help="Input directories, fast5 files, or files of fast5 file names.")
args = parser.parse_args()
numeric_log_level = getattr(logging, args.log_level.upper(), None)
if not isinstance(numeric_log_level, int):
raise ValueError("Invalid log level: '%s'" % args.log_level)
logging.basicConfig(level=numeric_log_level,
format="%(asctime)s %(name)s.%(levelname)s %(message)s",
datefmt="%Y/%m/%d %H:%M:%S")
logger = logging.getLogger(os.path.basename(__file__))
fast5.Logger.set_levels_from_options([args.log_level.lower()])
# fix delim
args.delim = list(args.delim)
while len(args.delim) < 2:
args.delim.append("")
logger.debug("args: " + str(args))
fl = add_paths(args.inputs[0], args)
for ifn in fl:
list_file(ifn, len(fl) > 1, args)
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