1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
|
# -*- coding: utf-8 -*-
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IMPORTS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Standard library imports
from collections import *
import warnings
import datetime
# Local lib import
from pycoQC.common import *
from pycoQC.pycoQC_parse import pycoQC_parse
from pycoQC.pycoQC_plot import pycoQC_plot
from pycoQC.pycoQC_report import pycoQC_report
from pycoQC import __name__ as package_name
from pycoQC import __version__ as package_version
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GLOBAL SETTINGS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Silence futurewarnings
warnings.filterwarnings("ignore", category=FutureWarning)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~MAIN CLASS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
def pycoQC (
summary_file:str,
barcode_file:str="",
bam_file:str="",
runid_list:list=[],
filter_calibration:bool=False,
filter_duplicated:bool=False,
min_barcode_percent:float=0.1,
min_pass_qual:float=7,
min_pass_len:int=0,
sample:int=100000,
html_outfile:str="",
report_title:str="PycoQC report",
config_file:str="",
template_file:str="",
json_outfile:str="",
skip_coverage_plot:bool=False,
verbose:bool=False,
quiet:bool=False):
"""
Parse Albacore sequencing_summary.txt file and clean-up the data
* summary_file
Path to a sequencing_summary generated by Albacore 1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+ (guppy_basecaller).
One can also pass multiple space separated file paths or a UNIX style regex matching multiple files
* barcode_file
Path to the barcode_file generated by Guppy 2.1.3+ (guppy_barcoder) or Deepbinner 0.2.0+. This is not a required file.
One can also pass multiple space separated file paths or a UNIX style regex matching multiple files
* bam_file
Path to a Bam file corresponding to reads in the summary_file. Preferably aligned with Minimap2
One can also pass multiple space separated file paths or a UNIX style regex matching multiple files
* runid_list
Select only specific runids to be analysed. Can also be used to force pycoQC to order the runids for
temporal plots, if the sequencing_summary file contain several sucessive runs. By default pycoQC analyses
all the runids in the file and uses the runid order as defined in the file.
* filter_calibration
If True read flagged as calibration strand by the software are removed
* filter_duplicated
If True duplicated read_ids are removed but the first occurence is kept (Guppy sometimes outputs the same read multiple times)
* min_barcode_percent
Minimal percent of total reads to retain barcode label. If below the barcode value is set as `unclassified`.
* min_pass_qual
Minimum quality to consider a read as 'pass'
* min_pass_len
Minimum read length to consider a read as 'pass'
* sample
If not None a n number of reads will be randomly selected instead of the entire dataset for ploting function (deterministic sampling)
* html_outfile
Path to an output html file report
* report_title
Title to use in the html report
* config_file
Path to a JSON configuration file for the html report.
If not provided, falls back to default parameters.
The first level keys are the names of the plots to be included.
The second level keys are the parameters to pass to each plotting function
* template_file
Jinja2 html template for the html report
* json_outfile
Path to an output json file report
* verbose
Increase verbosity
* quiet
Reduce verbosity
"""
# Save args and init options in dict for report
options_d = locals()
info_d = {"package_name":package_name, "package_version":package_version, "timestamp":str(datetime.datetime.now())}
# Set logging level
logger = get_logger (name=__name__, verbose=verbose, quiet=quiet)
logger.warning ("Checking arguments values")
# Save all verified values + type
runid_list = check_arg("runid_list", runid_list, required_type=list, allow_none=True)
filter_calibration = check_arg("filter_calibration", filter_calibration, required_type=bool, allow_none=False)
filter_duplicated = check_arg("filter_duplicated", filter_duplicated, required_type=bool, allow_none=False)
min_barcode_percent = check_arg("min_barcode_percent", min_barcode_percent, required_type=float, min=0, max=100, allow_none=False)
min_pass_qual = check_arg("min_pass_qual", min_pass_qual, required_type=float, min=0, max=60, allow_none=False)
min_pass_len = check_arg("min_pass_len", min_pass_len, required_type=int, min=0, allow_none=False)
sample = check_arg("sample", sample, required_type=int, min=0, allow_none=True)
html_outfile = check_arg("html_outfile", html_outfile, required_type=str, allow_none=True)
html_outfile = check_arg("html_outfile", html_outfile, required_type=str, allow_none=True)
report_title = check_arg("report_title", report_title, required_type=str, allow_none=True)
config_file = check_arg("config_file", config_file, required_type=str, allow_none=True)
template_file = check_arg("template_file", template_file, required_type=str, allow_none=True)
json_outfile = check_arg("json_outfile", json_outfile, required_type=str, allow_none=True)
skip_coverage_plot = check_arg("skip_coverage_plot", skip_coverage_plot, required_type=bool, allow_none=False)
# Print debug info
logger.debug("General info")
logger.debug(dict_to_str(info_d))
logger.debug("Runtime options")
logger.debug(dict_to_str(options_d))
#~~~~~~~~~~pycoQC_parse~~~~~~~~~~#
parser = pycoQC_parse (
summary_file=summary_file,
barcode_file=barcode_file,
bam_file=bam_file,
runid_list=runid_list,
filter_calibration=filter_calibration,
filter_duplicated=filter_duplicated,
min_barcode_percent=min_barcode_percent,
verbose=verbose,
quiet=quiet)
logger.debug("Parser stats")
logger.debug(parser)
#~~~~~~~~~~pycoQC_plot~~~~~~~~~~#
plotter = pycoQC_plot(
parser=parser,
min_pass_qual=min_pass_qual,
min_pass_len=min_pass_len,
sample=sample,
verbose=verbose,
quiet=quiet)
logger.debug("Plotter stats")
logger.debug(plotter)
#~~~~~~~~~~pycoQC_report~~~~~~~~~~#
if html_outfile or json_outfile:
reporter = pycoQC_report (
parser=parser,
plotter=plotter,
verbose=verbose,
quiet=quiet)
if html_outfile:
reporter.html_report(
outfile=html_outfile,
config_file=config_file,
template_file=template_file,
report_title=report_title,
skip_coverage_plot=skip_coverage_plot)
# Run json output function
if json_outfile:
reporter.json_report(
outfile=json_outfile)
#~~~~~~~~~~return plotting object for API~~~~~~~~~~#
return plotter
|
