-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathBamStat.py
executable file
·184 lines (163 loc) · 8.02 KB
/
BamStat.py
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
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
'''
***********************************************************
* @File : BamStat.py
* @Author : Zhou Wei *
* @Date : 2020/11/24 17:23:32 *
* @E-mail : [email protected] *
* @Version : -- *
* You are using the program scripted by Zhou Wei. *
* If you find some bugs, please *
* Please let me know and acknowledge in your publication. *
* Thank you! *
* Best wishes! *
***********************************************************
'''
import os
class STSTAT():
def __init__(self):
self.ST = 'a'
def CMD(self, INbam, Outpre):
pass
class GETSTAT():
def __init__(self):
self.ST = 'a'
def CMD(self, INbam, Outpre):
pass
import argparse
def Args():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
prefix_chars='-+',
conflict_handler='resolve',
description="",
epilog="")
parser.add_argument('-V','--version',action ='version',
version='EcDNA version 0.1')
subparsers = parser.add_subparsers(dest="commands",
help='models help.')
P_Common = subparsers.add_parser('Common',conflict_handler='resolve', #add_help=False,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
help='The common parameters used for other models.')
P_Common.add_argument("-f", "--infile",type=str,
help='''the input file or input number split by ",".''')
P_Common.add_argument("-i", "--indir",type=str,
help='''the input directory.''')
P_Common.add_argument("-o", "--outdir",type=str,default=os.getcwd(),
help="output file dir, default=current dir.")
P_Common.add_argument("-n", "--njob",type=int,default=5,
help="The maximum number of concurrently running jobs.")
P_Common.add_argument("-bd", "--bamdir", type=str, default='02.MiniMap',
help="input bam directory for fetch ")
P_Common.add_argument("-fd", "--fetchdir", type=str, default='03.SoftMap',
help="out directory for fetch")
P_Common.add_argument("-sd", "--searchdir", type=str, default='03.SoftMap',
help="out directory of search")
P_Common.add_argument("-md", "--mergedir", type=str, default='03.SoftMap',
help="out directory of merge")
P_Common.add_argument("-rd", "--regiondir", type=str, default='04.EcRegion',
help="out directory for region")
P_Common.add_argument("-cd", "--checkdir", type=str, default='05.CheakBP',
help="out directory for check breakpoint of plasmid")
P_Common.add_argument("-ch", "--Chrom", action='store_true', default=True,
help="only keep the specified chromosome: 1-22,X,Y,MT.")
P_Common.add_argument("-bt", "--bedtools", type=str, default='/share/home/share/software/bedtools2/bin/',
help="bedtools path")
P_Common.add_argument("-st", "--samtools", type=str, default='/share/home/share/software/samtools-1.10/bin/',
help="samtools path")
P_Common.add_argument("-gb", "--gtfbed", type=str, default='/share/home/share/Repository/GenomeDB/Reference/Homo_Sapiens/ENSEMBL/Homo_sapiens.GRCh38.100.gtf.gene.bed',
help="the gene bed file used for annotation of regions")
P_Common.add_argument("-ap", "--annopeak", type=str, default='/share/home/share/software/Homer/bin/annotatePeaks.pl',
help="the annotatePeaks.pl script")
P_Common.add_argument("-gt", "--gtf", type=str, default='/share/home/share/Repository/GenomeDB/Reference/Homo_Sapiens/ENSEMBL/Homo_sapiens.GRCh38.100.gtf',
help="the genome gtf file.")
P_Common.add_argument("-cb", "--checkbed", type=str, default='/share/home/zhou_wei/Workspace/11Project/02Plasmid/01analysescript/uniqueovr/BEDUniq.region.txt',
help="the bed file of plasmid unique region.")
P_Autopipe = subparsers.add_parser('Auto', conflict_handler='resolve', prefix_chars='-+',
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
parents=[P_Common, P_fetch, P_search, P_merge, P_region],
help='the auto-processing for all.')
P_Autopipe.add_argument("+P", "++pipeline",nargs='+',
help="the auto-processing: Fetch, Search, Region.")
P_Autopipe.add_argument('+M','++MODEL' , nargs='+', type=str, default=['Standard'],
help='''Chose more the one models from Standard, Fselect,Fitting and Predict used for DIY pipline.''')
args = parser.parse_args()
return args
import logging
class DispatchingFormatter:
def __init__(self, formatters, default_formatter):
self._formatters = formatters
self._default_formatter = default_formatter
def format(self, record):
formatter = self._formatters.get(record.name, self._default_formatter)
return formatter.format(record)
class Logger:
level_dict = {
'NOTSET' : logging.NOTSET,
'DEBUG' : logging.DEBUG,
'INFO' : logging.INFO,
'WARNING' : logging.WARNING,
'ERROR' : logging.ERROR,
'CRITICAL': logging.CRITICAL,
}
ChangeFrom = DispatchingFormatter(
{ 'c' : logging.Formatter( '[%(asctime)s] [%(levelname)-4s]: %(message)s', '%Y-%m-%d %H:%M:%S'),
'p' : logging.Formatter( '[%(levelname)-4s]: %(message)s'),
'n' : logging.Formatter( '%(message)s' ),
},
logging.Formatter('%(message)s')
)
def __init__(self, outpath, filemode='w', clevel = 'INFO', Flevel = 'INFO'):
logging.basicConfig(
level = Logger.level_dict[clevel] ,
format = '[%(asctime)s] [%(levelname)-4s]: %(message)s',
datefmt = '%Y-%m-%d %H:%M:%S',
filename = None,
)
File = logging.FileHandler(outpath, mode= filemode)
File.setLevel(Logger.level_dict[Flevel])
File.setFormatter(Logger.ChangeFrom)
logging.getLogger().addHandler(File)
self.R = logging
self.C = logging.getLogger('c')
self.P = logging.getLogger('p')
self.N = logging.getLogger('n')
self.CI = logging.getLogger('c').info
self.NI = logging.getLogger('n').info
self.CW = logging.getLogger('c').warning
self.NW = logging.getLogger('n').warning
import os
import time
import traceback
def Commands():
info ='''
***********************************************************
* Author : Zhou Wei *
* Date : %s *
* E-mail : [email protected] *
* You are using The scripted by Zhou Wei. *
* If you find some bugs, please email to me. *
* Please let me know and acknowledge in your publication. *
* Sincerely *
* Best wishes! *
***********************************************************
'''%(time.strftime("%a %b %d %H:%M:%S %Y", time.localtime()))
args = Args()
os.makedirs(args.outdir, exist_ok=True)
Log = Logger( '%s/%s_log.log'%(args.outdir, args.commands) )
Log.NI(info.strip())
Log.NI("The argument you have set as follows:".center(59, '*'))
_ml = max([ len(i) for i in vars(args).keys()] )
for i,(k,v) in enumerate(vars(args).items(), start=1):
Log.NI( '**{:0>{}}|{:<{}}: {}'.format(i,2, k,_ml, v) )
Log.NI(59 * '*')
try:
ecDNA(args, Log).Pipeline()
Log.CI('Success!!!')
except Exception:
Log.CW('Failed!!!')
traceback.print_exc()
finally:
Log.CI('You can check your progress in log file.')
Commands()