-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathpaths.py
137 lines (87 loc) · 4.84 KB
/
paths.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
qPathOrdered = OrderedDict([
('S_raw','inputFiles/sanger.total.aftertrim.removeCT.min500bp.fasta'),
('S_ass','inputFiles/SangerAssembledAndNonAssembled.min500bp.withoutCandT.fasta'),
('PB_raw','inputFiles/PB.Cell1and2.raw.fasta'),
('PB_ass','inputFiles/PacBio.Correct.C1.fasta'),
('MI_raw','inputFiles/LejlaControl.2D.min500bp.fasta'),
('MI_demux' , 'output/LejlaControl.2D.min500bp.afterBC.fasta'),
('MI_corr1' , 'output/LejlaControl.2D.min500bp.afterNC1.fasta'),
('MI_corr2' , 'output/LejlaControl.2D.min500bp.afterNC2.fasta'),
('MI_polish' , 'output/LejlaControl.2D.min500bp.afterNP.fasta'),
('MI_polishNoFilter' , 'output/LejlaControl.2D.min500bp.afterNPnofilter.fasta'), #This file will be generated by calculateResistome.ipynb
('MIpc_raw', 'inputFiles/poreCamp.2D.min500.fasta'),
('MIpc_demux' , 'output/poreCamp.2D.min500.afterBC.fasta'),
('MIpc_corr1' , 'output/poreCamp.2D.min500.afterNC1.fasta'),
('MIpc_corr2' , 'output/poreCamp.2D.min500.afterNC2.fasta'),
#('MIpc_polish' , 'output/poreCamp.2D.min500.afterNP.fasta'),
#('MIpc_polishNoFilter' , 'output/poreCamp.2D.min500.afterNPnofilter.fasta') #This file will be generated by calculateResistome.ipynb
])
annotationPathOrdered = OrderedDict([
('S_raw','output/annotation/sanger.total.aftertrim.removeCT.min500bp.fasta.annotated.csv'),
('S_ass','output/annotation/SangerAssembledAndNonAssembled.min500bp.withoutCandT.fasta.annotated.csv'),
('PB_raw','output/annotation/PB.Cell1and2.raw.fasta.annotated.csv'),
('PB_ass','output/annotation/PacBio.Correct.C1.fasta.annotated.csv'),
('MI_raw','output/annotation/LejlaControl.2D.min500bp/LejlaControl.2D.min500bp.annotated.csv'),
('MI_demux' , 'output/annotation/LejlaControl.2D.min500bp/LejlaControl.2D.min500bp.afterBC.annotated.csv'),
('MI_corr1' , 'output/annotation/LejlaControl.2D.min500bp/LejlaControl.2D.min500bp.afterNC1.annotated.csv'),
('MI_corr2' , 'output/annotation/LejlaControl.2D.min500bp/LejlaControl.2D.min500bp.afterNC2.annotated.csv'),
('MI_polishNoFilter' , 'output/annotation/LejlaControl.2D.min500bp.afterNPnofilter.fasta.annotated.csv'),
('MIpc_raw', 'output/annotation/poreCamp.2D.min500/poreCamp.2D.min500.annotated.csv'),
('MIpc_demux' , 'output/annotation/poreCamp.2D.min500/poreCamp.2D.min500.afterBC.annotated.csv'),
('MIpc_corr1' , 'output/annotation/poreCamp.2D.min500/poreCamp.2D.min500.afterNC1.annotated.csv'),
('MIpc_corr2' , 'output/annotation/poreCamp.2D.min500/poreCamp.2D.min500.afterNC2.annotated.csv'),
#('MIpc_polishNoFilter' , 'output/annotation/poreCamp.2D.min500.afterNPnofilter.fasta.annotated.csv'),
])
readLabels = OrderedDict([
('S_raw','Sanger raw'),
('S_ass','Sanger assembled'),
('PB_raw','PacBio raw'),
('PB_ass','PacBio assembled'),
('MIpc_raw', 'nanopore lib. B:\n2D reads'),
('MIpc_demux' , 'nanopore lib. B:\nafter debarcoding'),
('MIpc_corr1' , 'nanopore lib. B:\nafter nanocorrect round 1'),
('MIpc_corr2' , 'nanopore lib. B:\nafter nanocorrect round 2'),
#('MIpc_polishNoFilter' , 'nanopore lib. B:\nafter nanopolish') ,
('MI_raw','nanopore lib. A: 2D reads'),
('MI_demux' , 'nanopore lib. A:\nafter debarcoding'),
('MI_corr1' , 'nanopore lib. A:\nafter nanocorrect round 1'),
('MI_corr2' , 'nanopore lib. A:\nafter nanocorrect round 2') ,
('MI_polishNoFilter' , 'nanopore lib. A:\nafter nanopolish ')
])
readLabelsSample = OrderedDict([
('S_raw','Sanger'),
('S_ass','Sanger'),
('PB_raw','PacBio'),
('PB_ass','PacBio'),
('MIpc_raw' , 'nanopore lib. B'),
('MIpc_demux' , 'nanopore lib. B'),
('MIpc_corr1' , 'nanopore lib. B'),
('MIpc_corr2' , 'nanopore lib. B'),
#('MIpc_polishNoFilter' , 'nanopore lib. B') ,
('MI_raw' , 'nanopore lib. A'),
('MI_demux' , 'nanopore lib. A'),
('MI_corr1' , 'nanopore lib. A'),
('MI_corr2' , 'nanopore lib. A'),
('MI_polishNoFilter' , 'nanopore lib. A')
])
readLabelsWorkflow = OrderedDict([
('S_raw','raw'),
('S_ass','assembled'),
('PB_raw','raw'),
('PB_ass','assembled'),
('MIpc_raw', 'raw 2D'),
('MIpc_demux' , 'after debarcoding'),
('MIpc_corr1' , 'after nanocorrect round 1'),
('MIpc_corr2' , 'after nanocorrect round 2'),
#('MIpc_polishNoFilter' , 'after nanopolish') ,
('MI_raw','raw 2D'),
('MI_demux' , 'after debarcoding'),
('MI_corr1' , 'after nanocorrect round 1'),
('MI_corr2' , 'after nanocorrect round 2') ,
('MI_polishNoFilter' , 'after nanopolish')
])
pacbioMuxData = 'inputFiles/pacbioMux.p'
colorSet = {'MI': '#4daf4a',
'PB': '#377eb8',
'MIpc':'#ff7f00',
'S':'#984ea3'}