-
Notifications
You must be signed in to change notification settings - Fork 0
/
cf-branch-exampleRun.py
137 lines (136 loc) · 5.92 KB
/
cf-branch-exampleRun.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
#!/usr/bin/env python3
import libConfig
# ---- Configuration of Experiment Design ----
expRep = libConfig.config()
expRep.queryStr = "speciesTreatment"
expRep.folderStr = "config/"
# Arguments/Parameters below need to modify depend on
# your experiment design and naming style
expRep.queryDict = {
"branch" : "speciesTreatment",
"group" : ["control","treat1","treat2","treat3","treat4"],
"direction" : ["R1","R2"],
"replication" : ["1","2","3"],
"pairPostfix" : "pair",
"unpairPostfix" : "unpair",
"mode" : "pairEnd",
"thread" : "6",
"conditionsList" : [
{
"genome" : "speciesDatabase",
"trim" : "trimQ30",
"transcriptome" : "dsStringtie",
"map" : "hisat2ForStringtie",
},
{
"genome" : "speciesDatabase",
"trim" : "trimQ30",
"transcriptome" : "gffRead",
"map" : "hisat2ForCufflinks",
}
],
"gtfDict" : {
"Stringtie" : {
"folder" : "05-st-Stringtie",
"balgown" : "05-st-ballgown",
},
"dsStringtie" : {
"folder" : "05-ds-Stringtie",
"balgown" : "05-ds-ballgown",
},
"waStringtie" : {
"folder" : "05-wa-Stringtie",
"balgown" : "05-wa-ballgown",
},
"gffRead" : {
"folder" : "05-gr-transcriptomeConstruction",
"balgown" : "",
}
},
"checkFolder" : ["largeData/01-raw/","largeData/03-trimed/speciesTreatment/"],
"[trim]inputFileName" : "largeData/01-raw/speciesTreatment/{group}{replication}-{direction}{fileType}",
"[trim]outputFileName" : "largeData/03-trimed/speciesTreatment/{condition}-{group}{replication}-{direction}-{pairType}{fileType}",
"[trim]fileType" : ".fastq",
"[hisat2]direction" : { '1' : "R1",'2' : "R2" },
"[hisat2]inputFileName" : "largeData/03-trimed/speciesTreatment/{trim}-{group}{replication}-{direction}-{pairType}{fileType}",
"[hisat2]outputFolder" : "largeData/04-hisat2/speciesTreatment/{annotate}-{trim}/",
"[hisat2]outputFileName" : "largeData/04-hisat2/speciesTreatment/{annotate}-{trim}/{hisat2Condition}-{group}{replication}{fileType}",
"[CuffDiff]resultFolder" : "userData/07-cd-estimateExpression/{branch}-{method}/{annotate}-{trim}/",
"stringtieFolder" : "userData/{folder}/{branch}/{annotate}-{trim}/",
"stringtieGTF" : "userData/{folder}/{branch}/{annotate}-{trim}/{group}{replication}.gtf",
"stringtieTSV" : "userData/{transcriptome}/{branch}/{annotate}-{trim}/{group}{replication}-expression.tsv",
"transcriptomeFolder" : "userData/{folder}/{branch}/",
"transcriptomeGTF" : "userData/{folder}/{branch}/{annotate}-{trim}-final.gtf",
"ballgownFolder" : "userData/{folder}/{branch}/{annotate}-{trim}-{group}{replication}/",
"ballgownGTF" : "userData/{folder}/{branch}/{annotate}-{trim}-{group}{replication}/{group}{replication}-expression.gtf",
"testing" : False,
}
expRep.modeStr = "UPDATE"
expRep.save()
# ---- Configuration of Experiment Design ----
expRep = libConfig.config()
expRep.queryStr = "speciesTreatment2"
expRep.folderStr = "config/"
# Arguments/Parameters below need to modify depend on
# your experiment design and naming style
expRep.queryDict = {
"branch" : "speciesTreatment2",
"group" : ["Normal","treatI","treatJ"],
"direction" : ["R1","R2"],
"replication" : ["1","2","3"],
"pairPostfix" : "pair",
"unpairPostfix" : "unpair",
"mode" : "pairEnd",
"thread" : "6",
"conditionsList" : [
{
"genome" : "speciesDatabase",
"trim" : "trimQ30",
"transcriptome" : "dsStringtie",
"map" : "hisat2ForStringtie",
},
{
"genome" : "speciesDatabase",
"trim" : "trimQ30",
"transcriptome" : "gffRead",
"map" : "hisat2ForCufflinks",
}
],
"gtfDict" : {
"Stringtie" : {
"folder" : "05-st-Stringtie",
"balgown" : "05-st-ballgown",
},
"dsStringtie" : {
"folder" : "05-ds-Stringtie",
"balgown" : "05-ds-ballgown",
},
"waStringtie" : {
"folder" : "05-wa-Stringtie",
"balgown" : "05-wa-ballgown",
},
"gffRead" : {
"folder" : "05-gr-transcriptomeConstruction",
"balgown" : "",
}
},
"checkFolder" : ["largeData/01-raw/","largeData/03-trimed/speciesTreatment2/"], # H_S1_R1_001.fastq
"[trim]inputFileName" : "largeData/01-raw/speciesTreatment/{group}_S{replication}_{direction}_001{fileType}",
"[trim]outputFileName" : "largeData/03-trimed/speciesTreatment2/{condition}-{group}{replication}-{direction}-{pairType}{fileType}",
"[trim]fileType" : ".fastq",
"[hisat2]direction" : { '1' : "R1",'2' : "R2" },
"[hisat2]inputFileName" : "largeData/03-trimed/speciesTreatment2/{trim}-{group}{replication}-{direction}-{pairType}{fileType}",
"[hisat2]outputFolder" : "largeData/04-hisat2/speciesTreatment2/{annotate}-{trim}/",
"[hisat2]outputFileName" : "largeData/04-hisat2/speciesTreatment2/{annotate}-{trim}/{hisat2Condition}-{group}{replication}{fileType}",
"[CuffDiff]resultFolder" : "userData/07-cd-estimateExpression/{branch}-{method}/{annotate}-{trim}/",
"stringtieFolder" : "userData/{folder}/{branch}/{annotate}-{trim}/",
"stringtieGTF" : "userData/{folder}/{branch}/{annotate}-{trim}/{group}{replication}.gtf",
"stringtieTSV" : "userData/{transcriptome}/{branch}/{annotate}-{trim}/{group}{replication}-expression.tsv",
"transcriptomeFolder" : "userData/{folder}/{branch}/",
"transcriptomeGTF" : "userData/{folder}/{branch}/{annotate}-{trim}-final.gtf",
"ballgownFolder" : "userData/{folder}/{branch}/{annotate}-{trim}-{group}{replication}/",
"ballgownGTF" : "userData/{folder}/{branch}/{annotate}-{trim}-{group}{replication}/{group}{replication}-expression.gtf",
"testing" : False,
}
expRep.modeStr = "UPDATE"
expRep.save()