forked from YenLab/Tn5InsertPrefer
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path0.utilities.sh
231 lines (217 loc) · 9.58 KB
/
0.utilities.sh
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
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
#!/bin/bash
##########################################################################
#This script restore all species information
#Issue report on [email protected]
#Copyright (c) 2020 __YenLab@SKLEH__. All rights reserved.
##########################################################################
#Usage: Configuration_info ce11/ce/Worm
# ce11 mm10 dm6 hg38 danRer11 tair10 pfa2 zm3
function Configuration_info {
#Patches and scaffold in the genome
CONSENSUS_REMOVE="^GL|^JH|^KI|chrPt|KN|KZ|Scaffold|chr2110|chrrDNA|ctg"
motifPath=/public/home/zhy/Tn5_bias/fimo/motifs
if [ ${1} = "ce11" ] || [ ${1} = "ce" ] || [ ${1} = "Worm" ]
then
sp="Worm" #Alias
GENOME_NAME="ce11" #Genome assembly
sp_dir="/public/home/zhy/Genomes_info/Caenorhabditis_elegans/" #Dir for each species
FASTA_FILE="${sp_dir}/Caenorhabditis_elegans.WBcel235.dna.toplevel_chrM.fa" #genome sequence
GTF_FILE="${sp_dir}/Caenorhabditis_elegans.WBcel235.95_chrM.gtf" #genome anotation
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/ce11_index" #Bowtie2 mapping index
GENOME_SIZE="${sp_dir}/ce11.chrom.sizes.clean" #All chrs except Patch/scaffold/chrM
GENOME_SIZE_chrM="${sp_dir}/ce11.chrom.sizes.clean_chrM" #All chrs except Patch/scaffold
PATCH_PATTERN="" #Patch/scaffold in genome which need filtering
FEATURE_PATH="${sp_dir}/basic" # basic annotation of this species
GENOME_SIZE_NUM=100286401 #Effective genome size
COMPOSITION=35.44% #GC content
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist="${sp_dir}/ce11-blacklist.v2.bed" #Blacklist if avaliable
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0" # nucleotide frequency
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1" # Di-nucleotide frequency
Liftover_file="${sp_dir}/ce10ToCe11.over.chain"
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "mm10" ] || [ ${1} = "mm" ] || [ ${1} = "Mouse" ]
then
sp="Mouse"
GENOME_NAME="mm10"
sp_dir="/public/home/zhy/Genomes_info/Mus_musculus/"
FASTA_FILE="${sp_dir}/Mus_musculus.GRCm38.dna.primary_assembly_chrM.fa"
GTF_FILE="${sp_dir}/Mus_musculus.GRCm38.95_chrM.gtf"
GTF_FILE_rs="${sp_dir}/mm10.refGene.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/mm10_index"
STAR_INDEXES="${sp_dir}/STAR_index_150bp/"
RSEM_INDEX="${sp_dir}/rsem/mm10"
GENOME_SIZE="${sp_dir}/mm10.chrom.sizes.clean"
GENOME_SIZE_chrM="${sp_dir}/mm10.chrom.sizes.clean_chrM"
PATCH_PATTERN="GL|JH"
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=2730871774
COMPOSITION=40.48%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist="${sp_dir}/mm10-blacklist.v2.bed"
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0"
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1"
Liftover_file="${sp_dir}/mm9ToMm10.over.chain.gz"
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "hg38" ] || [ ${1} = "hg" ] || [ ${1} = "Human" ]
then
sp="Human"
GENOME_NAME="hg38"
sp_dir="/public/home/zhy/Genomes_info/homo_sapiens"
FASTA_FILE="${sp_dir}/Homo_sapiens.GRCh38.dna.primary_assembly_chrM.fa"
GTF_FILE="${sp_dir}/Homo_sapiens.GRCh38.95_chrM.gtf"
GTF_FILE_rs="${sp_dir}/hg38.refGene.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/hg38_index"
STAR_INDEXES="${sp_dir}/STAR_index_150bp/"
RSEM_INDEX="${sp_dir}/rsem/hg38"
GENOME_SIZE="${sp_dir}/hg38.chrom.sizes.clean"
GENOME_SIZE_chrM="${sp_dir}/hg38.chrom.sizes.clean_chrM"
PATCH_PATTERN="KI|GL"
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=3099750718
COMPOSITION=38.84%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist="${sp_dir}/hg38-blacklist.v2.bed"
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0"
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1"
Liftover_file="${sp_dir}/hg19ToHg38.over.chain.gz"
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "tair10" ] || [ ${1} = "tair" ] || [ ${1} = "Plant" ]
then
sp="Plant"
GENOME_NAME="tair10"
sp_dir="/public/home/zhy/Genomes_info/arabidopsis_thaliana"
FASTA_FILE="${sp_dir}/Arabidopsis_thaliana.TAIR10.dna.toplevel_chrM.fa"
GTF_FILE="${sp_dir}/Arabidopsis_thaliana.TAIR10.43_chrM.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/tair10_index"
GENOME_SIZE="${sp_dir}/tair10.chrom.sizes.clean"
GENOME_SIZE_chrM="${sp_dir}/tair10.chrom.sizes.clean_chrM"
PATCH_PATTERN="chrPt"
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=119667750
COMPOSITION=36.00%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist=""
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0"
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1"
Liftover_file=""
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "pfa2" ] || [ ${1} = "pfa" ] || [ ${1} = "huffia" ]
then
sp="huffia"
GENOME_NAME="pfa2"
sp_dir="/public/home/zhy/Genomes_info/plasmodium_falciparum"
FASTA_FILE="${sp_dir}/Plasmodium_falciparum.EPr1.dna.toplevel_chrM.fa"
GTF_FILE="${sp_dir}/Plasmodium_falciparum.EPr1.43_chrM.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/pfa2_index"
GENOME_SIZE="${sp_dir}/pfa2.chrom.sizes"
GENOME_SIZE_chrM="${sp_dir}/pfa2.chrom.sizes"
PATCH_PATTERN="na"
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=23292622
COMPOSITION=19.34%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist=""
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0"
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1"
Liftover_file=""
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "danRer11" ] || [ ${1} = "danRer" ] || [ ${1} = "Fish" ]
then
sp="Fish"
GENOME_NAME="danRer11"
sp_dir="/public/home/zhy/Genomes_info/danio_rerio"
FASTA_FILE="${sp_dir}/Danio_rerio.GRCz11.dna.primary_assembly_chrM.fa"
GTF_FILE="${sp_dir}/Danio_rerio.GRCz11.96_chrM.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/danRer11_index"
GENOME_SIZE="${sp_dir}/danRer11.chrom.sizes.clean"
GENOME_SIZE_chrM="${sp_dir}/danRer11.chrom.sizes.clean_chrM"
PATCH_PATTERN="KN|KZ"
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=1373471384
COMPOSITION=36.52%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist=""
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0"
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1"
Liftover_file="${sp_dir}/danRer10ToDanRer11.over.chain.gz"
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "dm6" ] || [ ${1} = "dm" ] || [ ${1} = "Fly" ]
then
sp="Fly"
GENOME_NAME="dm6"
sp_dir="/public/home/zhy/Genomes_info/Drosophila_melanogaster"
FASTA_FILE="${sp_dir}/Drosophila_melanogaster.BDGP6.22.dna.toplevel_chrM.fa"
GTF_FILE="${sp_dir}/Drosophila_melanogaster.BDGP6.22.96_chrM.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/dm6_index"
GENOME_SIZE="${sp_dir}/dm6.chrom.sizes.clean"
GENOME_SIZE_chrM="${sp_dir}/dm6.chrom.sizes.clean_chrM"
PATCH_PATTERN="Scaffold|chr2110|chrrDNA"
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=143726002
COMPOSITION=41.67%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist="${sp_dir}/dm6-blacklist.v2.bed"
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0"
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1"
Liftover_file=""
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "zm3" ] || [ ${1} = "zm" ] || [ ${1} = "maize" ]
then
sp="maize"
GENOME_NAME="zm3"
sp_dir="/public/home/zhy/Genomes_info/zea_mays"
FASTA_FILE="${sp_dir}/Zea_mays.B73_RefGen_v4.dna.toplevel_chrM.fa"
GTF_FILE="${sp_dir}/Zea_mays.B73_RefGen_v4.43_chrM.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/zm3_index"
GENOME_SIZE="${sp_dir}/zm3.chrom.sizes.clean"
GENOME_SIZE_chrM="${sp_dir}/zm3.chrom.sizes.clean_chrM"
PATCH_PATTERN="ctg|chrPt"
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=2135083061
COMPOSITION=46.19%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist=""
markov_bg0="${sp_dir}/${GENOME_NAME}_markov_bg_0"
markov_bg1="${sp_dir}/${GENOME_NAME}_markov_bg_1"
Liftover_file=""
Tn5MotifProb=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME_prob.txt
Tn5MotifMEME=${motifPath}/${GENOME_NAME}_Tn5_motif_MEME.txt
Tn5MotifMEME19=${motifPath}/${GENOME_NAME}_Tn5_motif19bp_MEME.txt
elif [ ${1} = "sacCer3" ] || [ ${1} = "sacCer" ] || [ ${1} = "yeast" ]
then
sp="yeast"
GENOME_NAME="sacCer3"
sp_dir="/public/home/zhy/Genomes_info/saccharomyces_cerevisiae"
FASTA_FILE="${sp_dir}/Saccharomyces_cerevisiae.EF4.67.dna.toplevel_chrM.fa"
GTF_FILE="${sp_dir}/Saccharomyces_cerevisiae.EF4.67_chrM.gtf"
BOWTIE2_INDEXES="${sp_dir}/bowtie2_index/sacCer3_index"
GENOME_SIZE="${sp_dir}/sacCer3.chrom.sizes"
GENOME_SIZE_chrM="${sp_dir}/sacCer3.chrom.sizes"
PATCH_PATTERN=""
FEATURE_PATH="${sp_dir}/basic"
GENOME_SIZE_NUM=12157105
COMPOSITION=38.15%
PREFIX="/public/home/zhy/Tn5_bias/${sp}/"
blacklist=""
markov_bg0=""
Liftover_file=""
else
echo "Your genome is not found!"
exit 1
fi
}