Y1000_Repo/prepare_data.sh at master · HittingerLab/Y1000_Repo · GitHub

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
#!/bin/bash

unzip Y1000dataV1.0.zip
mv 'Y1000+ Data Release 1.0.0'/Y1000dataV1.0_20250430.tar.gz .
rm -rf 'Y1000+ Data Release 1.0.0'

tar zxvf Y1000dataV1.0_20250430.tar.gz

tar zxvf genomes.tar.gz
tar zxvf pep.tar.gz
tar zxvf cds.tar.gz
tar zxvf gtf.tar.gz
tar zxvf gff3.tar.gz
tar zxvf y1000.outgroups.tar.gz
tar zxvf orthofinder.tar.gz

mkdir ./data
mkdir ./data/original

mv genomes ./data/original/genomes
mv pep ./data/original/pep
mv cds ./data/original/cds
mv gtf ./data/original/gtf
mv gff3 ./data/original/gff3
mv y1000.outgroups ./data/original/y1000.outgroups
mv orthofinder ./data/original/orthofinder


mkdir ./data/BySpecies

mkdir ./data/ByDataType
mkdir ./data/ByDataType/genomes
mkdir ./data/ByDataType/pep
mkdir ./data/ByDataType/cds
mkdir ./data/ByDataType/gtf
mkdir ./data/ByDataType/gff3

IFS=""

echo -e "SpID\tGenome\tPep\tCDS\tGFF3\tGTF" > File_paths.tsv


tail -n +2 File_guide.tsv > temp
while read line ; do
	spID=$(echo $line | cut -f 1)
	genome=$(echo $line | cut -f 2)
	pep=$(echo $line | cut -f 3)
	cds=$(echo $line | cut -f 4)
	gtf=$(echo $line | cut -f 6)
	gff3=$(echo $line | cut -f 5)

	mkdir ./data/BySpecies/$spID

	ln -s $(pwd)/data/original/genomes/$genome ./data/ByDataType/genomes/$spID.fsa
	ln -s $(pwd)/data/original/genomes/$genome ./data/BySpecies/$spID/$spID.fsa
	newgenome="$(echo $PWD)""/data/ByDataType/genomes/$spID.fsa"

	ln -s $(pwd)/data/original/pep/$pep ./data/ByDataType/pep/$spID.pep
	ln -s $(pwd)/data/original/pep/$pep ./data/BySpecies/$spID/$spID.pep
	newpep="$(echo $PWD)""/data/ByDataType/pep/$spID.pep"

	ln -s $(pwd)/data/original/cds/$cds ./data/ByDataType/cds/$spID.cds
	ln -s $(pwd)/data/original/cds/$cds ./data/BySpecies/$spID/$spID.cds
	newcds="$(echo $PWD)""/data/ByDataType/cds/$spID.cds"

	ln -s $(pwd)/data/original/gtf/$gtf ./data/ByDataType/gtf/$spID.gtf
	ln -s $(pwd)/data/original/gtf/$gtf ./data/BySpecies/$spID/$spID.gtf
	newgtf="$(echo $PWD)""/data/ByDataType/gtf/$spID.gtf"

	ln -s $(pwd)/data/original/gff3/$gff3 ./data/ByDataType/gff3/$spID.gff3
	ln -s $(pwd)/data/original/gff3/$gff3 ./data/BySpecies/$spID/$spID.gff3
	newgff3="$(echo $PWD)""/data/ByDataType/gff3/$spID.gff3"

	echo -e "$spID\t$newgenome\t$newpep\t$newcds\t$newgff3\t$newgtf" >> File_paths.tsv

done < temp
rm temp


##Cleanup
rm genomes.tar.gz
rm pep.tar.gz
rm cds.tar.gz
rm gtf.tar.gz
rm gff3.tar.gz
rm y1000.outgroups.tar.gz
rm orthofinder.tar.gz
rm Y1000dataV1.0.zip
rm Y1000dataV1.0_20250430.tar.gz