Contact GitHub API Training Shop Blog About. © 2016 GitHub, Inc. ... 24. 25. Raw · Blame · History. #!/bin/bash. #write R script, needs biomaRt echo "#!/usr/bin/ ...
This repository
Search
Pull requests
Issues
Gist
milospjanic / ensembl2genename Code
Issues 0
Unwatch
Pull requests 0
Wiki
Pulse
Graphs
1
Star
0
Fork
0
Settings
Convert human ENSEMBL IDs to gene names — Edit 11 commits
Branch: master
1 branch
0 releases
New pull request
Create new file
1 contributor
Upload files
milospjanic Rename ensemble2genename.sh to ensembl2genename.sh
Find file
Clone or download
Latest commit f2c5a0b on May 13
README.md
Update README.md
4 months ago
ensembl2GeneNameMod2.sh
Rename ensemble2GeneNameMod2.sh to ensembl2GeneNameMod2.sh
4 months ago
ensembl2genename.sh
Rename ensemble2genename.sh to ensembl2genename.sh
4 months ago
README.md
ensembl2genename This is combined bash/R script that will use a file with human ENSEMBL geneIDs in a first column of a file and append a gene name to it, while keeping the structure of the file from other columns. Ensembl2genename sets its host to ensembl.org thus it could be especially useful when biomaRt site is down.
Dependencies Rscript, BiomaRt
Usage chmod 775 ensembl2genename.sh ./ensembl2genename.sh file.txt
Example head file.txt ENSG00000210077 ENSG00000210082 ENSG00000209082 ENSG00000198888 ENSG00000210100 ENSG00000210107 ENSG00000210112 ENSG00000198763 ENSG00000210117 ENSG00000210127
chrM chrM chrM chrM chrM chrM chrM chrM chrM chrM
1602 1671 3230 3307 4263 4329 4402 4470 5512 5587
1670 3229 3304 4262 4331 4400 4469 5511 5579 5655
+ + + + + + + + -
69 1559 75 956 69 72 68 1042 68 69
0 106043 1 29426 0 0 0 15914 0 0
chmod 775 ensembl2genename.sh ./ensembl2genename.sh file.txt
head file.txt.genename
MT-TV ENSG00000210077 MT-RNR2 ENSG00000210082 MT-TL1 ENSG00000209082 MT-ND1 ENSG00000198888 MT-TI ENSG00000210100 MT-TQ ENSG00000210107 MT-TM ENSG00000210112 MT-ND2 ENSG00000198763 MT-TW ENSG00000210117 MT-TA ENSG00000210127
© 2016 GitHub, Inc.
Terms
Privacy
chrM chrM chrM chrM chrM chrM chrM chrM chrM chrM
Security
Status
1602 1671 3230 3307 4263 4329 4402 4470 5512 5587
Help
1670 3229 3304 4262 4331 4400 4469 5511 5579 5655
+ + + + + + + + -
69 1559 75 956 69 72 68 1042 68 69
0 106043 1 29426 0 0 0 15914 0 0
Contact GitHub
API
Training
Shop
Blog
About
This repository
Search
Pull requests
Issues
Gist
milospjanic / ensembl2genename Code
Branch: master
Issues 0
Unwatch
Pull requests 0
Wiki
Pulse
Graphs
1
Star
0
Fork
0
Settings
ensembl2genename / ensembl2genename.sh
Find file
milospjanic Rename ensemble2genename.sh to ensembl2genename.sh
Copy path
f2c5a0b on May 13
1 contributor
26 lines (17 sloc) 1
Raw
655 Bytes
Blame
History
#!/bin/bash
2 3
#write R script, needs biomaRt
4 5
echo "#!/usr/bin/Rscript
6
library(biomaRt)
7
listMarts(host=\"grch37.ensembl.org\")
8
ensembl = useMart(\"ENSEMBL_MART_ENSEMBL\",dataset=\"hsapiens_gene_ensembl\", host=\"grch37.ensembl.org\")
9
id_merge = getBM(attributes=c(\"ensembl_gene_id\",\"external_gene_name\"),mart=ensembl)
10
write.table(id_merge, file=\"id_merge.txt\", sep = \"\t\", quote =F, col.names=F, row.names=F)
11
" > script.r
12 13
#run R script
14 15
chmod 775 script.r
16
./script.r
17 18
#Use awk to append gene names
19 20
awk 'NR==FNR {h[$1] = $1; h2[$1] = $2; next} {print h2[$1], $0}' id_merge.txt $1 >$1.genename
21 22
#remove temporary files
23 24
rm id_merge.txt
25
rm script.r
© 2016 GitHub, Inc.
Terms
Privacy
Security
Status
Help
Contact GitHub
API
Training
Shop
Blog
About
This repository
Search
Pull requests
Issues
Gist
milospjanic / ensembl2genename Code
Issues 0
Branch: master
Unwatch
Pull requests 0
Wiki
Pulse
Graphs
1
Star
0
Fork
0
Settings
ensembl2genename / ensembl2GeneNameMod2.sh
Find file
milospjanic Rename ensemble2GeneNameMod2.sh to ensembl2GeneNameMod2.sh
Copy path
78039d0 on May 13
1 contributor
Executable File 1
26 lines (17 sloc)
Raw
668 Bytes
Blame
History
#!/bin/bash
2 3
#write R script, needs biomaRt
4 5
echo "#!/usr/bin/Rscript
6
library(biomaRt)
7
listMarts(host=\"grch37.ensembl.org\")
8
ensembl = useMart(\"ENSEMBL_MART_ENSEMBL\",dataset=\"hsapiens_gene_ensembl\", host=\"grch37.ensembl.org\")
9
id_merge = getBM(attributes=c(\"ensembl_gene_id\",\"external_gene_name\"),mart=ensembl)
10
write.table(id_merge, file=\"id_merge.txt\", sep = \"\t\", quote =F, col.names=F, row.names=F)
11
" > script.r
12 13
#run R script
14 15
chmod 775 script.r
16
./script.r
17 18
#Use awk to append gene names
19 20
awk 'NR==FNR {h[$1] = $1; h2[$1] = $2; next} {if($1 in h2) print h2[$1], $0}' id_merge.txt $1 >$1.genename
21 22
#remove temporary files
23 24
rm id_merge.txt
25
rm script.r
© 2016 GitHub, Inc.
Terms
Privacy
Security
Status
Help
Contact GitHub
API
Training
Shop
Blog
About
