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fast-results

getGO.R

Get the ancestor of given level for given GO term.

Install required R packages

source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")     ## R version 2.15 or later
biocLite("GOstats")
biocLite("annotate")

Usage: Rscript --vanilla getGO.R <your_GO_ID> <level>
Example: Rscript --vanilla getGO.R GO:0000007 3
Output file: anc_GO:0000007.txt
GO:0000007 MF GO:0022857 transmembrane transporter activity

getSeqbyID.pl

Grep sequences from a fasta file by given IDs (one ID per line) in a file.

Usage: getSeqbyID.pl <seq> <ids> <out>

getSeqbyRegion.pl

Grep sequences from a tab separated file with regions information, one region per line.

Usage: getSeqbyRegion.pl <genome> <regions> <out>

regions file format:

chromosome start stop strand sequenceName

output fasta format:

>sequenceName chromosome_start_stop_strand_length
MAGNSDNEIGNDMNMDNSD.....Sequences..

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Scripts to get sequence works done FAST

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