tycheleturner / annotate_protein_domains

Using bedtools to annotate protein domains

annotate_protein_domains

Using bedtools to annotate protein domains

Example:

Rscript annotateDomains.R -i inputfile.txt -p PROTEIN_ARCHITECTURE.bed -b ~/software/bedtools/bedtools-2.17.0/bin/bedtools

Requirements: R/3.0.0 R optparse library

Example input file content (no header needed but shown for clarification):

GeneName ProteinName Phenotype AAposition Chromosome Position(hg19) RefAllele AltAllele AlleleFreq

NAT2 NP_000006.2 1000Genomes 114 chr8 18257854 T C 0.296703296703

PROTEIN_ARCHITECTURE.bed file is a bed file that looks like this:

Protein AAStart AAStop DomainName

NP_000680.2 4 12 A2M