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