blockToAlign: Convert blocks from blat into alignment

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Convert blocks from blat into alignment

Description

Convert blocks from blat into alignment

Usage

blockToAlign(seqs, tSeqs, qStarts, tStarts, sizes)

Arguments

seqs	vector of sequences
tSeqs	vector of target sequences or a single target
qStarts	comma separated starts of query matches e.g. from blat or cigarToBlock (1 based)
tStarts	comma separated starts of target matches e.g. from blat or cigarToBlock (1 based)
sizes	comma separated lengths of matches e.g. from blat or cigarToBlock

Value

data.frame with sequences aligned in columns qSeq and tSeq

Examples

blockToAlign('ABEC','BCD','2,4','1,2','1,1')
blockToAlign(c('ABC','CDE'),c('BCD','ABCDE'),c('1,3','1'),c('1,2','3'),c('1,1','3'))
blocks<-cigarToBlock(c('3M','2M1I1M'),1:2)
blockToAlign(
  c('ATC','ATGC'),
  c('ATCT','GATCT'),
  blocks$qStarts,blocks$tStarts,blocks$sizes
)

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.