README.md

In mutolisp/seqParser: Parsing DNA sequences (seqParser)

seqParser

DNA sequence parser

What does seqParser do

• clip by primers

related function: getCuttedPrimer(primer, len, direction='forward'), grepSeqByPrimer(seq, fprimer, rprimer)

• sort by groups

• BLAST+ wrapper for R

Installation

# assume you have devtools installed
devtools::install_github(repo = 'mutolisp/seqParser')

Dependencies: dplyr, Biostrings, data.table, stringr, seqinr

Use

Set up original primers

library(seqParser)
##### set up primers #####
fprimer <-  'AGATATTGGAAC[A|T]TTATATTTTATTT[A|T]TGG'
rprimer <-  'GGAGGATT[C|T]GG[A|T]AATTGATTAGT'

Adjust the length of each primer

##### grep by forward and reverse primers #####
fp <- getCuttedPrimer(fprimer, len=17, direction = 'forward')
rp <- getCuttedPrimer(rprimer, len=11, direction = 'reverse')

Grep sequences by given primers and export

ex.fasta <- outputSeq(fastaFile = 'example.fasta', 
                 outputFasta = 'example.fasta', 
                 fprimer = fp, 
                 rprimer = rp, 
                 duplinum = 5, 
                 fill = TRUE)

Blast+ (you need to install NCBI blast first)

# make blast database
makeblastdb(input = 'example.fasta',
            dbtype='nucl', title='example', out='/tmp/out/ab')

# blast: blast(type='blastn', ...) or blast(type='blastx', ...)
blast(type='blastn', query='query.fasta',
      db = '/path/to/the/sdb', out = '/tmp/output.txt',
      task='megablast', evalue=1, max_target_seqs=20, num_threads=8,

Citation

Cheng-Tao Lin (2018) seqParser: R package for DNA sequence parsing. URL: https://github.com/mutolisp/seqParser DOI: 10.5281/zenodo.1493692

mutolisp/seqParser documentation built on May 23, 2019, 10:52 a.m.