map_pep_ref: Amino mapping function

Description Usage Arguments Details Value Author(s) Examples

Description

This function calls PANDAseq and PAUDA for mapping the translated DNA reads

Usage

1
map_pep_ref(infile, outfile, par_list)

Arguments

infile

File path to the fastq file, better controlled by parameter given by the par_list(), see set_par_list

outfile

File path to the results dir

par_list

Parameter given by the par_list(), see set_par_list

Details

The function is the mapping control function for the AA mapping. Most importantly, paired reads are merged by PAUDAseq first. The mapping and translation of the sequence reads to amino reads is done by PAUDA. Finally, the blastx output is parsed by get_pauda_hits.

Value

pep_alignment_df list

Author(s)

Jochen Kruppa

Examples

1

jkruppa/viralDetectTools documentation built on May 30, 2019, 3:41 p.m.