abif_fasta: abif_fasta.R

In schyen/isolationWorkflow: Workflow for building strain libraries during isolation experiments

Description

Function to read Applied Biosystem Inc. Format (Ab1, ABIF) files and put into one FASTA files for easy blasting on NCBI

Usage

abif_fasta(folder = NULL, exclude = NULL, trim = TRUE,
  trim.check = FALSE, export.check = TRUE, show.prog = TRUE,
  output = "V3-V6seq.FASTA")

Arguments

folder	name of folder to where ab1 files are kept; need full path; if path uses backslashes, must use double backslashes (\) instead; must be in quotes.
exclude	= name of files that you wish to exclude from fasta file; must be in quotes, extention required, must be in a vector; example: c('file1.ab1','file2.ab1')
trim	logical, default TRUE; do you want to trim N's from beginning and end? trim determined by evaluating each nucleotide in the sequence to see if it it is an N or not. It will then look for when the number of non-N nucleotides is twice the number of Ns (meaning we are well into our gene sequence) and the trim to be the most recent N found. Both beginning and ends of the sequence are trimmed this way.
trim.check	logical; default FALSE; print sequence before and after trim to manually check the trim
export.check	logical, default TRUE; export sequences before and after trimming for convenience when examining trim job; exports as output_check.csv
show.prog	logical, default TRUE; Reports a message on what file is currently being converted
ouput	default is 'V3-V6seq.FASTA'; name of output file; fasta extension required; will be a FASTA file; will save in location of folder provided; can set to FALSE if no output desired

Value

a fasta file of trimmed sequences

schyen/isolationWorkflow documentation built on May 24, 2019, 2:03 a.m.