abif_fasta: abif_fasta

In schyen/somefxns: Generic Tools to Help with Analysis

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 of the sequence? 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 ouput_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

fasta file

schyen/somefxns documentation built on Aug. 6, 2019, 2:26 p.m.