gen_strainlib: gen_strainlib

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

Description

function to generate/update strain library and fasta file reads in blast result file from parse blast if no strain library supplied, creates a new one Species that are only found once and not already in strain library are added to library Generates strain library as csv Generates strain library as fasta also generates fasta file for each species, amalgamating results from current blast result and strain library

Usage

gen_strainlib(blast_file, lib_path, lib_file = NULL,
  lib_name = "mystrainlibrary")

Arguments

blast_file	string. file name. csv file containing blast results. Include path if necessary
lib_path	path. string. location of strain library file
lib_file	string. file name. defualt NULL. Name of strain library file. Creates a library file if none supplied.
lib_name	string. defaults to generic library name,name of strain library (only used if new one is being created)

Value

creates/updates strain library creates fasta file of strain library creates fasta files of species with multiple isolates found

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