cpblast: Generate NCBI BLAST Results by aligning input genome...

In ramadatta/CPgeneProfiler: Profiles the Carbapenamase genes from the genome assemblies (One Line, Title Case)

Generate NCBI BLAST Results by aligning input genome assemblies against Carbapenamase (CP) gene database

Description

Prior to running this command, the NCBI_BARRGD_CPG_DB.fasta file is expected to be downloaded and saved in the respective location on the local system. cpblast() helps to generate the location of the CP genes in the genomes.

Usage

cpblast(
  fastalocation,
  dblocation,
  num_threads = "4",
  evalue = "1e-6",
  word_size = "28",
  max_target_seqs = "500"
)

Arguments

fastalocation	Location of the folder with only fasta files. The files must end with either .fasta or .fa format
dblocation	Location of the NCBI_BARRGD_CPG_DB.fasta (CP gene database)
num_threads	Number of threads to run the blast (default = 16)
evalue	Cutoff e-value for blast hit (default = "1e-6")
word_size	<Integer, >=4> Word size for wordfinder algorithm (default = 28)
max_target_seqs	Maximum number of aligned sequences to keep (value of 5 or more is recommended, default = 500)

Examples

cpblast("/home/user/CPgeneProfiler/testData/fasta","/home/user/CPgeneProfiler/testData/db")
cpblast(fastalocation = "/home/user/CPgeneProfiler/testData/fasta",dblocation = "/home/user/CPgeneProfiler/testData/db",num_threads = 8,evalue = "1e-6")

ramadatta/CPgeneProfiler documentation built on Jan. 9, 2025, 4:22 a.m.