Author: Murat Buyukyoruk
genemap_generator help:
This script is developed to generate a dataframe that can be used to create alignment panel with phylogenetic trees (i.e., to use with Pylo2genemap.py script).
tqdm is required to provide a progress bar.
trimal is required for -a option.
Syntax:
genemap_generator.py -i demo_aligned.fasta -o demo_out.txt -d demo_hmmsearch_domtblout.txt -p genomic -a auto
genemap_generator dependencies:
Bio module and SeqIO available in this package refer to https://biopython.org/wiki/Download
tqdm refer to https://pypi.org/project/tqdm/
trimal refer to http://trimal.cgenomics.org/downloads
-i/--input FASTA Specify a fasta file used for generating phylogenetic tree and HMMER search. FASTA file requires headers starting with accession number. (i.e. >NZ_CP006019 [Prodigal Description])
-o/--output Output file Specify a output file name that should contain genemap info.
-d/--data HMMER domtblout Specify a hmmsearch or hmmscan domtblout file to parse the positions of predicted hmm hits.
-p/--position genomic or ORF Option to generate ORF-specific or genomic-based genemap positions. It is recommended to use "genomic" option if you are planning to perform Neighbourhood analysis.
-a/--anchor no or auto Option to generate ORF-specific or genomic-based genemap positions. It is recommended to use "genomic" option if you are planning to perform Neighbourhood analysis.
-h/--help HELP Shows this help text and exits the run.