A command-line tool for retrieving GenBank metadata and mapping coding sequences between query and subject FASTA files to identify their most similar counterparts.
Project description
A command-line tool for retrieving GenBank metadata and mapping coding sequences between query and subject FASTA files to identify their most similar counterparts.
Free software: MIT license
Documentation: https://genemapper.readthedocs.io
Features
Automated retrieval of GenBank metadata for query and reference sequences files in FASTA format.
Parallelized mapping of query CDS against subject CDS with scoring and threshold-based similarity.
Detailed log and Excel output of mapping results
Adjustable similarity thresholds and multi-processor usage.
Installation
pip install genemapperUsage - Metadata Retrieval
genemapper metadata --query my_query_gene_cds.fasta --reference my_subject_gene_cds.fasta --email you@example.comUsage - Gene Mapping
genemapper map --query my_query_gene_cds.fasta --subject my_subject_gene_cds.fasta --output LAbriniVersusCAETHG_Mapping.xlsx --similarityThreshold 0.99 --numProcesses 20
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