Overview

At it's core camlhmp is a library that provides a set of functions for typing organisms. It includes functions for running programs and parsing their outputs. In situations where the available CLI commands do not meet your needs, you can use the API functions to build your own custom workflows.

Currently the following modules are available in the camlhmp API:

Type	Module	Function	Description
Engine	camlhmp.engines.blast	run_blast	Run BLAST program
Engine	camlhmp.engines.blast	run_blast	Alias for run_blast with blastn specified
Engine	camlhmp.engines.blast	run_blast	Alias for run_blast with tblastn specified
Framework	camlhmp.framework	read_framework	Read the framework YAML file
Framework	camlhmp.framework	print_version	Print the version of the framework
Framework	camlhmp.framework	get_types	Get the types from the framework
Framework	camlhmp.framework	check_types	Check the types against the results
Framework	camlhmp.framework	check_regions	Check the region types against the results
Parser	camlhmp.parsers.blast	get_blast_allele_hits	Parse BLAST output for allele hits
Parser	camlhmp.parsers.blast	get_blast_region_hits	Parse BLAST output for region hits
Parser	camlhmp.parsers.blast	get_blast_target_hits	Parse BLAST output for target hits
Utils	camlhmp.utils	execute	Execute a command
Utils	camlhmp.utils	check_dependencies	Check if all dependencies are installed
Utils	camlhmp.utils	get_platform	Get the platform of the executing machine
Utils	camlhmp.utils	validate_file	Validate a file exists and not empty
Utils	camlhmp.utils	file_exists_error	Determine if a file exists and raise an error
Utils	camlhmp.utils	parse_seq	Parse a sequence file containing a single record
Utils	camlhmp.utils	parse_seqs	Parse a sequence file containing a multiple records
Utils	camlhmp.utils	parse_table	Parse a delimited file
Utils	camlhmp.utils	parse_yaml	Parse a YAML file
Utils	camlhmp.utils	write_tsv	Write the dictionary to a TSV file