homologfinder.hf

homologfinder.hf

Finds homologs in human and mouse.

About

hf or HomologFinder finds homologs in human and mouse. if the input gene or genelist is human, then it returns mouse homolog(s) and vice versa

Usage

$ hf -h

Examples

$ hf -g ZNF365

$ hf -l Wdr53,Zfp365

$ hf -f genelist.txt

Functions

Name	Description
check_help	check if usage needs to be printed
collect_args	collect all the cli arguments
create_homolog_table	Create the homolog lookup table.
exit_w_msg	Gracefully exit with proper message
hf	Run the homolog finder lookup.
main	Run the CLI.
print_results	Print the homolog finder results.
process_args	Process CLI arguments into a gene list.
process_genelist	Expand a gene list with homologs from the lookup table.
read_lookup	Read the homolog lookup table.

check_help

homologfinder.hf.check_help(parser)

check if usage needs to be printed

collect_args

homologfinder.hf.collect_args()

collect all the cli arguments

create_homolog_table

homologfinder.hf.create_homolog_table(
    rpt_file=importlib.resources.files(__package__) / 'HOM_MouseHumanSequence.rpt',
)

Create the homolog lookup table.

exit_w_msg

homologfinder.hf.exit_w_msg(message)

Gracefully exit with proper message

hf

homologfinder.hf.hf(args)

Run the homolog finder lookup.

main

homologfinder.hf.main()

Run the CLI.

print_results

homologfinder.hf.print_results(result)

Print the homolog finder results.

process_args

homologfinder.hf.process_args(args, lookup)

Process CLI arguments into a gene list.

process_genelist

homologfinder.hf.process_genelist(gl, lookup)

Expand a gene list with homologs from the lookup table.

read_lookup

homologfinder.hf.read_lookup()

Read the homolog lookup table.