Command line interface to pmotools-python with pmotools-runner.py

See installation instruction page for how to install pmotools-python which comes with a command line interact called pmotools-runner.py

Code

pmotools-runner.py

pmotools v1.0.0 - A suite of tools for interacting with Portable Microhaplotype Object (pmo) file format

Available functions organized by groups are
convertors_to_json
    text_meta_to_json_meta - Convert text file meta to JSON Meta
    excel_meta_to_json_meta - Convert excel file meta to JSON Meta
    microhaplotype_table_to_json_file - Convert microhaplotype table to JSON Meta
    terra_amp_output_to_json - Convert terra output table to JSON seq table

extractors_from_pmo
    extract_pmo_with_selected_meta - Extract from PMO samples and associated haplotypes with selected meta
    extract_pmo_with_select_specimen_ids - Extract from PMO specific samples from the specimens table
    extract_pmo_with_select_experiment_sample_ids - Extract from PMO specific experiment sample ids from the experiment_info table
    extract_pmo_with_select_targets - Extract from PMO specific targets
    extract_pmo_with_read_filter - Extract from PMO with a read filter
    extract_allele_table - Extract allele tables which can be as used as input to such tools as dcifer or moire

working_with_multiple_pmos
    combine_pmos - Combine multiple pmos of the same panel into a single pmo

extract_basic_info_from_pmo
    list_experiment_sample_ids_per_specimen_id - Each specimen_id can have multiple experiment_sample_ids, list out all in a PMO
    list_specimen_meta_fields - List out the specimen meta fields in the specimen_info section
    list_tar_amp_bioinformatics_info_ids - List out all the tar_amp_bioinformatics_info_ids in a PMO file
    count_specimen_meta - Count the values of specific specimen meta fields in the specimen_info section
    count_targets_per_sample - Count the number of targets per sample
    count_samples_per_target - Count the number of samples per target

extract_panel_info_from_pmo
    extract_insert_of_panels - Extract the insert of panels from a PMO
    extract_refseq_of_inserts_of_panels - Extract the ref_seq of panels from a PMO