Command line interface to pmotools-python with pmotools-python

See installation instruction page for how to install pmotools-python which comes with a commandline interface called pmotools-python

Code

pmotools-python

extractors_from_pmo
- ways to extract specific portions of a PMO
  - extract_pmo_with_selected_meta - Extract samples + haplotypes using selected meta
  - extract_pmo_with_select_specimen_names - Extract specific samples from the specimens table
  - extract_pmo_with_select_library_sample_names - Extract experiment sample names from experiment_info table
  - extract_pmo_with_select_targets - Extract specific targets
  - extract_pmo_with_read_filter - Extract with a read filter
  - extract_allele_table - Extract allele tables for tools like dcifer or moire
  - extract_insert_of_panels - Extract inserts of panels from a PMO
  - extract_refseq_of_inserts_of_panels - Extract ref_seq of panel inserts from a PMO
working_with_multiple_pmos
- How to work with multiple PMOs
  - combine_pmos - Combine multiple PMOs of the same panel
extract_basic_info_from_pmo
- Getting some basic infomartion about your data stored in a PMO
  - list_library_sample_names_per_specimen_name - List experiment_sample_ids per specimen_id
  - list_specimen_meta_fields - List specimen meta fields in the specimen_info section
  - list_bioinformatics_run_names - List all tar_amp_bioinformatics_info_ids in a PMO
  - count_specimen_meta - Count values of selected specimen meta fields
  - count_targets_per_library_sample - Count number of targets per sample
  - count_library_samples_per_target - Count number of samples per target
validation
- Function for validating PMOs against a schema to ensure it meets the standards of the file
  - validate_pmo - Validate a PMO file against a JSON Schema

--- title: Command line interface to pmotools-python with pmotools-python --- ```{r setup, echo=F} source("../common.R") ``` See [installation instruction page](../Tools_Installation/pmotools-python_installation.qmd) for how to install `pmotools-python` which comes with a commandline interface called `pmotools-python` ```{bash, eval = F} pmotools-python ``` ```{bash, echo = F, eval = F} pmotools-python | perl -pe 's/\e\[[0-9;]*m(?:\e\[K)?//g' ``` * **extractors_from_pmo** * ways to extract specific portions of a PMO * [extract_pmo_with_selected_meta](subsetting_from_PMO.qmd#subsetting-by-samples-within-specific-metafields) - Extract samples + haplotypes using selected meta * [extract_pmo_with_select_specimen_names](subsetting_from_PMO.qmd#subsetting-by-specific-specimen_names) - Extract specific samples from the specimens table * [extract_pmo_with_select_library_sample_names](subsetting_from_PMO.qmd#subsetting-by-specific-library_sample_names) - Extract experiment sample names from experiment_info table * [extract_pmo_with_select_targets](subsetting_from_PMO.qmd#subsetting-by-specific-targets) - Extract specific targets * [extract_pmo_with_read_filter](subsetting_from_PMO.qmd#subsetting-by-samples-within-specific-metafields) - Extract with a read filter * [extract_allele_table](extracting_allele_tables.qmd#pmotools-python-extract_allele_table) - Extract allele tables for tools like dcifer or moire * [extract_insert_of_panels](extracting_panel_info_from_pmo.qmd#extract-insert-locations-of-panels-from-pmo) - Extract inserts of panels from a PMO * [extract_refseq_of_inserts_of_panels](extracting_panel_info_from_pmo.qmd#extract-ref-sequences-of-insert-locations-of-panels-from-pmo) - Extract ref_seq of panel inserts from a PMO * **working_with_multiple_pmos** * How to work with multiple PMOs * [combine_pmos](handling_multiple_pmos.qmd#pmotools-python-combine_pmos) - Combine multiple PMOs of the same panel * **extract_basic_info_from_pmo** * Getting some basic infomartion about your data stored in a PMO * [list_library_sample_names_per_specimen_name](getting_basic_info_from_pmo.qmd#list_specimen_meta_fields) - List experiment_sample_ids per specimen_id * [list_specimen_meta_fields](getting_basic_info_from_pmo.qmd#list_specimen_meta_fields) - List specimen meta fields in the specimen_info section * [list_bioinformatics_run_names](getting_basic_info_from_pmo.qmd#list_bioinformatics_run_names) - List all tar_amp_bioinformatics_info_ids in a PMO * [count_specimen_meta](getting_basic_info_from_pmo.qmd#list_specimen_meta_fields) - Count values of selected specimen meta fields * [count_targets_per_library_sample](getting_basic_info_from_pmo.qmd#count_targets_per_library_sample) - Count number of targets per sample * [count_library_samples_per_target](getting_basic_info_from_pmo.qmd#count_targets_per_library_sample) - Count number of samples per target * **validation** * Function for validating PMOs against a schema to ensure it meets the standards of the file * [validate_pmo](validating_pmos.qmd#pmotools-python-validate_pmo) - Validate a PMO file against a JSON Schema