Pmo To Table

export_pmo_into_xlsx

export all parts of a PMO into a .xlsx file

usage: pmotools-python export_pmo_into_xlsx [-h] --pmo PMO --output OUTPUT
                                            [--overwrite]

Named Arguments

--pmo

PMO file

--output

output file

--overwrite

If output file exists, overwrite it

Default: False

export_specimen_meta_table

export the specimen meta table from a PMO file

usage: pmotools-python export_specimen_meta_table [-h] --file FILE
                                                  [--output OUTPUT]
                                                  [--delim DELIM]
                                                  [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_library_sample_meta_table

export the library_sample meta table from a PMO file

usage: pmotools-python export_library_sample_meta_table [-h] --file FILE
                                                        [--output OUTPUT]
                                                        [--delim DELIM]
                                                        [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_project_info_meta_table

export the project_info meta table from a PMO file

usage: pmotools-python export_project_info_meta_table [-h] --file FILE
                                                      [--output OUTPUT]
                                                      [--delim DELIM]
                                                      [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_sequencing_info_meta_table

export the sequencing_info meta table from a PMO file

usage: pmotools-python export_sequencing_info_meta_table [-h] --file FILE
                                                         [--output OUTPUT]
                                                         [--delim DELIM]
                                                         [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_specimen_travel_meta_table

export the specimen travel_info meta table from a PMO file

usage: pmotools-python export_specimen_travel_meta_table [-h] --file FILE
                                                         [--output OUTPUT]
                                                         [--delim DELIM]
                                                         [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_targeted_genomes_meta_table

export the targeted genomes info meta table from a PMO file

usage: pmotools-python export_targeted_genomes_meta_table [-h] --file FILE
                                                          [--output OUTPUT]
                                                          [--delim DELIM]
                                                          [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_target_info_meta_table

export the target info meta table from a PMO file

usage: pmotools-python export_target_info_meta_table [-h] --file FILE
                                                     [--output OUTPUT]
                                                     [--delim DELIM]
                                                     [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_panel_info_meta_table

export the panel info meta table from a PMO file

usage: pmotools-python export_panel_info_meta_table [-h] --file FILE
                                                    [--output OUTPUT]
                                                    [--delim DELIM]
                                                    [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_bioinformatics_run_info_meta_table

export the bioinformatics_run_info meta table from a PMO file

usage: pmotools-python export_bioinformatics_run_info_meta_table
       [-h] --file FILE [--output OUTPUT] [--delim DELIM] [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

export_bioinformatics_methods_info_meta_table

export the bioinformatics_methods_info meta table from a PMO file

usage: pmotools-python export_bioinformatics_methods_info_meta_table
       [-h] --file FILE [--output OUTPUT] [--delim DELIM] [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--delim

the delimiter of the output text file, examples input tab,comma but can also be the actual delimiter

Default: 'tab'

--overwrite

If output file exists, overwrite it

Default: False

extract_allele_table

Extract allele tables for tools like dcifer or moire

usage: pmotools-python extract_allele_table [-h] --file FILE
                                            [--jsonschema JSONSCHEMA]
                                            [--delim DELIM] --output OUTPUT
                                            [--overwrite] [--skip_validation]
                                            [--allele_freqs_output ALLELE_FREQS_OUTPUT]
                                            [--specimen_info_meta_fields SPECIMEN_INFO_META_FIELDS]
                                            [--library_sample_info_meta_fields LIBRARY_SAMPLE_INFO_META_FIELDS]
                                            [--microhap_fields MICROHAP_FIELDS]
                                            [--representative_haps_fields REPRESENTATIVE_HAPS_FIELDS]
                                            [--default_base_col_names DEFAULT_BASE_COL_NAMES]

Named Arguments

--file

PMO file

--jsonschema

the jsonschema to check the PMO against

Default: '/home/runner/work/pmotools-python/pmotools-python/src/pmotools/schemas/portable_microhaplotype_object_v1.1.0.schema.json'

--delim

the delimiter of the input text file, examples tab,comma

Default: 'tab'

--output

Output allele table file name path

--overwrite

If output file exists, overwrite it

Default: False

--skip_validation

skip validation of PMO

Default: False

--allele_freqs_output

if also writing out allele frequencies, write to this file

--specimen_info_meta_fields

Meta Fields if any to include from the specimen table

--library_sample_info_meta_fields

Meta Fields if any to include from the library sample table

--microhap_fields

additional optional fields from the detected microhaplotype object to include

--representative_haps_fields

additional optional fields from the detected representative object to include

--default_base_col_names

default base column names, must be length 3

Default: 'library_sample_name,target_name,mhap_id'

Examples:
%(prog)s –file input.pmo –output output.tsv %(prog)s –file input.pmo.gz –output output.tsv –delim comma %(prog)s –file input.pmo –output output.tsv –allele_freqs_output freqs.tsv –overwrite %(prog)s –file input.pmo –output output.tsv –microhap_fields reads,mhap_id %(prog)s –file input.pmo –output output.tsv –specimen_info_meta_fields collection_date,collection_country

extract_insert_of_panels

Extract inserts of panels from a PMO

usage: pmotools-python extract_insert_of_panels [-h] --file FILE
                                                [--output OUTPUT]
                                                [--overwrite] [--add_ref_seqs]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--overwrite

If output file exists, overwrite it

Default: False

--add_ref_seqs

add ref seqs to the output as ref_seq

Default: False

extract_refseq_of_inserts_of_panels

extract ref_seq of inserts of panels, but if no ref_seq is saved in the PMO will just be blank

usage: pmotools-python extract_refseq_of_inserts_of_panels [-h] --file FILE
                                                           [--output OUTPUT]
                                                           [--overwrite]

Named Arguments

--file

PMO file

--output

output file

Default: 'STDOUT'

--overwrite

If output file exists, overwrite it

Default: False