Extractors From Pmo

extract_pmo_with_selected_meta

Extract samples + haplotypes using selected meta

usage: pmotools-python extract_pmo_with_selected_meta [-h] --file FILE
                                                      --output OUTPUT
                                                      [--overwrite]
                                                      [--verbose]
                                                      --metaFieldsValues
                                                      METAFIELDSVALUES

Named Arguments

--file

PMO file

--output

Output json file path

--overwrite

If output file exists, overwrite it

Default: False

--verbose

write out various messages about extraction

Default: False

--metaFieldsValues

Meta Fields to include, should either be a table with columns field, values (and optionally group) or supplied command line as field1=value1,value2,value3:field2=value1,value2

extract_pmo_with_select_specimen_names

Extract specific samples from the specimens table

usage: pmotools-python extract_pmo_with_select_specimen_names
       [-h] --file FILE --output OUTPUT [--overwrite] [--verbose]
       --specimen_names SPECIMEN_NAMES

Named Arguments

--file

PMO file

--output

Output json file path

--overwrite

If output file exists, overwrite it

Default: False

--verbose

write out various messages about extraction

Default: False

--specimen_names

Can either comma separated specimen_names, or a plain text file where each line is a specimen_name

extract_pmo_with_select_library_sample_names

Extract library sample names from library_sample_info table

usage: pmotools-python extract_pmo_with_select_library_sample_names
       [-h] --file FILE --output OUTPUT [--overwrite] [--verbose]
       --library_sample_names LIBRARY_SAMPLE_NAMES

Named Arguments

--file

PMO file

--output

Output json file path

--overwrite

If output file exists, overwrite it

Default: False

--verbose

write out various messages about extraction

Default: False

--library_sample_names

Can either comma separated library_sample_names, or a plain text file where each line is a library_sample_name

extract_pmo_with_select_targets

Extract specific targets

usage: pmotools-python extract_pmo_with_select_targets [-h] --file FILE
                                                       --output OUTPUT
                                                       [--overwrite]
                                                       [--verbose] --targets
                                                       TARGETS

Named Arguments

--file

PMO file

--output

Output json file path

--overwrite

If output file exists, overwrite it

Default: False

--verbose

write out various messages about extraction

Default: False

--targets

Can either comma separated target_names, or a plain text file where each line is a target_name

extract_pmo_with_read_filter

Extract with a read filter

usage: pmotools-python extract_pmo_with_read_filter [-h] --file FILE --output
                                                    OUTPUT [--overwrite]
                                                    --read_count_minimum
                                                    READ_COUNT_MINIMUM

Named Arguments

--file

PMO file

--output

Output json file path

--overwrite

If output file exists, overwrite it

Default: False

--read_count_minimum

the minimum read count (inclusive) for detected haplotypes to be kept