Extract Basic Info From Pmo

list_library_sample_names_per_specimen_name

List library_sample_names per specimen_name

usage: pmotools-python list_library_sample_names_per_specimen_name
       [-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

list_specimen_meta_fields

List specimen meta fields in the specimen_info section

usage: pmotools-python list_specimen_meta_fields [-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

list_bioinformatics_run_names

List all bioinformatics_run_names in a PMO

usage: pmotools-python list_bioinformatics_run_names [-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

count_specimen_meta

Count values of selected specimen meta fields

usage: pmotools-python count_specimen_meta [-h] --file FILE [--output OUTPUT]
                                           [--delim DELIM] [--overwrite]
                                           --meta_fields META_FIELDS

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

--meta_fields

the fields to count the subfields of, can supply multiple separated by commas, e.g. –meta_fields collection_country,collection_date

count_targets_per_library_sample

Count number of targets per sample

usage: pmotools-python count_targets_per_library_sample [-h] --file FILE
                                                        [--output OUTPUT]
                                                        [--delim DELIM]
                                                        [--overwrite]
                                                        [--read_count_minimum READ_COUNT_MINIMUM]

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

--read_count_minimum

the minimum read count (inclusive) to be counted as covered by sample

Default: 0.0

count_library_samples_per_target

Count number of samples per target

usage: pmotools-python count_library_samples_per_target [-h] --file FILE
                                                        [--output OUTPUT]
                                                        [--delim DELIM]
                                                        [--overwrite]
                                                        [--read_count_minimum READ_COUNT_MINIMUM]

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

--read_count_minimum

the minimum read count (inclusive) to be counted as covered by sample

Default: 0.0