Internal API

ProjectDF

The ProjectDF class is the core back-end class of spacemake.

class spacemake.project_df.ProjectDF(file_path, config: Optional[spacemake.config.ConfigFile] = None)

ProjectDF: class responsible for managing spacemake projects.

Parameters:
  • file_path – path to the project_df.csv file, where we will save the project list.
  • config (ConfigFile) – config file object
  • df (pd.DataFrame) – A pandas dataframe, containing one row per sample
add_sample_sheet(sample_sheet_path, basecalls_dir)

add_sample_sheet.

Parameters:
  • sample_sheet_path –
  • basecalls_dir –
add_samples_from_yaml(projects_yaml_file)

add_samples_from_yaml.

Parameters:projects_yaml_file –
add_update_sample(action=None, project_id=None, sample_id=None, R1=None, R2=None, dge=None, longreads=None, longread_signature=None, sample_sheet=None, basecalls_dir=None, is_merged=False, return_series=False, puck_barcode_file=None, puck_barcode_file_id=None, **kwargs)

add_update_sample.

Parameters:
  • action –
  • project_id –
  • sample_id –
  • R1 –
  • R2 –
  • dge –
  • longreads –
  • longread_signature –
  • sample_sheet –
  • basecalls_dir –
  • is_merged –
  • return_series –
  • kwargs –
assert_projects_samples_exist(project_id_list=[], sample_id_list=[])

assert_projects_samples_exist.

Parameters:
  • project_id_list –
  • sample_id_list –
compute_max_barcode_mismatch(indices: List[str]) → int

compute_max_barcode_mismatch.

Parameters:indices (List[str]) – List of illumina I7 index barcodes
Returns:the maximum mismatch to be allowed for this set of index barcodes
Return type:int
delete_sample(project_id, sample_id)

delete_sample.

Parameters:
  • project_id –
  • sample_id –
dump()

dump.

find_barcode_file(puck_barcode_file_id: str) → str

Tries to find path of a barcode file, using the puck_barcode_file_id.

Parameters:puck_barcode_file_id (str) – puck_barcode_file_id of the puck we are looking for.
Returns:path of the puck file, containing barcodes, or None
Return type:str
get_ix_from_project_sample_list(project_id_list=[], sample_id_list=[])

get_ix_from_project_sample_list.

Parameters:
  • project_id_list –
  • sample_id_list –
get_metadata(field, project_id=None, sample_id=None, **kwargs)

get_metadata.

Parameters:
  • field –
  • project_id –
  • sample_id –
  • kwargs –
get_puck_variables(project_id: str, sample_id: str, return_empty=False) → Dict

get_puck_variables.

Parameters:
  • project_id (str) – project_id of a sample
  • sample_id (str) – sample_id of a sample
  • return_empty –
Returns:

A dictionary containing the puck variables of a given sample
Return type:

Dict
get_sample_info(project_id: str, sample_id: str) → Dict

get_sample_info.

Parameters:
  • project_id (str) –
  • sample_id (str) –
Returns:

A dictionary containing all the values of a given sample, from the ProjectDF.
Return type:

Dict
hamming_distance(string1: str, string2: str) → int

Cacluate hamming distance between two strings

Parameters:
  • string1 (str) –
  • string2 (str) –
Return type:

int
has_dge(project_id: str, sample_id: str) → bool

Returns True if a has dge. for Pacbio only samples returns False.

Parameters:
  • project_id (str) –
  • sample_id (str) –
Return type:

bool
is_external(project_id: str, sample_id: str) → bool

is_external.

Parameters:
  • project_id (str) –
  • sample_id (str) –
Return type:

bool
is_spatial(project_id: str, sample_id: str, puck_barcode_file_id: str) → bool

Returns true if a sample with index (project_id, sample_id) is spatial, meaning that it has spatial barcodes attached.

Parameters:
  • project_id (str) –
  • sample_id (str) –
Return type:

bool
merge_samples(merged_project_id, merged_sample_id, project_id_list=[], sample_id_list=[], **kwargs)

merge_samples.

Parameters:
  • merged_project_id –
  • merged_sample_id –
  • project_id_list –
  • sample_id_list –
  • kwargs –
remove_variable(ix, variable_name, variable_key)

remove_variable.

Parameters:
  • ix –
  • variable_name –
  • variable_key –
sample_exists(project_id=None, sample_id=None)

sample_exists.

Parameters:
  • project_id –
  • sample_id –
set_remove_variable(variable_name, variable_key, action, project_id_list=[], sample_id_list=[], keep_old=False)

set_remove_variable.

Parameters:
  • variable_name –
  • variable_key –
  • action –
  • project_id_list –
  • sample_id_list –
  • keep_old –
set_variable(ix, variable_name, variable_key, keep_old=False)

set_variable.

Parameters:
  • ix –
  • variable_name –
  • variable_key –
  • keep_old –
spacemake.project_df.add_sample_sheet_cmdline(pdf, args)

add_sample_sheet_cmdline.

Parameters:
  • pdf –
  • args –
spacemake.project_df.add_samples_from_yaml_cmdline(pdf, args)

add_samples_from_yaml_cmdline.

Parameters:
  • pdf –
  • args –
spacemake.project_df.add_update_delete_sample_cmdline(pdf, args)

add_update_delete_sample_cmdline.

Parameters:
  • pdf –
  • args –
spacemake.project_df.get_action_sample_parser(parent_parser, action, func)

get_action_sample_parser.

Parameters:
  • parent_parser –
  • action –
  • func –
spacemake.project_df.get_add_sample_sheet_parser()

Returns parser for sample sheet addition

Returns:parser
Return type:argparse.ArgumentParser
spacemake.project_df.get_data_parser(reads_required=False)

Returns a parser which contain extra arguments for a given sample. The returned parser will contain the –R1, –R2, –longreads, –longread-signature, –barcode_flavor, –species, –puck, –puck_barcode_file_id, –puck_barcode_file, –investigator, –experiment, –sequencing_date, –run_mode arguments.

Parameters:
  • species_required – if true, the –species argument will be required during parsing.
  • reads_required – if true, –R1, –R2, and –longreads arguments will be required during parsing.
spacemake.project_df.get_project_sample_parser(allow_multiple=False, prepend='', help_extra='')

Return a parser for project_id’s and sample_id’s

Parameters:
  • allow_multiple – if true, we allow multiple projects and samples, and the parser will have a –project_id_list and a –sample_id_list parameter
  • prepend – a string that will be prepended before the arguments
  • help_extra – extra help message
Returns:

a parser object
Return type:

argparse.ArgumentParser
spacemake.project_df.get_set_remove_variable_subparsers(parent_parser, variable_name, func, prepend='', allow_multiple=False)

get_set_remove_variable_subparsers.

Parameters:
  • parent_parser –
  • variable_name –
  • func –
  • prepend –
  • allow_multiple –
spacemake.project_df.list_projects_cmdline(pdf, args)

list_projects_cmdline.

Parameters:
  • pdf –
  • args –
spacemake.project_df.merge_samples_cmdline(pdf, args)

merge_samples_cmdline.

Parameters:
  • pdf –
  • args –
spacemake.project_df.set_remove_variable_cmdline(pdf, args)

set_remove_variable_cmdline.

Parameters:
  • pdf –
  • args –
spacemake.project_df.setup_project_parser(pdf, parent_parser_subparsers)

setup_project_parser.

Parameters:
  • pdf –
  • attach_to –

ConfigFile

This class is responsible for updating spacemake’s configuration.