LIMS module

Benchling API module

Easy to use benchling functions to fetch sequences and objects

teemi.lims.benchling_api.from_benchling(bname: str, schema: str = '')[source]

Extract information of object on benchling. :param bname: The name of the object on Benchling. :type bname: str :param schema: The schema of the object, by default “” :type schema: str, optional

Returns

The extracted object from Benchling.

Return type

object

teemi.lims.benchling_api.sequence_to_benchling(folder_name, oligo_name, oligo_bases, schema)[source]

This function uploads sequences to Benchling.

Parameters

  • folder_name (str) – The name of the folder in which to upload the sequence.

  • oligo_name (str) – The name of the oligo.

  • oligo_bases (str) – The base sequence of the oligo.

  • schema (str) – The schema to use for the oligo. Should be one of the following: “Primer”, “DNA Fragment”, “Plasmid”, “Gene”, “gRNA”, “Marker”,”Promoter”, “Terminator”, “Tag”, “Origin of Replication”.

Returns

Return type

None

teemi.lims.benchling_api.session = <benchlingapi.session.Session object>

This part of the LIMS module is used for importing sequences and exporting sequences to benchling

teemi.lims.benchling_api.update_loc_vol_conc(seqRecord, DBpath: str = '')[source]

Update with location volume and concentration information downloaded from benchling if possible.

Parameters

  • seqRecord (Bio.SeqRecord.SeqRecord) – The SeqRecord object to update.

  • DBpath (str, optional) – The path to the csv file containing the location, volume and concentration information.

  • Returns –

  • -------- –

  • seqRecord – The updated SeqRecord object.

CSV database module

Easy to use functions to fetch sequences and objects from local csv database

teemi.lims.csv_database.add_annotations(list_of_parts: list, concentration: float = 0.0, reference: str = '', volume: float = 0.0, comments: str = '', location: str = '') → list[source]

Adds the neccessary annotations to a list of SeqRecord objects to be uploaded to the database

teemi.lims.csv_database.add_sequences_to_dataframe(list_of_DNA: list, csv_database_as_df, index=0) → None[source]

Adds sequences to local csv databse.

Parameters

  • list_of_DNA (list) – BioSeqrecord objects

  • csv_database_as_df (pd.DataFrame) – your temporary csv database made into a pandas dataframe

  • index (int) – designating which index you want the dna i.e could choose index= 288 which is plate 3 A1

Returns

updates the dateframe with your sequences

Return type

None

teemi.lims.csv_database.add_unique_ids(list_of_parts: list, path='../data/csv_database') → None[source]

Adds unique ids to a list of SeqRecords.

teemi.lims.csv_database.change_row(row_index: int, csv_database_as_df, biopython_object)[source]

inserts a biopyton object into the database at a specific index

teemi.lims.csv_database.delete_row_df(row_index, which_df)[source]

Deletes a row in the database without changing the namse of

teemi.lims.csv_database.get_box(box_number: int, csv_database_as_df)[source]

Returns the plate from a specified csv_database. :param box_number: designating which plate to fetch :type box_number: int :param csv_database_as_df: your temporary csv database made into a pandas dataframe :type csv_database_as_df: pd.DataFrame

Returns

dataframe with the specified plate

Return type

pd.Dataframe

teemi.lims.csv_database.get_database(name: str, path='../data/csv_database/')[source]

Fetches the csv database as a pd.dataframe

teemi.lims.csv_database.get_dna_from_box_name(name: str, database_name: str, database_path='../data/csv_database/', genbank_files_path='../data/genbank_files/', genbank=False) → Bio.SeqRecord.SeqRecord[source]

fetch dna based on the name from the BOX database of choice.

Parameters

  • name (str) – name of the sequence you want to fetch

  • database_name (str) – name of the database u want the sequence to be fetched from

  • genbank_files_path (str) – filepath to your genbank files

  • genbank (bool) – if True the function will fetch thegenbank file based on the unique ID.

Returns

Record – biopython object with values attached to its instances.

Return type

Bio.SeqRecord

teemi.lims.csv_database.get_dna_from_plate_name(name: str, database_name: str, database_path='../data/csv_database/', genbank_files_path='../data/genbank_files/', genbank=False) → Bio.SeqRecord.SeqRecord[source]

fetch dna based on the name from the PLATE database of choice.

Parameters

  • name (str) – name of the sequence you want to fetch

  • database_name (str) – name of the database u want the sequence to be fetched from

  • genbank_files_path (str) – filepath to your genbank files

  • genbank (bool) – if True the function will fetch thegenbank file based on the unique ID.

Returns

Record – biopython object with values attached to its instances.

Return type

Bio.SeqRecord

teemi.lims.csv_database.get_plate(plate_number: int, csv_database_as_df)[source]

Returns the plate from a specified csv_database. :param plate_number: designating which plate to fetch :type plate_number: int :param csv_database_as_df: your temporary csv database made into a pandas dataframe :type csv_database_as_df: pd.DataFrame

Returns

dataframe with the specified plate

Return type

pd.Dataframe

teemi.lims.csv_database.get_unique_id(path='../data/csv_database') → int[source]

Makes a single unique ID from the csv_database files.

Parameters

path (str) – path to the local csv database

Returns

Unique_id – a unique ID starting from 10000

Return type

int

teemi.lims.csv_database.update_database(dataframe, which_database: str, path='../data/csv_database/') → None[source]

Updates the database of choosing