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Souradipto Choudhuri edited this page Feb 7, 2023 · 1 revision

File Handler

The package is designed for reading and writing the data. This is documentation for file handler package. Functions for general use:

Detailed Description of Functions

Detailed description of functions are given below.

Detailed description for functions of general usage

get_gb

Retrieves the Sequence Record object from a given accession number

  • accession_id: Provided accession number

Returns the retrieved genebank (gb) file as a SeqRecord object. For details about SeqRecord object click here.

make_dir

Makes a directory if not present already

  • path: Path of the directory

read_file

Returns a dataframe from given csv file

  • file_name: Name or path to csv file

Returns the read cvs file in the pandas DataFrame object. For details about pd.DataFrame click here.

set_entrez_param

Sets entrez parameters, viz. email id and API key.

  • email: Email of the user (optional)
  • api_key: API key of the user (optional)

This function can show the following warning

  • EmailWarning: If no email is provided
  • ApiWarning: If no API key is provided

Note

It is advised to add your email to NCBI before using the function. You can have your own API key. For details about how to get API key click here.

write_exome_fasta

Creates a fasta file of exome if not exists previously or is empty

  • file_name: The name or path of the file to be created
  • nuc_file_path: The path of nucleotide file from where the exome is tobe extracted
  • organism_name: Name of the organism

This function can show the following warning

  • FileNotEmptyError: If the given file to write is not empty

write_nucleotide_fasta

Creates a fasta file of nucleotides if not exists previously or is empty

  • file_name: The name or path of the file to be created
  • cds_lst: The tuple of FeatureLocation objects
  • record: The SeqRecord object containing whole sequence
  • organism_name: Name of the organism

This function can show the following warning

  • FileNotEmptyError: If the given file to write is not empty

For details about FeatureLocation object click here. For details about SeqRecord object click here.

write_protein_fasta

Creates a fasta file of proteins if not exists previously or is empty

  • file_name: The name or path of the file to be created
  • cds_lst: The tuple of FeatureLocation objects
  • record: The SeqRecord object containing whole sequence

This function can show the following warning

  • FileNotEmptyError: If the given file to write is not empty

© 2023 Souradipto Choudhuri

© 2023 Souradipto Choudhuri

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