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

Extractor

The package is designed for extracting the data. This is documentation for extractor package. Functions for general use:

Functions for advanced use:

Detailed Description of Functions

Detailed description of functions are given below.

Detailed description for functions of general usage

extract_cds

Extracts the CDS as a Sequence Record object from a given Sequence Record object

  • record: Original Sequence Record object from where the CDS is to be extracted
  • feature_location: The location of CDS, which is a Feature Location object
  • cds_no: Number of CDS

For details about SeqRecord object click here. For details about FeatureLocation object click here. The function returns a new Sequence Record object containing the CDS

extract_cds_lst

Extracts the list of features if their type is CDS

  • record: Original Sequence Record object from where the CDS is to be extracted

For details about SeqRecord object click here. Returns a tuple containing FeatureLocation objects. For details about FeatureLocation object click here.

extract_exome

Extracts the exome from given nucleotides

  • nuc_file_path: The path to the nucleotide file
  • organism_name: Name of the organism

Returns the exome as a Sequence Record object. For details about SeqRecord object click here.

extract_prot

Extracts protein sequences from given sequence feature object.

  • feature: The CDS, which is a SeqFeature object
  • organism_name: Name of the organism
  • cds_no: Number of the CDS

For details about SeqFeature object click here. The function returns the protein sequence as a SeqRecord object. For details about SeqRecord object click here.

Detailed descriptions of functions for advanced usage

extract_cds_seq

Extracts the CDS sequence from a given sequence

  • seq: Provided sequence
  • feature_location: The location of the CDS

feature_location is an object of type FeatureLocation. For details about FeatureLocation object click here. The function returns the sequence of CDS which is of type Seq. For details about Seq object click here.

extract_prot_seq

Extracts the protein sequence reported in the report for the provided cds.

  • feature: The CDS, which is a SeqFeature object

For details about SeqFeature object click here. The function returns the protein sequence, which is of type Seq. For details about Seq object click here.

© 2023 Souradipto Choudhuri

© 2023 Souradipto Choudhuri

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