itpseq.Replicate.load_data#

Replicate.load_data(how='aax', min_peptide=None, max_peptide=None, limit=None, sample=None)[source]#

Reads the nucleotide/aminoacid inverse-toeprint file as a pandas Series, filters entries based on peptide length and stop codons.

Parameters:

  • how (str, optional) – Defines which type of inverse toeprints to load: - ‘nuc’: loads the nucleotide data - ‘aa’: loads the amino acid data - ‘aax’: loads the amino acid data, removes peptides with a stop in the coding sequence (before the A-site)

  • filename (Path or str) – Path to the nucleotide/amino-acid file

  • min_peptide (int, optional) – Minimum peptide length to keep, by default None

  • max_peptide (int, optional) – Maximum peptide length to keep, by default None

  • limit (int or None, optional) – If not None, limits the number of reads to process. This is useful to perform quick tests.

  • sample (str or None, optional) – If not None, samples <sample> reads randomly.

Returns:

Series of inverse-toeprints for the replicate.

Return type:

Series

Examples

Load the inverse-toeprints with a minimum peptide length of 3 and keep the internal stops.
>>> replicate.load_data(min_peptide=3, how='aa')
0           mFIVRGWQV
1                 mWQ
2                 m*T
3          mEVHATTSGQ
4          mHPNYTS*PV
              ...
2828877          mTGA
2828878     mRSATINLQ
2828879    mSLMPHHRGN
2828880          mHWH
2828881     mSSTRSSRS
Length: 2828882, dtype: object
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