itpseq.Replicate¶
- class itpseq.Replicate(*, replicate: str | None = None, filename: Path | None = None, sample: Sample | None = None, labels: dict | None = None, **kwargs)¶
Replicate instances represent a specific biological or experimental replicate of a Sample.
The purpose of the class is to handle, process, and analyze data corresponding to a replicate. Replicate objects provide methods to load associated data, compute statistical measures, and generate graphical representations such as sequence logos.
- filename¶
Path to the file associated with the replicate. This file is expected to contain raw data relevant to the replicate.
- Type:
Optional[Path]
- replicate¶
Identifier or label for the replicate (e.g., “1”).
- Type:
Optional[str]
- labels¶
Dictionary of labels or metadata associated with the replicate.
- Type:
Optional[dict]
- name¶
Name of the sample, derived from sample.name if provided.
- Type:
str
- dataset¶
The DataSet the Sample belongs to, derived from sample.dataset if provided.
- Type:
Any
- kwargs¶
Additional keyword arguments and metadata stored as “meta” during initialization.
- Type:
dict
- Attributes:
- dataset
- sample_name
Methods
get_counts
([pos])Counts the number of reads for each motif or combination of amino-acid/position.
load_data
([min_peptide, max_peptide, how, ...])Reads the aminoacid inverse-toeprint file as a pandas Series, filters entries based on peptide length and stop codons.
logo
([logo_kwargs, ax, fMet, type])Generates a sequence logo based on the aligned inverse-toeprints, using the logomaker library.
rename
([name])Sets the name of the replicate from a parameter or automatically.
- __init__(*, replicate: str | None = None, filename: Path | None = None, sample: Sample | None = None, labels: dict | None = None, **kwargs)¶
Methods
__init__
(*[, replicate, filename, sample, ...])get_counts
([pos])Counts the number of reads for each motif or combination of amino-acid/position.
load_data
([min_peptide, max_peptide, how, ...])Reads the aminoacid inverse-toeprint file as a pandas Series, filters entries based on peptide length and stop codons.
logo
([logo_kwargs, ax, fMet, type])Generates a sequence logo based on the aligned inverse-toeprints, using the logomaker library.
rename
([name])Sets the name of the replicate from a parameter or automatically.
Attributes
sample_name