thtools.fasta.FParser

class thtools.fasta.FParser(text)

A basic FASTA parser with miRBase built in.

Extracts main FASTA sub-components. Supports slice syntax and summation.

Parameters
textstr

The FASTA text to parse.

Notes

Upon instantiation, the text attribute is formatted using the format() method.

Examples

>>> import thtools as tt
>>> ths = "UUAGCCGCUGUCACACGCACAGGGAUUUACAAAAAGAGGAGAGUAAAAUGCUGUGCGUGCACCAUAAAACGAACAUAGAC"
>>> rbs = "AGAGGAGA"
>>> fasta = tt.FParser.fromspecies("Homo sapiens")[295:305] # slice a small chunk of the database
>>> triggers = fasta.seqs
>>> trigger_names = fasta.ids
>>> my_test = tt.autoconfig(ths, rbs, triggers, names=trigger_names)
>>> my_result = my_test.run(max_size=3, n_samples=100)
>>> my_result.specificity
0.9999981076197236
Attributes
idsList[str]
seqsList[str]
headersList[str]
descriptionsList[str]
numint
textstr
sourceset, defaults to set()
line_lengthint, defaults to 70
copy()

Implement copy protocol.

Returns
FParser

A copy of self.

format(line_length=70)

Format the text of a FASTA to be a certain line length in each sequence.

Parameters
linelengthint, default=FParser.line_length

The max length of each sequence line.

Returns
str

The formatted text of the FParser object.

classmethod fromfile(path, *args, **kwargs)

Open a FASTA file and parse it into a FParser object.

Parameters
pathstr

The path to the FASTA file.

*args

Any extra arguments to pass to open().

**kwargs

Any extra keyword arguments to pass to open().

Returns
FParser
classmethod fromregistry(part=None, parts=None, retries=0)

Create a FParser instance from a part or list of parts in the Registry of Standard Biological Parts.

Parameters
partstr, optional
partsCollection[str], optional
retriesint, default=0
Returns
FParser | list[FParser]
Raises
ValueError

If neither part nor parts is supplied.

classmethod fromspecies(species)

Create a FParser instance based on the miRNAs in miRBase.

Full species list available via FParser.specieslist.

Parameters
speciesstr
Returns
FParser
index(key)

Get the index of a key in IDs, sequences, descriptions or headers.