fasta_2_dict

yoda_powers.bio.fasta_2_dict(fasta_file)[source]

Function that take a file name (fasta), and return a dictionnary of sequence

Notes

function need modules:

  • pathlib

  • BioPython

Parameters

fasta_file (str) – a path to fasta file directory

Returns

the fasta dict with sequence extract

Return type

dict

Raises

  • ValueError – If fasta_file does not exist.

  • ValueError – If fasta_file is not a valid file.

Example

>>> filename = "sequence.fasta"
>>> fasta_2_dict(filename)
{'Seq1': SeqRecord(seq=Seq('ATGCTGCAGTAG', SingleLetterAlphabet()), id='Seq1', name='Seq1', description='Seq1', dbxrefs=[]),
'Seq2': SeqRecord(seq=Seq('ATGCCGATCGATG', SingleLetterAlphabet()), id='Seq2', name='Seq2', description='Seq2', dbxrefs=[]),
'Seq3': SeqRecord(seq=Seq('ATGCTCAGTCAGTAG', SingleLetterAlphabet()), id='Seq3', name='Seq3', description='Seq3', dbxrefs=[])}