bioseq.utils

bioseq.utils.fetchENS(uid: str) → DNA[source]

bioseq.utils.fetchENS(uid: List[str]) → List[DNA]

Fetch sequence corresponding to UID from Ensemble REST api.

Parameters: uid (str | List[str]) – One or list of ENS’s unique id
Returns: One or list of DNA sequence corresponding to UID
Return type: DNA | List[DNA]

bioseq.utils.fetchNCBI(uid: str) → Union[DNA, RNA, Peptide][source]

bioseq.utils.fetchNCBI(uid: List[str]) → List[Sequence]

Fetch sequence corresponding to UID from NCBI E-utilities. Only support RNA, mRNA(DNA), Protein.

Prefix	Explanation
NM_(mRNA)	Protein-coding transcripts (usually curated)
NR_(RNA )	Non-protein-coding transcripts
XM_(mRNA)	Predicted model protein-coding transcript
XR_(RNA )	Predicted model non-protein-coding transcript
AP_(Protein)	Annotated on AC alternate assembly
NP_(Protein)	Associated with an NM or NC accession
YP_(Protein)	Annotated on genomic molecules without an instantiated transcript record
XP_(Protein)	Predicted model, associated with an XM accession
WP_(Protein)	Non-redundant across multiple strains and species

Parameters: uid (str|List[str]) – One or list of NCBI’s unique id
Returns: If uid is a list, the return is a list of Sequence(excluded the uid not found data on NCBI) without ensure sequence’s type, else the return is a Sequence corresponding to UID.
Return type: DNA | RNA | Peptide | List[Sequence]

bioseq.utils.loadFasta(filename: str) → List[Sequence][source]

bioseq.utils.loadFasta(filename: str, iterator: Literal[True]) → Iterator[Sequence]

Load fasta file

Parameters

Returns

List[Sequence] | Iterator

bioseq.utils.parseFasta(fasta_text: str) → List[Sequence][source]

Parse a FASTA formatted string.

bioseq.utils.printAlign(sequence1: str, sequence2: str, spacing: int = 10, line_width: int = 30, show_seq: bool = True)[source]

Print two sequence by a pretty format

Parameters