Transcript

class alphagenome.data.transcript.Transcript(exons, cds=None, start_codon=None, stop_codon=None, transcript_id=None, gene_id=None, protein_id=None, uniprot_id=None, info=<factory>)

Represents transcript object containing attributes from a GTF file.

A transcript is a region of DNA that encodes a single RNA molecule. The Transcript dataclass contains attributes that describe the structure and content of a transcript, namely:

exons

A list of genome.Interval instances representing exons within a transcript. Each Transcript must contain exons.

cds

An optional list of genome.Interval instances representing coding sequences (CDS) within a transcript. CDS include start codon and exclude stop codon.

start_codon

An optional list of genome.Interval instances representing a single start codon. Start codons can be split by introns, therefore might have more than one genomic interval. Some coding transcripts are missing start codons, e.g., ENST00000455638.6.

stop_codon

An optional list of genome.Interval instances representing a single stop codon. Stop codon can be split by introns, therefore might have more than one genomic interval. Some transcripts coding transcripts are missing stop codons, e.g., ENST00000574051.5.

transcript_id

An optional string representing a transcript id.

gene_id

An optional string representing a gene id.

protein_id

An optional string representing a protein id which is encoded by the transcript.

uniprot_id

An optional UniprotKB-AC id string.

info

a dictionary of additional information on a transcript.

chromosome

chromosome name on which the transcript is present. Must be the same for all genomic intervals within a transcript.

is_mitochondrial

whether the transcript is on the mitochondria chromosome.

strand_int

strand on which transcript is present as an int. -1 for negative strand +1 for positive strand

strand

strand (positive or negative) on which transcript is present. Must be the same for all genomic intervals within a transcript.

is_negative_strand

a boolean value indicating whether transcript is on negative strand.

is_positive_strand

a boolean value indicating whether transcript is on positive strand.

transcript_interval

a genomic interval of a transcript.

selenocysteines

a list of intervals where selenocysteines are present within a transcript.

selenocysteine_pos_in_protein

a list of 0-based positions of selenocysteines in protein encoded by the transcript.

is_coding

a value indicating whether a Transcript contains coding sequences (CDS) or not.

cds_including_stop_codon

a list of CDS and stop_codon intervals with overlapping intervals merged.

utr5

A list of genomic intervals representing 5’ untranslated region. 5’ UTR doesn’t include start codon. There may be no 5’ UTR present in the transcript or UTRs can be split by introns.

utr3

A list of genomic intervals representing 3’ untranslated region. 3’ UTR doesn’t include stop codon. There may be no 3’ UTR present in the transcript or UTRs can be split by introns.

splice_regions

a list of splice regions within a transcript.

splice_donor_sites

a list of splice donor sites. Commonly, the RNA sequence that is removed begins with the dinucleotide GU at its 5′ end.

splice_acceptor_sites

a list of splice acceptor sites. Commonly, the RNA sequence that is removed ends with AG at its 3′ end.

splice_donors

a list of splice donors. The first nucleotide of the intron (0-based).

splice_acceptors

a list of splice acceptors. The last nucleotide of the intron (0-based).

Methods

fix_truncation(transcript)	Fixes CDS start and stop positions to be within coding frame.
from_gtf_df(transcript_df[, ignore_info, ...])	Initializes a Transcript object from a transcript DataFrame.
offset_in_cds(genome_position)	Return the offset within the set of CDS exons of genome_position.