Source code for velocyto.transcript_model

from typing import *
import velocyto as vcy


[docs]class TranscriptModel: """A simple object representing a transcript model as a list of `vcy.Feature` objects """ __slots__ = ["trid", "trname", "geneid", "genename", "chromstrand", "list_features"] def __init__(self, trid: str, trname: str, geneid: str, genename: str, chromstrand: str) -> None: self.trid = trid self.trname = trname self.geneid = geneid self.genename = genename self.chromstrand = chromstrand self.list_features: List[vcy.Feature] = [] def __iter__(self) -> vcy.Feature: for i in self.list_features: yield i def __lt__(self, other: Any) -> bool: assert self.chromstrand == other.chromstrand, "`<`(.__lt__) not implemented for different chromosomes" return self.list_features[0].start < other.list_features[0].start def __gt__(self, other: Any) -> bool: assert self.chromstrand == other.chromstrand, "`>` (.__gt__) not implemented for different chromosomes" return self.list_features[0].start > other.list_features[0].start @property def start(self) -> int: """ NOTE: This should be accessed only after the creation of the transcript model is finished (i.e.) after append_exon has been called to add all the exons/introns """ return self.list_features[0].start @property def end(self) -> int: """NOTE: This should be accessed only after the creation of the transcript model is finished (i.e.) after append_exon has been called to add all the exons/introns """ return self.list_features[-1].end
[docs] def ends_upstream_of(self, read: vcy.Read) -> bool: # one could consider to add TOLERANCE # note that ``self.list_features[-1]`` is the last exon if strand + and first exons for strand -
return self.list_features[-1].end < read.pos
[docs] def intersects(self, segment: Tuple[int, int], minimum_flanking: int=vcy.MIN_FLANK) -> bool: return (segment[-1] - minimum_flanking > self.start) and\
(segment[0] + minimum_flanking < self.end) # and ((segment[-1] - segment[0]) > minimum_flanking)
[docs] def append_exon(self, exon_feature: vcy.Feature) -> None: """Append an exon and create an intron when needed Arguments --------- exon_feature: vcy.Feature A feature object represneting an exon to add to the transcript model. """ exon_feature.transcript_model = self if len(self.list_features) == 0: # first/last exon self.list_features.append(exon_feature) else: # Some exon already exissted if self.chromstrand[-1] == "+": intron_number = self.list_features[-1].exin_no else: intron_number = self.list_features[-1].exin_no - 1 self.list_features.append(vcy.Feature(start=self.list_features[-1].end + 1, end=exon_feature.start - 1, kind=ord("i"), exin_no=intron_number, transcript_model=self))
self.list_features.append(exon_feature)
[docs] def chop_if_long_intron(self, maxlen: int=vcy.LONGEST_INTRON_ALLOWED) -> None: """Modify a Transcript model choppin the 5' region upstram of a very long intron To avoid that extremelly long intron mask the counting of interal genes Arguments --------- maxlen: int, default=vcy.LONGEST_INTRON_ALLOWED transcript model tha contain one or more intronic interval of len == maxlen will be chopped Returns ------- Nothing it will call `_remove_upstream_of` or `_remove_downstream_of` on the transcript model its name will be changed appending `_mod` to both trid and trname """ long_feats = [i for i in self.list_features if len(i) > maxlen and i.kind == ord("i")] if len(long_feats): if self.chromstrand[-1] == "+": self._remove_upstream_of(long_feats[-1]) else: # self.chromstrand[-1] == "-" self._remove_downstream_of(long_feats[0]) self.trid = self.trid + "_mod"
self.trname = self.trname + "_mod" def _remove_upstream_of(self, longest_feat: vcy.Feature) -> None: tmp = [] ec = 1 ic = 1 for feat in self.list_features: if feat > longest_feat: if feat.kind == ord("e"): feat.exin_no = ec ec += 1 tmp.append(feat) elif feat.kind == ord("i"): feat.exin_no = ic ic += 1 tmp.append(feat) self.list_features = tmp def _remove_downstream_of(self, longest_feat: vcy.Feature) -> None: tmp = [] ec = 1 ic = 1 for feat in self.list_features[::-1]: if feat < longest_feat: if feat.kind == ord("e"): feat.exin_no = ec ec += 1 tmp.append(feat) elif feat.kind == ord("i"): feat.exin_no = ic ic += 1 tmp.append(feat) self.list_features = tmp[::-1] def __repr__(self) -> str: list_feats = '-'.join(f"{chr(i.kind)}{i.exin_no}" for i in self.list_features)
return f"<TrMod {self.trid}\t{list_feats}\tat {hex(id(self))}>"