Models

cruzdb.models contains the per-feature objects that give you attributes on each row of a table

This is used to create a Model with the appropriate methods from a UCSC table. It uses sqlalchemy reflection to do the lifiting.

class cruzdb.models.ABase

Base object that wraps returned database rows

Methods

bed(*attrs, **kwargs)	return a bed formatted string of this feature
bed12([score, rgb])	return a bed12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
blat([db, sequence, seq_type])	make a request to the genome-browsers BLAT interface
distance([other_or_start, end, features])	check the distance between this an another interval
downstream(distance)	return the (start, end) of the region before the geneStart
features(other_start, other_end)	return e.g. “intron;exon” if the other_start, end overlap introns and
globalize(position[, cdna])
is_downstream_of(other)	return a boolean indicating whether this feature is downstream of
is_upstream_of(other)	return a boolean indicating whether this feature is upstream of other
localize(*positions, **kwargs)	convert global coordinate(s) to local taking
ncbi_blast([db, megablast, sequence])	perform an NCBI blast against the sequence of this feature
promoter([up, down])	Return a start, end tuple of positions for the promoter region of this
sequence([per_exon])	Return the sequence for this feature.
tss([up, down])	Return a start, end tuple of positions around the transcription-start
upstream(distance)	return the (start, end) of the region before the geneStart

bed(*attrs, **kwargs)

return a bed formatted string of this feature

bed12(score='0', rgb='.')

return a bed12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) representation of this interval

bins

return the bins for efficient querying

blat(db=None, sequence=None, seq_type='DNA')

make a request to the genome-browsers BLAT interface sequence is one of None, “mrna”, “cds” returns a list of features that are hits to this sequence.

cds

just the parts of the exons that are translated

cds_sequence

a list of genomic sequences for the CDS’s

cdss

just the parts of the exons that are translated

coding_exons

includes the entire exon as long as any of it is > cdsStart and < cdsEnd

distance(other_or_start=None, end=None, features=False)

check the distance between this an another interval Parameters ———-

other_or_start : Interval or int

either an integer or an Interval with a start attribute indicating the start of the interval

end : int

if other_or_start is an integer, this must be an integer indicating the end of the interval

features : bool

if True, the features, such as CDS, intron, etc. that this feature overlaps are returned.

downstream(distance)

return the (start, end) of the region before the geneStart

exons

return a list of exons [(start, stop)] for this object if appropriate

features(other_start, other_end)

return e.g. “intron;exon” if the other_start, end overlap introns and exons

gene_features

return a list of features for the gene features of this object. This would include exons, introns, utrs, etc.

is_downstream_of(other)

return a boolean indicating whether this feature is downstream of other taking the strand of other into account

is_gene_pred

http://genome.ucsc.edu/FAQ/FAQformat.html#format9

is_upstream_of(other)

return a boolean indicating whether this feature is upstream of other taking the strand of other into account

localize(*positions, **kwargs)

convert global coordinate(s) to local taking introns into account and cds/tx-Start depending on cdna=True kwarg

mrna_sequence

a list of genomic sequences for the mRNA’s

ncbi_blast(db='nr', megablast=True, sequence=None)

perform an NCBI blast against the sequence of this feature

position

a chrom:start-stop representation of this feature

promoter(up=2000, down=0)

Return a start, end tuple of positions for the promoter region of this gene

Parameters :

up : int

this distance upstream that is considered the promoter

down : int

the strand is used to add this many downstream bases into the gene.

sequence(per_exon=False)

Return the sequence for this feature. if per-exon is True, return an array of exon sequences This sequence is never reverse complemented

tss(up=0, down=0)

Return a start, end tuple of positions around the transcription-start site

Parameters :

up : int

if greature than 0, the strand is used to add this many upstream bases in the appropriate direction

down : int

if greature than 0, the strand is used to add this many downstream bases into the gene.

upstream(distance)

return the (start, end) of the region before the geneStart

utr3

return the 3’ UTR if appropriate

utr5

return the 5’ UTR if appropriate

class cruzdb.models.Interval(start, end, chrom=None, name=None)

Interval class for convenience

Parameters :

start : int

end : int

chrom : str

name : str

optional name for the interval

Methods

distance([other_or_start, end, features])	check the distance between this an another interval
is_upstream_of(other)	check if this is upstream of the other interval taking the strand of
overlaps(other)	check for overlap with the other interval

distance(other_or_start=None, end=None, features=False)

check the distance between this an another interval Parameters ———-

other_or_start : Interval or int

either an integer or an Interval with a start attribute indicating the start of the interval

end : int

if other_or_start is an integer, this must be an integer indicating the end of the interval

features : bool

if True, the features, such as CDS, intron, etc. that this feature overlaps are returned.

is_upstream_of(other)

check if this is upstream of the other interval taking the strand of the other interval into account

overlaps(other)

check for overlap with the other interval