Reference

ce_detector.detector

class for detecting junction reads

class ce_detector.detector.JunctionDetector(bam_file, reference, quality, output=None)

class for detecting junction reads and record position

Parameters

• bam_file (str) – bam file

• output (str) – filename of output

• reference (str) – filename of genome reference

• quality (int) – quality for filtering junction reads

static check_strand(anchor, acceptor)

check type of strand

Parameters

• anchor (str) – anchor of read

• acceptor (str) – acceptor of read

Returns

type of strand (-|+)

Return type

str

run(chrom, ann_chrom, logger, verbose=False)

detect junction reads and annotate slice site, write results to file

Returns

instance from junctionmap

Return type

instance

worker(bam_file, reference, chrom, ann_chrom, quality, idn, junctionmap)

find junction reads and annotate slice site

Parameters

• ann_chrom –

• bam_file (instance) – handle of bam_file

• reference (instance) – handle of reference

• chrom (str) – chromosome

• quality (int) – quality for filtering reads

• idn (int) – identifier of reads

• junctionmap (instance) – instance from junctionmap

Returns

instance from junctionmap

Return type

instance

class ce_detector.detector.JunctionMap(chrom)

build a class to store information of all junction reads

add_read(read)

add read to junctionlist

Parameters

read (instance) – instance from Read

write2file(output, header=None)

write all reads in junctionlist to file

Parameters

• output (str or TextIo) – file name of output

• header (str) – header of output

class ce_detector.detector.Read(chrom, start, end, idn, score, strand, anchor, acceptor, pvalue)

build a read class for storing information of every junction read

Parameters

• chrom (str) – chromosome of genome

• start (int) – start position of junction read

• end (int) – end position of junction read

• idn (int) – index of junction read

• score (int) – support of junction read

• strand (str) – direction of junction read (-|+)

• anchor (str) – anchor of junction read

• acceptor (str) – acceptor of junction read

ce_detector.annotator

class for annotating junction reads

class ce_detector.annotator.Annotator(database: Any, output=None)

annotate junction reads

Parameters

• junctionmap (instance) – instance return ce_detector.detector.JunctionMap

• database (Any) – database of annotation files

• output (TestIo) – filename of annotated junction reads. Defaults to None

annotate_junction(read, result, db)

annotate junction reads and write results to file

Parameters

• read (instance) – junction read return ce_detector.detector.Read

• result (defaultdict[Any, Any]) – gene list used for annotation

• db (instance of file) – database of annotation file

static detect_property(start, end, junction_list)

detect type of slice, number of skipped donors and number of skipped acceptors

type of slice including D A DA N NDA

Parameters

• start (int) – start of junction read

• end (int) – end of junction read

• junction_list (numpy.array) – gene list of junction reads

Returns

type of slice, number of skipped donors, number of skipped acceptors

run(junctionmap, logger, verbose=False)

main function used to annotate junction reads

pick all genes covered by one junction read and annotate all of them: type of slice, number of skipped donors and number of skipped acceptors

ce_detector.scanner

class for scanning cryptic exons based on previous _result :: Junction detector and junction annotator

class ce_detector.scanner.Scanner(cutoff, output=None)

class for scanning cryptic exons based on annotated junction reads

Parameters

• cutoff (int) – cutoff used to filter junction reads with relatively low score or depth

• output (str) – filename of _result

run(junctionmap, logger, verbose=False) → Iterable

run program to scan cryptic exons

Parameters

• verbose –

• logger –

• junctionmap (instance) – instance from ce_detector.detector.JunctionMap

Returns

temporary result used to store cryptic exons

Return type

Iterable

write2file(logger, verbose=False)

start iterator and write _result to file

ce_detector.scanner.assign_value(df_ce, ces, ns, ce_id, ns_id) → None

assign value of child column for every cryptic exons that contains junction reads with N type

Given the start and end of cryptic exons and junction reads, Note: types of junction reads contains N, D, A, DA, NDA. For details: https://regtools.readthedocs.io/en/latest/commands/junctions-annotate/

Parameters

• df_ce (pandas.DataFrame) – pandas.DataFrame of cryptic exons

• ces (pandas.DataFrame) – cryptic exons’ pandas.DataFrame, which has gene ids that both cryptic exon and junction read own. It only contain gene id, start and end

• ns (pandas.DataFrame) – pandas.DataFrame of junction reads whose type is N, as well as has same gene id as cryptic exons

• ce_id (numpy.array) – index of gene id of cryptic exons which has junction reads as children

• ns_id (numpy.array) – index of gene id of junction reads with N type, which have junction reads as children

ce_detector.scanner.check(axis) → numpy.array

check if cryptic exon has children

Which means that check if the cryptic exon is split by others junction reads in terms of start and end position

Parameters

axis (numpy.array) – an array, a junction read, included start and end

Returns

whether junction read can split cryptic exon

Return type

bool

ce_detector.scanner.find_ce(groups) → Iterable

parse _result getting from annotations in order to detect cryptic exons

Parameters

groups (Groupby object return from Dataframe.groupby) – annotated junction reads are grouped by strand and type

Returns

pd.DataFrame of two strands

Return type

Iterable

ce_detector.scanner.split_ce(df_ce, df_n) → Iterable

Iterator: check whether detected cryptic exons are split by other junction reads

Parameters

• df_ce (pandas.DataFrame) – pandas.DataFrame of cryptic exons return from find_ce()

• df_n (pandas.DataFrame) – pandas.DataFrame of junction reads with N type

Returns

param:df_ce with new column children

Return type

iterator