MACS3.IO.Parser module

Input parsers used across MACS3 for reading alignment-like formats.

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License (see the file LICENSE included with the distribution).

class MACS3.IO.Parser.BAMPEParser

Bases: BAMParser

Parser for paired-end BAM files that yields fragment spans.

n: Total number of fragments.

d: Average fragment length.

append_petrack(petrack)

Append inferred fragments to an existing PETrackI.

Parameters:: petrack – Existing paired-end track to append to.
Returns:: The updated track instance.
Return type:: PETrackI

Examples

from MACS3.IO.Parser import BAMPEParser
parser = BAMPEParser("reads.bam")
petrack = parser.build_petrack()
# Later, append more fragments from another file:
parser2 = BAMPEParser("more_reads.bam")
petrack = parser2.append_petrack(petrack)

build_petrack()

Return a PETrackI populated with inferred fragments.

Returns:: Paired-end track populated from BAM pairs.
Return type:: PETrackI

Examples

from MACS3.IO.Parser import BAMPEParser
parser = BAMPEParser("reads.bam")
petrack = parser.build_petrack()

class MACS3.IO.Parser.BAMParser

Bases: GenericParser

Parser for BAM binary alignment files.

append_fwtrack(fwtrack): Append uniquely mapped reads to an existing FWTrack.

build_fwtrack(): Append uniquely mapped reads to an existing FWTrack.

get_references(): Return (references, lengths) extracted from the BAM header.

sniff(): Return True if the file begins with the BAM magic string.

tsize()

Get tag size from BAM file – read l_seq field.

Refer to: http://samtools.sourceforge.net/SAM1.pdf

This may not work for BAM file from bedToBAM (bedtools),

since the l_seq field seems to be 0.

class MACS3.IO.Parser.BEDPEParser

Bases: GenericParser

Parser for three-column BEDPE-style fragments (chrom, left, right).

append_petrack(petrack): Append fragments from the stream to an existing PETrackI.

build_petrack()

Return a PETrackI constructed from the entire stream.

Returns:: Paired-end track populated from the input stream.
Return type:: PETrackI

Examples

from MACS3.IO.Parser import BEDPEParser
parser = BEDPEParser("fragments.bedpe")
petrack = parser.build_petrack()

class MACS3.IO.Parser.BEDParser

Bases: GenericParser

Parser for standard BED records with optional strand column.

class MACS3.IO.Parser.BowtieParser

Bases: GenericParser

Parser for Bowtie or Maqview single-end map files.

class MACS3.IO.Parser.ELANDExportParser

Bases: GenericParser

Parser for ELAND export tab-delimited files.

class MACS3.IO.Parser.ELANDMultiParser

Bases: GenericParser

Parser for ELAND multi-hit reports (s_N_eland_multi format).

class MACS3.IO.Parser.ELANDResultParser

Bases: GenericParser

Parser for single-end ELAND result tables.

class MACS3.IO.Parser.FragParser

Bases: GenericParser

Parser for scATAC fragment TSV files with barcode counts.

append_petrack(petrack, max_count=0)

Append barcode-aware fragments to an existing PETrackI.

Parameters:

petrack – Existing paired-end track to append to.
max_count – Optional cap applied to per-fragment count values.

Returns:

The updated track instance.

Return type:

PETrackII

Examples

from MACS3.IO.Parser import FragParser
parser = FragParser("fragments.tsv.gz")
petrack = parser.build_petrack()
parser2 = FragParser("more_fragments.tsv.gz")
petrack = parser2.append_petrack(petrack, max_count=10)

build_petrack(max_count=0)

Return a PETrackII populated with fragments and barcodes.

Parameters:: max_count – Optional cap applied to per-fragment count values.
Returns:: Paired-end track with barcode and count metadata.
Return type:: PETrackII

Examples

from MACS3.IO.Parser import FragParser
parser = FragParser("fragments.tsv.gz")
petrack = parser.build_petrack(max_count=10)

class MACS3.IO.Parser.GenericParser

Bases: object

Base parser with helpers for streaming alignment-like text files.

filename: Path to the input file.

gzipped: Whether the input stream is gzipped. (bool)

tag_size: tag size.

fhd: Open file handle for the input stream.

buffer_size: Buffer size for streaming reads.

append_fwtrack(fwtrack): Append parsed locations to an existing FWTrack.

build_fwtrack(): Create a new FWTrack populated from the underlying stream.

close(): Close the underlying file handle.

is_gzipped(): Report whether the underlying input stream is gzip compressed.

sniff(): Return True when the input appears compatible with this parser.

tsize(): Estimate tag length from a sample of valid alignments.

class MACS3.IO.Parser.SAMParser

Bases: GenericParser

Parser for SAM alignment text files with standard SAM flags.

MACS3.IO.Parser.guess_parser(fname, buffer_size=100000)

Return the first parser that recognises fname as a supported format.

Parameters:

fname – Path to inspect.
buffer_size (cython.long) – Buffer size handed to candidate parser constructors.

Returns:

Parser instance configured for the detected format.

Raises:

Exception – If no parser can identify the file structure.