Bio.Sequencing.Ace module

Parser for ACE files output by PHRAP.

Written by Frank Kauff (fkauff@duke.edu) and Cymon J. Cox (cymon@duke.edu)

Usage:

There are two ways of reading an ace file:

  1. The function ‘read’ reads the whole file at once;

  2. The function ‘parse’ reads the file contig after contig.

First option, parse whole ace file at once:

from Bio.Sequencing import Ace
acefilerecord = Ace.read(open('my_ace_file.ace'))
This gives you:

  • acefilerecord.ncontigs (the number of contigs in the ace file)

  • acefilerecord.nreads (the number of reads in the ace file)

  • acefilerecord.contigs[] (one instance of the Contig class for each contig)

The Contig class holds the info of the CO tag, CT and WA tags, and all the reads used for this contig in a list of instances of the Read class, e.g.:

contig3 = acefilerecord.contigs[2]
read4 = contig3.reads[3]
RD_of_read4 = read4.rd
DS_of_read4 = read4.ds

CT, WA, RT tags from the end of the file can appear anywhere are automatically sorted into the right place.

see _RecordConsumer for details.

The second option is to iterate over the contigs of an ace file one by one in the ususal way:

from Bio.Sequencing import Ace
contigs = Ace.parse(open('my_ace_file.ace'))
for contig in contigs:
    print(contig.name)
    ...

Please note that for memory efficiency, when using the iterator approach, only one contig is kept in memory at once. However, there can be a footer to the ACE file containing WA, CT, RT or WR tags which contain additional meta-data on the contigs. Because the parser doesn’t see this data until the final record, it cannot be added to the appropriate records. Instead these tags will be returned with the last contig record. Thus an ace file does not entirerly suit the concept of iterating. If WA, CT, RT, WR tags are needed, the ‘read’ function rather than the ‘parse’ function might be more appropriate.

class Bio.Sequencing.Ace.rd

Bases: object

RD (reads), store a read with its name, sequence etc.

The location and strand each read is mapped to is held in the AF lines.

__init__(self)

Initialize the class.

class Bio.Sequencing.Ace.qa(line=None)

Bases: object

QA (read quality), including which part if any was used as the consensus.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.ds(line=None)

Bases: object

DS lines, include file name of a read’s chromatogram file.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.af(line=None)

Bases: object

AF lines, define the location of the read within the contig.

Note attribute coru is short for complemented (C) or uncomplemented (U), since the strand information is stored in an ACE file using either the C or U character.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.bs(line=None)

Bases: object

BS (base segment), which read was chosen as the consensus at each position.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.rt(line=None)

Bases: object

RT (transient read tags), generated by crossmatch and phrap.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.ct(line=None)

Bases: object

CT (consensus tags).

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.wa(line=None)

Bases: object

WA (whole assembly tag), holds the assembly program name, version, etc.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.wr(line=None)

Bases: object

WR lines.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.Reads(line=None)

Bases: object

Holds information about a read supporting an ACE contig.

__init__(self, line=None)

Initialize the class.

class Bio.Sequencing.Ace.Contig(line=None)

Bases: object

Holds information about a contig from an ACE record.

__init__(self, line=None)

Initialize the class.

Bio.Sequencing.Ace.parse(handle)

Iterate of ACE file contig by contig.

Argument handle is a file-like object.

This function returns an iterator that allows you to iterate over the ACE file record by record:

records = parse(handle)
for record in records:
    # do something with the record

where each record is a Contig object.

class Bio.Sequencing.Ace.ACEFileRecord

Bases: object

Holds data of an ACE file.

__init__(self)

Initialize the class.

sort(self)

Sorts wr, rt and ct tags into the appropriate contig / read instance, if possible.

Bio.Sequencing.Ace.read(handle)

Parse a full ACE file into a list of contigs.