# 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 usual 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__()

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 61
  __static_attributes__ = ('info_items', 'name', 'padded_bases', 'read_tags', 'sequence')

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

  Bases: `object`

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

  __init__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 76
  __static_attributes__ = ('align_clipping_end', 'align_clipping_start', 'qual_clipping_end', 'qual_clipping_start')

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

  Bases: `object`

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

  __init__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 93
  __static_attributes__ = ('chem', 'chromat_file', 'direction', 'dye', 'phd_file', 'template', 'time')

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__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 128
  __static_attributes__ = ('coru', 'name', 'padded_start')

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

  Bases: `object`

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

  __init__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 148
  __static_attributes__ = ('name', 'padded_end', 'padded_start')

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

  Bases: `object`

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

  __init__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 163
  __static_attributes__ = ('comment', 'date', 'name', 'padded_end', 'padded_start', 'program', 'tag_type')

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

  Bases: `object`

  CT (consensus tags).

  __init__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 185
  __static_attributes__ = ('comment', 'date', 'info', 'name', 'notrans', 'padded_end', 'padded_start', 'program', 'tag_type')

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

  Bases: `object`

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

  __init__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 211
  __static_attributes__ = ('date', 'info', 'program', 'tag_type')

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

  Bases: `object`

  WR lines.

  __init__(line=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 227
  __static_attributes__ = ('aligned', 'date', 'name', 'program')

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

  Bases: `object`

  Holds information about a read supporting an ACE contig.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 244
  __init__(line=None)

    Initialize the class.

  __static_attributes__ = ('ds', 'qa', 'rd', 'rt', 'wr')

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

  Bases: `object`

  Holds information about a contig from an ACE record.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 263
  __static_attributes__ = ('af', 'bs', 'ct', 'name', 'nbases', 'nreads', 'nsegments', 'quality', 'reads', 'sequence', 'uorc', 'wa')
  __init__(line=None)

    Initialize the class.

Bio.Sequencing.Ace.parse(source)

  Iterate of ACE file contig by contig.

  Argument source is a file-like object or a path to a file.

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

      records = parse(source)
      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.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 519
  __static_attributes__ = ('contigs', 'ncontigs', 'nreads', 'wa')
  __init__()

    Initialize the class.

  sort()

    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.

Biopython v: 1.86

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