# Bio.Restriction.PrintFormat module

Print the results of restriction enzyme analysis.

PrintFormat prints the results from restriction analysis in 3 different format: list, column or map.

The easiest way to use it is:

    >>> from Bio.Restriction.PrintFormat import PrintFormat
    >>> from Bio.Restriction.Restriction import RestrictionBatch
    >>> from Bio.Seq import Seq
    >>> pBs_mcs = Seq('GGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTC')
    >>> restriction_batch = RestrictionBatch(['EcoRI', 'BamHI', 'ApaI'])
    >>> result = restriction_batch.search(pBs_mcs)
    >>> my_map = PrintFormat()
    >>> my_map.print_that(result, 'My pBluescript mcs analysis:\n',
    ...               'No site:\n')
    My pBluescript mcs analysis:
    ApaI       :  12.
    EcoRI      :  50.
    No site:
    BamHI

    >>> my_map.sequence = pBs_mcs
    >>> my_map.print_as("map")
    >>> my_map.print_that(result)
               12 ApaI
               |
               |                                     50 EcoRI
               |                                     |
    GGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTC
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||
    CCATGGCCCGGGGGGGAGCTCCAGCTGCCATAGCTATTCGAACTATAGCTTAAG
    1                                                   54

       Enzymes which do not cut the sequence.

    BamHI

    >>>

Some of the methods of PrintFormat are meant to be overridden by derived class.

Use the following parameters to control the appearance:

- ConsoleWidthwidth of the console used default to 80.

    should never be less than 60.

- NameWidth : space attributed to the name in PrintList method.

- Indent : Indent of the second line.

- MaxSizeMaximal size of the sequence (default=6:

    -> 99 999 bp + 1 trailing ‘,’ people are unlikely to ask for restriction map of sequences bigger than 100.000 bp. This is needed to determine the space to be reserved for sites location.

    - MaxSize = 5 => 9.999 bp

    - MaxSize = 6 => 99.999 bp

    - MaxSize = 7 => 999.999 bp

Example output:

    <------------ ConsoleWidth --------------->
    <- NameWidth ->
    EcoRI         :   1, 45, 50, 300, 400, 650,
                          700, 1200, 2500.
                      <-->
                        Indent

class Bio.Restriction.PrintFormat.PrintFormat

  Bases: `object`

  PrintFormat allow the printing of results of restriction analysis.

  ConsoleWidth = 80
  NameWidth = 10
  MaxSize = 6
  Cmodulo = 0
  PrefWidth = 80
  Indent = 4
  linesize = 70
  print_as(what='list')

    Print the results as specified.

    Valid format are:

      ‘list’ -> alphabetical order ‘number’ -> number of sites in the sequence ‘map’ -> a map representation of the sequence with the sites.

    If you want more flexibility over-ride the virtual method make_format.

  format_output(dct, title='', s1='')

    Summarise results as a nicely formatted string.

    Arguments:

      - dct is a dictionary as returned by a RestrictionBatch.search()

      - title is the title of the map. It must be a formatted string, i.e. you must include the line break.

      - s1 is the title separating the list of enzymes that have sites from those without sites.

      - s1 must be a formatted string as well.

    The format of print_that is a list.

  print_that(dct, title='', s1='')

    Print the output of the format_output method (OBSOLETE).

    Arguments:

      - dct is a dictionary as returned by a RestrictionBatch.search()

      - title is the title of the map. It must be a formatted string, i.e. you must include the line break.

      - s1 is the title separating the list of enzymes that have sites from those without sites.

      - s1 must be a formatted string as well.

    This method prints the output of A.format_output() and it is here for backwards compatibility.

  make_format(cut=(), title='', nc=(), s1='')

    Virtual method used for formatting results.

    Virtual method. Here to be pointed to one of the _make_* methods. You can as well create a new method and point make_format to it.

  __annotations_cache__ = {}
  __firstlineno__ = 85
  __static_attributes__ = ('make_format',)

Biopython v: 1.86

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