biopython v1.71.0 Bio.Restriction.PrintFormat.PrintFormat

PrintFormat allow the printing of results of restriction analysis.

Link to this section Summary

Functions

__init__()

Initialise

__next_section()

Next section (PRIVATE)

_make_list()

Summarise a list of positions by enzyme (PRIVATE)

_make_list_only()

Summarise list of positions per enzyme (PRIVATE)

_make_map()

Summarise mapping information as a string (PRIVATE)

_make_map_only()

Make string describing cutting map (PRIVATE)

_make_nocut()

Summarise non-cutting enzymes (PRIVATE)

_make_nocut_only()

Summarise non-cutting enzymes (PRIVATE)

_make_number()

Format cutting position information as a string (PRIVATE)

_make_number_only()

Summarise number of cuts as a string (PRIVATE)

format_output()

Summarise results as a nicely formatted string

make_format()

Virtual method used for formatting results

print_as()

Print the results as specified

print_that()

Print the output of the format_output method (OBSOLETE)

Link to this section Functions

__init__()

Initialise.

__next_section()

Next section (PRIVATE).

Arguments:

ls is a tuple/list of tuple (string, [int, int]).
into is a string to which the formatted ls will be added.

Format ls as a string of lines: The form is::

enzyme1     :   position1.
enzyme2     :   position2, position3.

then add the formatted ls to tot return tot.

_make_list()

Summarise a list of positions by enzyme (PRIVATE).

Return a string of form::

title.

enzyme1     :   position1, position2.
enzyme2     :   position1, position2, position3.

Arguments:

ls is a tuple or list of cutting enzymes.
title is the title.
nc is a tuple or list of non cutting enzymes.
s1 is the sentence before the non cutting enzymes.

_make_list_only()

Summarise list of positions per enzyme (PRIVATE).

Return a string of form::

title.

enzyme1     :   position1, position2.
enzyme2     :   position1, position2, position3.
...

Arguments:

ls is a tuple or list of results.
title is a string.
Non cutting enzymes are not included.

_make_map()

Summarise mapping information as a string (PRIVATE).

Return a string of form::

| title.
|
|     enzyme1, position
|     |
| AAAAAAAAAAAAAAAAAAAAA...
| |||||||||||||||||||||
| TTTTTTTTTTTTTTTTTTTTT...

Arguments:

ls is a list of cutting enzymes.
title is the title.
nc is a list of non cutting enzymes.
s1 is the sentence before the non cutting enzymes.

_make_map_only()

Make string describing cutting map (PRIVATE).

Return a string of form::

| title.
|
|     enzyme1, position
|     |
| AAAAAAAAAAAAAAAAAAAAA...
| |||||||||||||||||||||
| TTTTTTTTTTTTTTTTTTTTT...

Arguments:

ls is a list of results.
title is a string.
Non cutting enzymes are not included.

_make_nocut()

Summarise non-cutting enzymes (PRIVATE).

Return a formatted string of the non cutting enzymes.

ls is a list of cutting enzymes -> will not be used. Here for compatibility with make_format.

Arguments:

title is the title.
nc is a list of non cutting enzymes.
s1 is the sentence before the non cutting enzymes.

_make_nocut_only()

Summarise non-cutting enzymes (PRIVATE).

Return a formatted string of the non cutting enzymes.

Arguments:

nc is a tuple or list of non cutting enzymes.
s1 is the sentence before the non cutting enzymes.

_make_number()

Format cutting position information as a string (PRIVATE).

Returns a string in the form::

title.

enzyme which cut 1 time:

enzyme1     :   position1.

enzyme which cut 2 times:

enzyme2     :   position1, position2.
...

Arguments:

ls is a list of cutting enzymes.
title is the title.
nc is a list of non cutting enzymes.
s1 is the sentence before the non cutting enzymes.

_make_number_only()

Summarise number of cuts as a string (PRIVATE).

Return a string of form::

title.

enzyme which cut 1 time:

enzyme1     :   position1.

enzyme which cut 2 times:

enzyme2     :   position1, position2.
...

Arguments:

ls is a list of results.
title is a string.
Non cutting enzymes are not included.

format_output()

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.

make_format()

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.

print_as()

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.

print_that()

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.