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#!/usr/bin/env python
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
r"""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 AllEnzymes
>>> from Bio import Entrez
>>> from Bio import SeqIO
>>> handle = Entrez.efetch(db="nucleotide", rettype="fasta", id="SYNPBR322")
>>> pBR322 = SeqIO.read(handle, "fasta")
>>> handle.close()
>>> dct = AllEnzymes.search(pBR322.seq)
>>> new = PrintFormat()
>>> new.print_that(dct, 'My pBR322 analysis:\n', 'No site:\n')
My pBR322 analysis:
AasI : 2169, 2582.
AatII : 4289.
...
ZraI : 4287.
ZrmI : 3847.
No site:
AarI AatI Acc65I AcsI AcvI AdeI AflII AgeI
...
Vha464I XapI XbaI XcmI XhoI XmaCI XmaI XmaJI
Zsp2I
>>> new.sequence = pBR322.seq
>>> new.print_as("map")
>>> new.print_that(dct)
...
Some of the methods of PrintFormat are meant to be overridden by derived
class.
"""
from __future__ import print_function
import re
from Bio._py3k import range
from Bio.Restriction import RanaConfig as RanaConf
class PrintFormat(object):
"""PrintFormat allow the printing of results of restriction analysis."""
ConsoleWidth = RanaConf.ConsoleWidth
NameWidth = RanaConf.NameWidth
MaxSize = RanaConf.MaxSize
Cmodulo = ConsoleWidth % NameWidth
PrefWidth = ConsoleWidth - Cmodulo
Indent = RanaConf.Indent
linesize = PrefWidth - NameWidth
def __init__(self):
"""PrintFormat() -> new PrintFormat Instance"""
pass
def print_as(self, what='list'):
"""PF.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.
"""
if what == 'map':
self.make_format = self._make_map
elif what == 'number':
self.make_format = self._make_number
else:
self.make_format = self._make_list
return
def print_that(self, dct, title='', s1=''):
"""PF.print_that(dct, [title[, s1]]) -> Print dct nicely formatted.
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."""
if not dct:
dct = self.results
ls, nc = [], []
for k, v in dct.items():
if v:
ls.append((k, v))
else:
nc.append(k)
print(self.make_format(ls, title, nc, s1))
return
def make_format(self, cut=(), title='', nc=(), s1=''):
"""PF.make_format(cut, nc, title, s) -> string
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.
"""
return self._make_list(cut, title, nc, s1)
# _make_* methods to be used with the virtual method make_format
def _make_list(self, ls, title, nc, s1):
"""PF._make_number(ls,title, nc,s1) -> string.
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.
"""
return self._make_list_only(ls, title) + self._make_nocut_only(nc, s1)
def _make_map(self, ls, title, nc, s1):
"""PF._make_number(ls,title, nc,s1) -> string.
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.
"""
return self._make_map_only(ls, title) + self._make_nocut_only(nc, s1)
def _make_number(self, ls, title, nc, s1):
"""PF._make_number(ls,title, nc,s1) -> string.
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.
"""
return self._make_number_only(ls, title) + self._make_nocut_only(nc, s1)
def _make_nocut(self, ls, title, nc, s1):
"""PF._make_nocut(ls,title, nc,s1) -> string.
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.
"""
return title + self._make_nocut_only(nc, s1)
def _make_nocut_only(self, nc, s1, ls=(), title=''):
"""PF._make_nocut_only(nc, s1) -> string.
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.
"""
if not nc:
return s1
st = ''
stringsite = s1 or '\n Enzymes which do not cut the sequence.\n\n'
Join = ''.join
for key in sorted(nc):
st = Join((st, str.ljust(str(key), self.NameWidth)))
if len(st) > self.linesize:
stringsite = Join((stringsite, st, '\n'))
st = ''
stringsite = Join((stringsite, st, '\n'))
return stringsite
def _make_list_only(self, ls, title, nc=(), s1=''):
"""PF._make_list_only(ls, title) -> string.
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.
"""
if not ls:
return title
return self.__next_section(ls, title)
def _make_number_only(self, ls, title, nc=(), s1=''):
"""PF._make_number_only(ls, title) -> string.
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.
"""
if not ls:
return title
# TODO: Use key to sort!
ls.sort(lambda x, y: cmp(len(x[1]), len(y[1])))
iterator = iter(ls)
cur_len = 1
new_sect = []
for name, sites in iterator:
l = len(sites)
if l > cur_len:
title += "\n\nenzymes which cut %i times :\n\n" % cur_len
title = self.__next_section(new_sect, title)
new_sect, cur_len = [(name, sites)], l
continue
new_sect.append((name, sites))
title += "\n\nenzymes which cut %i times :\n\n" % cur_len
return self.__next_section(new_sect, title)
def _make_map_only(self, ls, title, nc=(), s1=''):
"""PF._make_map_only(ls, title) -> string.
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.
"""
if not ls:
return title
resultKeys = sorted(str(x) for x, y in ls)
map = title or ''
enzymemap = {}
for (enzyme, cut) in ls:
for c in cut:
if c in enzymemap:
enzymemap[c].append(str(enzyme))
else:
enzymemap[c] = [str(enzyme)]
mapping = sorted(enzymemap.keys())
cutloc = {}
x, counter, length = 0, 0, len(self.sequence)
for x in range(60, length, 60):
counter = x - 60
l = []
cutloc[counter] = l
remaining = []
for key in mapping:
if key <= x:
l.append(key)
else:
remaining.append(key)
mapping = remaining
cutloc[x] = mapping
sequence = str(self.sequence)
revsequence = str(self.sequence.complement())
a = '|'
base, counter = 0, 0
emptyline = ' ' * 60
Join = ''.join
for base in range(60, length, 60):
counter = base - 60
line = emptyline
for key in cutloc[counter]:
s = ''
if key == base:
for n in enzymemap[key]:
s = ' '.join((s, n))
l = line[0:59]
lineo = Join((l, str(key), s, '\n'))
line2 = Join((l, a, '\n'))
linetot = Join((lineo, line2))
map = Join((map, linetot))
break
for n in enzymemap[key]:
s = ' '.join((s, n))
k = key % 60
lineo = Join((line[0:(k - 1)], str(key), s, '\n'))
line = Join((line[0:(k - 1)], a, line[k:]))
line2 = Join((line[0:(k - 1)], a, line[k:], '\n'))
linetot = Join((lineo, line2))
map = Join((map, linetot))
mapunit = '\n'.join((sequence[counter: base], a * 60,
revsequence[counter: base],
Join((str.ljust(str(counter + 1), 15), ' ' * 30,
str.rjust(str(base), 15), '\n\n'))
))
map = Join((map, mapunit))
line = ' ' * 60
for key in cutloc[base]:
s = ''
if key == length:
for n in enzymemap[key]:
s = Join((s, ' ', n))
l = line[0:(length - 1)]
lineo = Join((l, str(key), s, '\n'))
line2 = Join((l, a, '\n'))
linetot = Join((lineo, line2))
map = Join((map, linetot))
break
for n in enzymemap[key]:
s = Join((s, ' ', n))
k = key % 60
lineo = Join((line[0:(k - 1)], str(key), s, '\n'))
line = Join((line[0:(k - 1)], a, line[k:]))
line2 = Join((line[0:(k - 1)], a, line[k:], '\n'))
linetot = Join((lineo, line2))
map = Join((map, linetot))
mapunit = ''
mapunit = Join((sequence[base: length], '\n'))
mapunit = Join((mapunit, a * (length - base), '\n'))
mapunit = Join((mapunit, revsequence[base:length], '\n'))
mapunit = Join((mapunit, Join((str.ljust(str(base + 1), 15), ' ' * (
length - base - 30), str.rjust(str(length), 15),
'\n\n'))))
map = Join((map, mapunit))
return map
# private method to do lists:
def __next_section(self, ls, into):
"""FP.__next_section(ls, into) -> string.
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.
"""
indentation = '\n' + (self.NameWidth + self.Indent) * ' '
linesize = self.linesize - self.MaxSize
pat = re.compile("([\w,\s()]){1,%i}[,\.]" % linesize)
several, Join = '', ''.join
for name, sites in sorted(ls):
stringsite = ''
l = Join((', '.join(str(site) for site in sites), '.'))
if len(l) > linesize:
#
# cut where appropriate and add the indentation
#
l = [x.group() for x in re.finditer(pat, l)]
stringsite = indentation.join(l)
else:
stringsite = l
into = Join((into,
str(name).ljust(self.NameWidth), ' : ', stringsite, '\n'))
return into
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