Last login: Mon Feb  6 10:18:54 on console
John-Flanagans-MacBook-Pro:~ johnflanagan$ ls
Desktop/
Documents/
Downloads/
EMAN2DB/
GRC2011pics/
LabMeetingTalk/
Library/
MP900314296.JPG
MP900422793.JPG
Movies/
Music/
NCMInonretreat/
Office_Mac_2008_English_MLF_X14-18333.iso*
P22nomissingwedge.png
Pictures/
Public/
Sites/
Syn5MissingWedge.png
Syn5convmissingwedge.png
Syn5convmissingwedgeBest.png
emd_1975.map
gl_functions.js~
me.jpg
pp_periodic_noise.png
termal.png
tomo.ai
John-Flanagans-MacBook-Pro:~ johnflanagan$ clear

John-Flanagans-MacBook-Pro:~ johnflanagan$ ipython
Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) 
Type "copyright", "credits" or "license" for more information.

IPython 0.10 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object'. ?object also works, ?? prints more.

In [1]: from re import *

In [2]: patern = compile('car')

In [3]: print patern
------> print(patern)
<_sre.SRE_Pattern object at 0x1012ada30>

In [4]: dir(patern)
Out[4]: 
['__copy__',
 '__deepcopy__',
 'findall',
 'finditer',
 'match',
 'scanner',
 'search',
 'split',
 'sub',
 'subn']

In [5]: mo = patern.search('blue carport')

In [6]: print mo
------> print(mo)
<_sre.SRE_Match object at 0x1012c36b0>

In [7]: dir(mo)
Out[7]: 
['__copy__',
 '__deepcopy__',
 'end',
 'expand',
 'group',
 'groupdict',
 'groups',
 'span',
 'start']

In [8]: print mo.groups()
------> print(mo.groups())
()

In [9]: print mo.group()
------> print(mo.group())
car

In [10]: print mo.start()
-------> print(mo.start())
5

In [11]: print mo.end()
-------> print(mo.end())
8

In [12]: print patern.findall('blue carport')
-------> print(patern.findall('blue carport'))
['car']

In [13]: print patern.findall('blue car carport') 
-------> print(patern.findall('blue car carport'))
['car', 'car']

In [14]: print patern.sub('air', 'blue carport')
-------> print(patern.sub('air', 'blue carport'))
blue airport

In [15]: print patern.sub('air', 'blue arport')
-------> print(patern.sub('air', 'blue arport'))
blue arport

In [16]: string = 'blue carport'

In [17]: print patern.sub('air', string)
-------> print(patern.sub('air', string))
blue airport

In [18]: print string
-------> print(string)
blue carport

In [19]: airport = patern.sub('air', string)

In [20]: print airport
-------> print(airport)
blue airport

In [21]: sub('car', 'air', 'blue carport')
Out[21]: 'blue airport'

In [22]: print search('^car', 'carport')
-------> print(search('^car', 'carport'))
<_sre.SRE_Match object at 0x1012c3780>

In [23]: print search('^car', 'blue car')
-------> print(search('^car', 'blue car'))
None

In [24]: print search('car$', 'blue car')
-------> print(search('car$', 'blue car'))
<_sre.SRE_Match object at 0x1012c3780>

In [25]: print search('car$', 'carport')
-------> print(search('car$', 'carport'))
None

In [26]: search('gr*', 'gift')
Out[26]: <_sre.SRE_Match object at 0x1012c3780>

In [27]: search('gr*', 'great')
Out[27]: <_sre.SRE_Match object at 0x1012c37e8>

In [28]: search('gr*', 'grrrrr')
Out[28]: <_sre.SRE_Match object at 0x1012c38b8>

In [29]: search('gr*', 'apple')

In [30]: search('gr+', 'gift')

In [31]: search('gr+', 'great')
Out[31]: <_sre.SRE_Match object at 0x1012c3920>

In [32]: search('gr+', 'grrrr')
Out[32]: <_sre.SRE_Match object at 0x1012c3988>

In [33]: search('g+', 'grrrr')
Out[33]: <_sre.SRE_Match object at 0x1012c39f0>

In [34]: search('g+', 'grrrr').group()
Out[34]: 'g'

In [35]: search('gr+', 'grrrr').group()
Out[35]: 'grrrr'

In [36]: search('gr*', 'grrrr').group()
Out[36]: 'grrrr'

In [37]: search('gr*', 'great').group()
Out[37]: 'gr'

In [38]: search('gr*', 'gift').group()
Out[38]: 'g'

In [39]: search('gr?', 'gift').group()
Out[39]: 'g'

In [40]: search('gr?', 'great').group()
Out[40]: 'gr'

In [41]: search('gr?', 'grrrr').group()
Out[41]: 'gr'

In [42]: search('gr+', 'grrrr').group()
Out[42]: 'grrrr'

In [43]: search('gr*', 'grrrr').group()
Out[43]: 'grrrr'

In [44]: search('gr{3}', 'grrrr').group()
Out[44]: 'grrr'

In [45]: search('gr{3}', 'grr').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [46]: search('gr{2,3}', 'grr').group()
Out[46]: 'grr'

In [47]: search('gr{2,3}', 'grrr').group()
Out[47]: 'grrr'

In [48]: search('gr{2,3}', 'great').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [49]: search('gr{2,3}', 'grrrr').group()
Out[49]: 'grrr'

In [50]: search('A+', 'AAA').group()
Out[50]: 'AAA'

In [51]: search('A+?', 'AAA').group()
Out[51]: 'A'

In [52]: search('A+', 'AAAZA').group()
Out[52]: 'AAA'

In [53]: search('A+', 'AAAZA').groups()
Out[53]: ()

In [54]: search('A+', 'AAAZA').group()
Out[54]: 'AAA'

In [55]: search('A+', 'AAAZAAA').group()
Out[55]: 'AAA'

In [56]: search('A+', 'AAAZAAA').groups()
Out[56]: ()

In [57]: search('A+', 'AAA AAA').groups()
Out[57]: ()

In [58]: search('A+', 'AAA AAA').group()
Out[58]: 'AAA'

In [59]: search('A+', 'AAA AAAA').group()
Out[59]: 'AAA'

In [60]: search('A+?', 'AAA').group()
Out[60]: 'A'

In [61]: search('A*?', 'AAA').group()
Out[61]: ''

In [62]: search('A{2}?', 'AAA').group()
Out[62]: 'AA'

In [63]: search('car.', 'cart').group()
Out[63]: 'cart'

In [64]: search('car.', 'oxcart').group()
Out[64]: 'cart'

In [65]: search('car.', 'cartwheel').group()
Out[65]: 'cart'

In [66]: search('car.*', 'cartwheel').group()
Out[66]: 'cartwheel'

In [67]: search('car.*', 'artwheel').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [68]: search('\dcar', 'car').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [69]: search('\dcar', '2car').group()
Out[69]: '2car'

In [70]: search('\dcar', '2 car').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [71]: search('\d\scar', '2 car').group()
Out[71]: '2 car'

In [72]: search('\d\scar', '2car').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [73]: search('\d\scar', '2  car').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [74]: search('\d\s*car', '2  car').group()
Out[74]: '2  car'

In [75]: search('\d\s*car', '2 car').group()
Out[75]: '2 car'

In [76]: search('\d\s*car', '2car').group()
Out[76]: '2car'

In [77]: search('\d\s+car', '2car').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [78]: search('\d\s+car', '2 car').group()
Out[78]: '2 car'

In [79]: search('\w\s+car', 'b car').group()
Out[79]: 'b car'

In [80]: search('\w\s+car', 'blue car').group()
Out[80]: 'e car'

In [81]: search('\w+\s+car', 'blue car').group()
Out[81]: 'blue car'

In [82]: search('\w+car', 'blue car').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [83]: search('\w+car', 'bluecar').group()
Out[83]: 'bluecar'

In [84]: search([abc].{2}, 'ape').group()
------------------------------------------------------------
   File "<ipython console>", line 1
     search([abc].{2}, 'ape').group()
                  ^
SyntaxError: invalid syntax


In [85]: search('[abc].{2}', 'ape').group()
Out[85]: 'ape'

In [86]: search('[abc].{2}', 'dog').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [87]: search('[abc].{2}', 'cat').group()
Out[87]: 'cat'

In [88]: search('[abc].{2}', 'cattle').group()
Out[88]: 'cat'

In [89]: search('[abc].*', 'cattle').group()
Out[89]: 'cattle'

In [90]: search('[abc].*', 'cattle drive').group()
Out[90]: 'cattle drive'

In [91]: search('[abc].*/s', 'cattle drive').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [92]: search('[abc].*/s', 'cattle drive').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [93]: search('[abc].*\s', 'cattle drive').group()
Out[93]: 'cattle '

In [94]: search('[^abc].{2}', 'dog').group()Out[94]: 'dog'

In [95]: search('[^abc].{2}', 'cat').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [96]: search('[^abc].{2}', 'ape').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [97]: search('[a-m].{2}', 'dog').group()
Out[97]: 'dog'

In [98]: search('[a-m].{2}', 'pat').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [99]: search('[0-5]', '2').group()
Out[99]: '2'

In [100]: search('[0-5]', '7').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [101]: search('[0-5]{1,2}', '50').group()
Out[101]: '50'

In [102]: search('[0-5]{1,2}', '55').group()
Out[102]: '55'

In [103]: search('[0-5]{1,2}', '59').group()
Out[103]: '5'

In [104]: search('[0-5]{1,2}', '60').group()
Out[104]: '0'

In [105]: search('[0-5]{2}', '60').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [106]: search('[0-5]{2}', '55').group()
Out[106]: '55'

In [107]: search('[0-5]{2}', '56').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [108]: search(r'(?:abc){2}123', 'abcabc123').group()
Out[108]: 'abcabc123'

In [109]: search(r'(?:abc){2}123', 'abc123').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [110]: search(r'(?:abc){2}123', 'abc123abc').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [111]: search(r'(?:abc)+123', 'abc123abc').group()
Out[111]: 'abc123'

In [112]: search(r'(?:abc)+123', 'abcabc').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [113]: search(r'(?:abc)+', 'abcabc').group()Out[113]: 'abcabc'

In [114]: search(r'(?:abc)+', 'abcabcabcabc').group()
Out[114]: 'abcabcabcabc'

In [115]: findall(r'(?:abc)+', 'abcabcabcabc')Out[115]: ['abcabcabcabc']

In [116]: findall(r'(?:abc)+', 'abcabc123abc')
Out[116]: ['abcabc', 'abc']

In [117]: search(r'(AT).*\1', 'ATGCAT').group()
Out[117]: 'ATGCAT'

In [118]: search(r'(AT).*\1', 'ATGCA').group()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [119]: search(r'(AT).*\1*', 'ATGCA').group()
Out[119]: 'ATGCA'

In [120]: dnareo = compile(r'(AT).*\1')

In [121]: mo = dnareo.search('ATCGCATA')

In [122]: print mo.group(0)
--------> print(mo.group(0))
ATCGCAT

In [123]: print mo.group(1)
--------> print(mo.group(1))
AT

In [124]: dnareo = compile(r'(A[CT]).*\1')

In [125]: print dnareo.search('ATCGCATA').group(0)
--------> print(dnareo.search('ATCGCATA').group(0))
ATCGCAT

In [126]: print dnareo.search('ACCGCACA').group(0)
--------> print(dnareo.search('ACCGCACA').group(0))
ACCGCAC

In [127]: print dnareo.search('ACCGCATA').group(0)
--------> print(dnareo.search('ACCGCATA').group(0))
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/johnflanagan/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'group'

In [128]: