P3 2018 python_regexes
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The document provides a recap of Python programming concepts like conditions and statements, while loops, for loops, break and continue statements, and working with strings. It also introduces regular expressions as a way to match patterns in strings using a formal language that can be interpreted by a regular expression processor. [SUMMARY
![RECAP: Lists
• Flexible arrays, not Lisp-like linked
lists
• a = [99, "bottles of beer", ["on", "the",
"wall"]]
• Same operators as for strings
• a+b, a*3, a[0], a[-1], a[1:], len(a)
• Item and slice assignment
• a[0] = 98
• a[1:2] = ["bottles", "of", "beer"]
-> [98, "bottles", "of", "beer", ["on", "the", "wall"]]
• del a[-1] # -> [98, "bottles", "of", "beer"]](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-7-320.jpg)
![RECAP: Dictionaries
• Hash tables, "associative arrays"
• d = {"duck": "eend", "water": "water"}
• Lookup:
• d["duck"] -> "eend"
• d["back"] # raises KeyError exception
• Delete, insert, overwrite:
• del d["water"] # {"duck": "eend", "back": "rug"}
• d["back"] = "rug" # {"duck": "eend", "back":
"rug"}
• d["duck"] = "duik" # {"duck": "duik", "back":
"rug"}](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-8-320.jpg)
![RECAP
if condition:
statements
[elif condition:
statements] ...
else:
statements
while condition:
statements
for var in sequence:
statements
break
continue
Strings
REGULAR EXPRESSIONS](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-9-320.jpg)
![Regular Expression Quick Guide
^ Matches the beginning of a line
$ Matches the end of the line
. Matches any character
s Matches whitespace
S Matches any non-whitespace character
* Repeats a character zero or more times
*? Repeats a character zero or more times (non-greedy)
+ Repeats a chracter one or more times
+? Repeats a character one or more times (non-greedy)
[aeiou] Matches a single character in the listed set
[^XYZ] Matches a single character not in the listed set
[a-z0-9] The set of characters can include a range
( Indicates where string extraction is to start
) Indicates where string extraction is to end](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-12-320.jpg)
![Matching and Extracting Data
• The re.search() returns a True/False
depending on whether the string matches
the regular expression
• If we actually want the matching strings
to be extracted, we use re.findall()
>>> import re
>>> x = 'My 2 favorite numbers are 19 and 42'
>>> y = re.findall('[0-9]+',x)
>>> print y
['2', '19', '42']](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-15-320.jpg)
![Warning: Greedy Matching
• The repeat characters (* and +) push outward in both directions
(greedy) to match the largest possible string
>>> import re
>>> x = 'From: Using the : character'
>>> y = re.findall('^F.+:', x)
>>> print y
['From: Using the :']
^F.+:
One or more
characters
First character in the
match is an F
Last character in the
match is a :](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-16-320.jpg)
![Non-Greedy Matching
• Not all regular expression repeat codes are
greedy! If you add a ? character - the + and *
chill out a bit...
>>> import re
>>> x = 'From: Using the : character'
>>> y = re.findall('^F.+?:', x)
>>> print y
['From:']
^F.+?:
One or more
characters but
not greedily
First character in the
match is an F
Last character in the
match is a :](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-17-320.jpg)
![Fine Tuning String Extraction
• Parenthesis are not part of the match -
but they tell where to start and stop what
string to extract
From stephen.marquard@uct.ac.za Sat Jan 5 09:14:16
2008
>>> y = re.findall('S+@S+',x)
>>> print y
['stephen.marquard@uct.ac.za']
>>> y = re.findall('^From (S+@S+)',x)
>>> print y
['stephen.marquard@uct.ac.za']
^From (S+@S+)](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-18-320.jpg)
![The Double Split Version
• Sometimes we split a line one way and then grab
one of the pieces of the line and split that piece
again
From stephen.marquard@uct.ac.za Sat Jan 5 09:14:16
2008
words = line.split()
email = words[1]
pieces = email.split('@')
print pieces[1]
stephen.marquard@uct.ac.za
['stephen.marquard', 'uct.ac.za']
'uct.ac.za'](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-19-320.jpg)
![The Regex Version
From stephen.marquard@uct.ac.za Sat Jan 5 09:14:16
2008
import re
lin = 'From stephen.marquard@uct.ac.za Sat Jan 5 09:14:1
y = re.findall('@([^ ]*)',lin)
print y['uct.ac.za']
'@([^ ]*)'
Look through the string until you find an at-sign
Match non-blank character
Match many of them](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-20-320.jpg)
![Escape Character
• If you want a special regular expression
character to just behave normally (most
of the time) you prefix it with ''
>>> import re
>>> x = 'We just received $10.00 for cookies.'
>>> y = re.findall('$[0-9.]+',x)
>>> print y
['$10.00']
$[0-9.]+
A digit or periodA real dollar sign
At least one
or more](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-21-320.jpg)
![Regex.py
text = 'abbaaabbbbaaaaa'
pattern = 'ab'
for match in re.finditer(pattern, text):
s = match.start()
e = match.end()
print ('Found "%s" at %d:%d' % (text[s:e], s, e))](https://image.slidesharecdn.com/p32018pythonregexes-181022204927/85/P3-2018-python_regexes-26-320.jpg)
P3 2018 python_regexes
- 7. RECAP: Lists • Flexible arrays, not Lisp-like linked lists • a = [99, "bottles of beer", ["on", "the", "wall"]] • Same operators as for strings • a+b, a*3, a[0], a[-1], a[1:], len(a) • Item and slice assignment • a[0] = 98 • a[1:2] = ["bottles", "of", "beer"] -> [98, "bottles", "of", "beer", ["on", "the", "wall"]] • del a[-1] # -> [98, "bottles", "of", "beer"]
- 8. RECAP: Dictionaries • Hash tables, "associative arrays" • d = {"duck": "eend", "water": "water"} • Lookup: • d["duck"] -> "eend" • d["back"] # raises KeyError exception • Delete, insert, overwrite: • del d["water"] # {"duck": "eend", "back": "rug"} • d["back"] = "rug" # {"duck": "eend", "back": "rug"} • d["duck"] = "duik" # {"duck": "duik", "back": "rug"}
- 9. RECAP if condition: statements [elif condition: statements] ... else: statements while condition: statements for var in sequence: statements break continue Strings REGULAR EXPRESSIONS
- 10. Regular Expressions http://en.wikipedia.org/wiki/Regular_expression In computing, a regular expression, also referred to as "regex" or "regexp", provides a concise and flexible means for matching strings of text, such as particular characters, words, or patterns of characters. A regular expression is written in a formal language that can be interpreted by a regular expression processor. Really clever "wild card" expressions for matching and parsing strings.
- 11. Understanding Regular Expressions • Very powerful and quite cryptic • Fun once you understand them • Regular expressions are a language unto themselves • A language of "marker characters" - programming with characters • It is kind of an "old school" language - compact
- 12. Regular Expression Quick Guide ^ Matches the beginning of a line $ Matches the end of the line . Matches any character s Matches whitespace S Matches any non-whitespace character * Repeats a character zero or more times *? Repeats a character zero or more times (non-greedy) + Repeats a chracter one or more times +? Repeats a character one or more times (non-greedy) [aeiou] Matches a single character in the listed set [^XYZ] Matches a single character not in the listed set [a-z0-9] The set of characters can include a range ( Indicates where string extraction is to start ) Indicates where string extraction is to end
- 13. The Regular Expression Module • Before you can use regular expressions in your program, you must import the library using "import re" • You can use re.search() to see if a string matches a regular expression similar to using the find() method for strings • You can use re.findall() extract portions of a string that match your regular expression similar to a combination of find() and slicing
- 14. Wild-Card Characters • The dot character matches any character • If you add the asterisk character, the character is "any number of times" ^X.*: Match the start of the line Match any character Many times
- 15. Matching and Extracting Data • The re.search() returns a True/False depending on whether the string matches the regular expression • If we actually want the matching strings to be extracted, we use re.findall() >>> import re >>> x = 'My 2 favorite numbers are 19 and 42' >>> y = re.findall('[0-9]+',x) >>> print y ['2', '19', '42']
- 16. Warning: Greedy Matching • The repeat characters (* and +) push outward in both directions (greedy) to match the largest possible string >>> import re >>> x = 'From: Using the : character' >>> y = re.findall('^F.+:', x) >>> print y ['From: Using the :'] ^F.+: One or more characters First character in the match is an F Last character in the match is a :
- 17. Non-Greedy Matching • Not all regular expression repeat codes are greedy! If you add a ? character - the + and * chill out a bit... >>> import re >>> x = 'From: Using the : character' >>> y = re.findall('^F.+?:', x) >>> print y ['From:'] ^F.+?: One or more characters but not greedily First character in the match is an F Last character in the match is a :
- 18. Fine Tuning String Extraction • Parenthesis are not part of the match - but they tell where to start and stop what string to extract From [email protected] Sat Jan 5 09:14:16 2008 >>> y = re.findall('S+@S+',x) >>> print y ['[email protected]'] >>> y = re.findall('^From (S+@S+)',x) >>> print y ['[email protected]'] ^From (S+@S+)
- 19. The Double Split Version • Sometimes we split a line one way and then grab one of the pieces of the line and split that piece again From [email protected] Sat Jan 5 09:14:16 2008 words = line.split() email = words[1] pieces = email.split('@') print pieces[1] [email protected] ['stephen.marquard', 'uct.ac.za'] 'uct.ac.za'
- 20. The Regex Version From [email protected] Sat Jan 5 09:14:16 2008 import re lin = 'From [email protected] Sat Jan 5 09:14:1 y = re.findall('@([^ ]*)',lin) print y['uct.ac.za'] '@([^ ]*)' Look through the string until you find an at-sign Match non-blank character Match many of them
- 21. Escape Character • If you want a special regular expression character to just behave normally (most of the time) you prefix it with '' >>> import re >>> x = 'We just received $10.00 for cookies.' >>> y = re.findall('$[0-9.]+',x) >>> print y ['$10.00'] $[0-9.]+ A digit or periodA real dollar sign At least one or more
- 22. Real world problems • Match IP Addresses, email addresses, URLs • Match balanced sets of parenthesis • Substitute words • Tokenize • Validate • Count • Delete duplicates • Natural Language processing
- 25. RE in Python • Unleash the power - built-in re module • Functions – to compile patterns • compile – to perform matches • match, search, findall, finditer – to perform operations on match object • group, start, end, span – to substitute • sub, subn • - Metacharacters
- 26. Regex.py text = 'abbaaabbbbaaaaa' pattern = 'ab' for match in re.finditer(pattern, text): s = match.start() e = match.end() print ('Found "%s" at %d:%d' % (text[s:e], s, e))
- 27. 27 Reading Files name = open("filename") – opens the given file for reading, and returns a file object name.read() - file's entire contents as a string name.readline() - next line from file as a string name.readlines() - file's contents as a list of lines – the lines from a file object can also be read using a for loop >>> f = open("hours.txt") >>> f.read() '123 Susan 12.5 8.1 7.6 3.2n 456 Brad 4.0 11.6 6.5 2.7 12n 789 Jenn 8.0 8.0 8.0 8.0 7.5n'
- 28. 28 File Input Template • A template for reading files in Python: name = open("filename") for line in name: statements >>> input = open("hours.txt") >>> for line in input: ... print(line.strip()) # strip() removes n 123 Susan 12.5 8.1 7.6 3.2 456 Brad 4.0 11.6 6.5 2.7 12 789 Jenn 8.0 8.0 8.0 8.0 7.5
- 29. 29 Writing Files name = open("filename", "w") name = open("filename", "a") – opens file for write (deletes previous contents), or – opens file for append (new data goes after previous data) name.write(str) - writes the given string to the file name.close() - saves file once writing is done >>> out = open("output.txt", "w") >>> out.write("Hello, world!n") >>> out.write("How are you?") >>> out.close() >>> open("output.txt").read() 'Hello, world!nHow are you?'
- 30. Question 4 • Program your own prosite parser ! • Download prosite pattern database (prosite.dat) • Automatically generate >2000 search patterns, and search in sequence set from question 1
- 31. >SEQ1 MGNLFENCTHRYSFEYIYENCTNTTNQCGLIRNVASSIDVFHWLDVYISTTIFVISGILNFYCLFIALYT YYFLDNETRKHYVFVLSRFLSSILVIISLLVLESTLFSESLSPTFAYYAVAFSIYDFSMDTLFFSYIMIS LITYFGVVHYNFYRRHVSLRSLYIILISMWTFSLAIAIPLGLYEAASNSQGPIKCDLSYCGKVVEWITCS LQGCDSFYNANELLVQSIISSVETLVGSLVFLTDPLINIFFDKNISKMVKLQLTLGKWFIALYRFLFQMT NIFENCSTHYSFEKNLQKCVNASNPCQLLQKMNTAHSLMIWMGFYIPSAMCFLAVLVDTYCLLVTISILK SLKKQSRKQYIFGRANIIGEHNDYVVVRLSAAILIALCIIIIQSTYFIDIPFRDTFAFFAVLFIIYDFSILSLLGSFTGVA M MTYFGVMRPLVYRDKFTLKTIYIIAFAIVLFSVCVAIPFGLFQAADEIDGPIKCDSESCELIVKWLLFCI ACLILMGCTGTLLFVTVSLHWHSYKSKKMGNVSSSAFNHGKSRLTWTTTILVILCCVELIPTGLLAAFGK SESISDDCYDFYNANSLIFPAIVSSLETFLGSITFLLDPIINFSFDKRISKVFSSQVSMFSIFFCGKR >SEQ2 MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN VVGLLRDAIK RRGDFEMDVV AMVNDTVATM ISCYYEDHQC EVGMIVGTGC NACYMEEMQN VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES SANPGQQLYE KLIGGKYMGE LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ >SEQ3 MESDSFEDFLKGEDFSNYSYSSDLPPFLLDAAPCEPESLEINKYFVVIIYVLVFLLSLLGNSLVMLVILY SRVGRSGRDNVIGDHVDYVTDVYLLNLALADLLFALTLPIWAASKVTGWIFGTFLCKVVSLLKEVNFYSGILLLA CISVDRY LAIVHATRTLTQKRYLVKFICLSIWGLSLLLALPVLIFRKTIYPPYVSPVCYEDMGNNTANWRMLLRILP QSFGFIVPLLIMLFCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTWVIQET CERRNDIDRALEATEILGILGRVNLIGEHWDYHSCLNPLIYAFIGQKFRHGLLKILAIHGLISKDSLPKDSRPSFVGS SSGH TSTTL >SEQ4 MEANFQQAVK KLVNDFEYPT ESLREAVKEF DELRQKGLQK NGEVLAMAPA FISTLPTGAE TGDFLALDFG GTNLRVCWIQ LLGDGKYEMK HSKSVLPREC VRNESVKPII DFMSDHVELF IKEHFPSKFG CPEEEYLPMG FTFSYPANQV SITESYLLRW TKGLNIPEAI NKDFAQFLTE GFKARNLPIR IEAVINDTVG TLVTRAYTSK ESDTFMGIIF GTGTNGAYVE QMNQIPKLAG KCTGDHMLIN MEWGATDFSC LHSTRYDLLL DHDTPNAGRQ IFEKRVGGMY LGELFRRALF HLIKVYNFNE GIFPPSITDA WSLETSVLSR MMVERSAENV RNVLSTFKFR FRSDEEALYL WDAAHAIGRR AARMSAVPIA SLYLSTGRAG KKSDVGVDGS LVEHYPHFVD MLREALRELI GDNEKLISIG IAKDGSGIGA ALCALQAVKE KKGLA MEANFQQAVK KLVNDFEYPT ESLREAVKEF DELRQKGLQK NGEVLAMAPA FISTLPTGAE TGDFLALDFG GTNLRVCWIQ LLGDGKYEMK HSKSVLPREC VRNESVKPII DFMSDHVELF IKEHFPSKFG CPEEEYLPMG FTFSYPANQV SITESYLLRW TKGLNIPEAI NKDFAQFLTE GFKARNLPIR IEAVINDTVG TLVTRAYTSK ESDTFMGIIF GTGTNGAYVE QMNQIPKLAG KCTGDHMLIN MEWGATDFSC LHSTRYDLLL DHDTPNAGRQ IFEKRVGGMY LGELFRRALF HLIKVYNFNE GIFPPSITDA WSLETSVLSR MMVERSAENV RNVLSTFKFR FRSDEEALYL WDAAHAIGRR AARMSAVPIA SLYLSTGRAG KKSDVGVDGS LVEHYPHFVD MLREALRELI GDNEKLISIG IAKDGSGIGA ALCALQAVKE KKGLA Oefening 1
- 32. Question 3. Swiss-Knife.py • Using a database as input ! Parse the entire Swiss Prot collection – How many entries are there ? – Average Protein Length (in aa and MW) – Relative frequency of amino acids • Compare to the ones used to construct the PAM scoring matrixes from 1978 – 1991
- 33. Question 3: Getting the database Uniprot_sprot.dat.gz – 528Mb (on Github onder Files) https://github.ugent.be/wvcrieki/Bioinformatics blob/script_branch/Files/swiss-prot.dat http://www.ebi.ac.uk/uniprot/download-center
- 34. Amino acid frequencies 1978 1991 L 0.085 0.091 A 0.087 0.077 G 0.089 0.074 S 0.070 0.069 V 0.065 0.066 E 0.050 0.062 T 0.058 0.059 K 0.081 0.059 I 0.037 0.053 D 0.047 0.052 R 0.041 0.051 P 0.051 0.051 N 0.040 0.043 Q 0.038 0.041 F 0.040 0.040 Y 0.030 0.032 M 0.015 0.024 H 0.034 0.023 C 0.033 0.020 W 0.010 0.014 Second step: Frequencies of Occurence
- 35. Extra Questions • How many records have a sequence of length 260? • What are the first 20 residues of 143X_MAIZE? • What is the identifier for the record with the shortest sequence? Is there more than one record with that length? • What is the identifier for the record with the longest sequence? Is there more than one record with that length? • How many contain the subsequence "ARRA"? • How many contain the substring "KCIP-1" in the description?