Biopython Tutorial and Cookbook

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Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck,Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy′nskiLast Update – 8 June 2016 (Biopython 1.67)

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http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

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关键词：Tutorial Cookbook python tutor Book Peter

1. 5.1.1 Reading Sequence Files
   
2. In general Bio.SeqIO.parse() is used to read in sequence files as SeqRecord objects, and is typically used
   
3. with a for loop like this:
   
4. 
   
5. from Bio import SeqIO
   
6. for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
   
7. print(seq_record.id)
   
8. print(repr(seq_record.seq))
   
9. print(len(seq_record

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1. 5.1.2 Iterating over the records in a sequence file
   
2. In the above examples, we have usually used a for loop to iterate over all the records one by one. You can use
   
3. the for loop with all sorts of Python objects (including lists, tuples and strings) which support the iteration
   
4. interface.
   
5. The object returned by Bio.SeqIO is actually an iterator which returns SeqRecord objects. You get to
   
6. see each record in turn, but once and only once. The plus point is that an iterator can save you memory
   
7. when dealing with large files.
   
8. Instead of using a for loop, can also use the next() function on an iterator to step through the entries,
   
9. like this:
   
10. from Bio import SeqIO
    
11. record_iterator = SeqIO.parse("ls_orchid.fasta", "fasta")
    
12. first_record = next(record_iterator)
    
13. print(first_record.id)
    
14. print(first_record.description)
    
15. second_record = next(record_iterator)
    
16. print(second_record.id)
    
17. print(second_record.description)

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1. 5.1.3 Getting a list of the records in a sequence file
   
2. In the previous section we talked about the fact that Bio.SeqIO.parse() gives you a SeqRecord iterator,
   
3. and that you get the records one by one. Very often you need to be able to access the records in any order.
   
4. The Python list data type is perfect for this, and we can turn the record iterator into a list of SeqRecord
   
5. objects using the built-in Python function list() like so:
   
6. from Bio import SeqIO
   
7. records = list(SeqIO.parse("ls_orchid.gbk", "genbank"))
   
8. print("Found %i records" % len(records))
   
9. print("The last record")
   
10. last_record = records[-1] #using Python’s list tricks
    
11. print(last_record.id)
    
12. print(repr(last_record.seq))
    
13. print(len(last_record))
    
14. print("The first record")
    
15. first_record = records[0] #remember, Python counts from zero
    
16. print(first_record.id)
    
17. print(repr(first_record.seq))
    
18. print(len(first_record)

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1. 5.2 Parsing sequences from compressed files
   
2. In the previous section, we looked at parsing sequence data from a file. Instead of using a filename, you
   
3. can give Bio.SeqIO a handle (see Section 24.1), and in this section we’ll use handles to parse sequence from
   
4. compressed files.
   
5. As you’ll have seen above, we can use Bio.SeqIO.read() or Bio.SeqIO.parse() with a filename - for
   
6. instance this quick example calculates the total length of the sequences in a multiple record GenBank file
   
7. using a generator expression:
   
8. >>> from Bio import SeqIO
   
9. >>> print(sum(len(r) for r in SeqIO.parse("ls_orchid.gbk", "gb")))
   
10. 67518
    
11. Here we use a file handle instead, using the with statement to close the handle automatically:
    
12. >>> from Bio import SeqIO
    
13. >>> with open("ls_orchid.gbk") as handle:
    
14. ... print(sum(len(r) for r in SeqIO.parse(handle, "gb")))
    
15. 67518
    
16. Or, the old fashioned way where you manually close the handle:
    
17. >>> from Bio import SeqIO
    
18. >>> handle = open("ls_orchid.gbk")
    
19. >>> print(sum(len(r) for r in SeqIO.parse(handle, "gb")))
    
20. 67518
    
21. >>> handle.close()
    
22. Now, suppose we have a gzip compressed file instead? These are very commonly used on Linux. We can
    
23. use Python’s gzip module to open the compressed file for reading - which gives us a handle object:
    
24. >>> import gzip
    
25. >>> from Bio import SeqIO
    
26. >>> handle = gzip.open("ls_orchid.gbk.gz", "r")
    
27. >>> print(sum(len(r) for r in SeqIO.parse(handle, "gb")))
    
28. 67518
    
29. >>> handle.close()
    
30. Similarly if we had a bzip2 compressed file (sadly the function name isn’t quite as consistent):
    
31. >>> import bz2
    
32. >>> from Bio import SeqIO
    
33. >>> handle = bz2.BZ2File("ls_orchid.gbk.bz2", "r")
    
34. >>> print(sum(len(r) for r in SeqIO.parse(handle, "gb")))
    
35. 67518
    
36. >>> handle.close()

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thanks for sharing very much

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