Biopython - basics

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Introduction

From the biopython website their goal is to “make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and scripts.” These modules use the biopython tutorial as a template for what you will learn here.  Here is a list of some of the most common data formats in computational biology that are supported by biopython.

Some of the other principal functions of biopython.

• A standard sequence class that deals with sequences, ids on sequences, and sequence features.
• Tools for performing common operations on sequences, such as translation, transcription and weight calculations.
• Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines.
• Code for dealing with alignments, including a standard way to create and deal with substitution matrices.
• Code making it easy to split up parallelizable tasks into separate processes.
• GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc.

>>> import Bio
>>> Bio.__version__
‘1.58‘

>>> from Bio.Seq import Seq
>>> my_seq = Seq("AGTACACTGGT")
>>> my_seq
Seq(‘AGTACACTGGT‘, Alphabet())
>>> aStringSeq = str(my_seq)
>>> aStringSeq
‘AGTACACTGGT‘
>>> my_seq_complement = my_seq.complement()
>>> my_seq_complement
Seq(‘TCATGTGACCA‘, Alphabet())
>>> my_seq_reverse = my_seq.reverse()
>>> my_seq_rc = my_seq.reverse_complement()
>>> my_seq_rc
Seq(‘ACCAGTGTACT‘, Alphabet())

>>> for seq_record in SeqIO.parse(os.path.join("data","ls_orchid.fasta"), "fasta"):
...     print seq_record.id
...     print repr(seq_record.seq)
...     print len(seq_record)
...
gi|2765658|emb|Z78533.1|CIZ78533
Seq(‘CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC‘, SingleLetterAlphabet())
740

Biopython - basics

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原文地址：http://www.cnblogs.com/pennyy/p/4119574.html