1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
|
\chapter{Introduction}
\label{chapter:introduction}
\section{What is Biopython?}
The Biopython Project is an international association of developers of freely available Python (\url{https://www.python.org}) tools for computational molecular biology. Python is an object oriented, interpreted, flexible language that is becoming increasingly popular for scientific computing. Python is easy to learn, has a very clear syntax and can easily be extended with modules written in C, C++ or FORTRAN.
The Biopython web site (\url{http://www.biopython.org}) provides
an online resource for modules, scripts, and web links for developers
of Python-based software for bioinformatics use and research. Basically,
the goal of Biopython is to make it as easy as possible to use Python
for bioinformatics by creating high-quality, reusable modules and
classes. Biopython features include parsers for various Bioinformatics
file formats (BLAST, Clustalw, FASTA, Genbank,...), access to online
services (NCBI, Expasy,...), interfaces to common and not-so-common
programs (Clustalw, DSSP, MSMS...), a standard sequence class, various
clustering modules, a KD tree data structure etc. and even documentation.
Basically, we just like to program in Python and want to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and scripts.
\section{What can I find in the Biopython package}
The main Biopython releases have lots of functionality, including:
\begin{itemize}
\item The ability to parse bioinformatics files into Python utilizable data structures, including support for the following formats:
\begin{itemize}
\item Blast output -- both from standalone and WWW Blast
\item Clustalw
\item FASTA
\item GenBank
\item PubMed and Medline
\item ExPASy files, like Enzyme and Prosite
\item SCOP, including `dom' and `lin' files
\item UniGene
\item SwissProt
\end{itemize}
\item Files in the supported formats can be iterated over record by record or indexed and accessed via a Dictionary interface.
\item Code to deal with popular on-line bioinformatics destinations such as:
\begin{itemize}
\item NCBI -- Blast, Entrez and PubMed services
\item ExPASy -- Swiss-Prot and Prosite entries, as well as Prosite searches
\end{itemize}
\item Interfaces to common bioinformatics programs such as:
\begin{itemize}
\item Standalone Blast from NCBI
\item Clustalw alignment program
\item EMBOSS command line tools
\end{itemize}
\item A standard sequence class that deals with sequences, ids on sequences, and sequence features.
\item Tools for performing common operations on sequences, such as translation, transcription and weight calculations.
\item Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines.
\item Code for dealing with alignments, including a standard way to create and deal with substitution matrices.
\item Code making it easy to split up parallelizable tasks into separate processes.
\item GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc.
\item Extensive documentation and help with using the modules, including this file, on-line wiki documentation, the web site, and the mailing list.
\item Integration with BioSQL, a sequence database schema also supported by the BioPerl and BioJava projects.
\end{itemize}
We hope this gives you plenty of reasons to download and start using Biopython!
\section{Installing Biopython}
All of the installation information for Biopython was separated from
this document to make it easier to keep updated.
The short version is use \verb|pip install biopython|, see the
\href{https://github.com/biopython/biopython/blob/master/README.rst}{main README}
file for other options.
\section{Frequently Asked Questions (FAQ)}
\begin{enumerate}
\item \emph{How do I cite Biopython in a scientific publication?} \\
Please cite our application note \cite[Cock \textit{et al.}, 2009]{cock2009}
as the main Biopython reference.
In addition, please cite any publications from the following list if appropriate, in particular as a reference for specific modules within Biopython (more information can be found on our website):
\begin{itemize}
\item For the official project announcement: \cite[Chapman and Chang, 2000]{chapman2000};
\item For \verb+Bio.PDB+: \cite[Hamelryck and Manderick, 2003]{hamelryck2003a};
\item For \verb+Bio.Cluster+: \cite[De Hoon \textit{et al.}, 2004]{dehoon2004};
\item For \verb+Bio.Graphics.GenomeDiagram+: \cite[Pritchard \textit{et al.}, 2006]{pritchard2006};
\item For \verb+Bio.Phylo+ and \verb+Bio.Phylo.PAML+: \cite[Talevich \textit{et al.}, 2012]{talevich2012};
\item For the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava, and EMBOSS: \cite[Cock \textit{et al.}, 2010]{cock2010}.
\end{itemize}
\item \emph{How should I capitalize ``Biopython''? Is ``BioPython'' OK?} \\
The correct capitalization is ``Biopython'', not ``BioPython'' (even though
that would have matched BioPerl, BioJava and BioRuby).
\item \emph{How is the Biopython software licensed?} \\
Biopython is distributed under the \emph{Biopython License Agreement}.
However, since the release of Biopython 1.69, some files are explicitly
dual licensed under your choice of the \emph{Biopython License Agreement}
or the \emph{BSD 3-Clause License}. This is with the intention of later
offering all of Biopython under this dual licensing approach.
\item \emph{What is the Biopython logo and how is it licensed?} \\
As of July 2017 and the Biopython 1.70 release, the Biopython logo is a
yellow and blue snake forming a double helix above the word ``biopython''
in lower case. It was designed by Patrick Kunzmann and this logo is dual
licensed under your choice of the \emph{Biopython License Agreement} or
the \emph{BSD 3-Clause License}.
\begin{latexonly}
\includegraphics[width=6cm]{images/biopython_logo.pdf}\\
\end{latexonly}
\begin{rawhtml}
<IMG ALIGN="center" SRC="images/biopython_logo.svg" TITLE="Biopython Logo (2017 onwards)" ALT="[New Biopython Logo]" width="300" height="200" />
<IMG ALIGN="center" SRC="images/biopython_logo_old.jpg" TITLE="Old Biopython Logo (2003-2017)" ALT="[Old Biopython Logo]" width="512" height="144" />
\end{rawhtml}
Prior to this, the Biopython logo was two yellow snakes forming a double
helix around the word ``BIOPYTHON'', designed by Henrik Vestergaard and
Thomas Hamelryck in 2003 as part of an open competition.
\begin{latexonly}
\includegraphics[width=7cm]{images/biopython_logo_old.jpg}\\
\end{latexonly}
\item \emph{Do you have a change-log listing what's new in each release?} \\
See the file \verb|NEWS.rst| included with the source code (originally called
just \verb|NEWS|), or read the
\href{https://github.com/biopython/biopython/blob/master/NEWS.rst}{latest NEWS file on GitHub}.
\item \emph{What is going wrong with my print commands?} \\
As of Biopython 1.77, we only support Python 3, so this tutorial
uses the Python 3 style print \emph{function}.
\item \emph{How do I find out what version of Biopython I have installed?} \\
Use this:
\begin{minted}{pycon}
>>> import Bio
>>> print(Bio.__version__)
...
\end{minted}
If the ``\verb|import Bio|'' line fails, Biopython is not installed.
Note that those are double underscores before and after version.
If the second line fails, your version is \emph{very} out of date.
If the version string ends with a plus like ``\verb|1.66+|'', you
don't have an official release, but an old snapshot of the in
development code \emph{after} that version was released. This naming
was used until June 2016 in the run-up to Biopython 1.68.
If the version string ends with ``\verb|.dev<number>|'' like
``\verb|1.68.dev0|'', again you don't have an official release,
but instead a snapshot of the in development code \emph{before}
that version was released.
\item \emph{Where is the latest version of this document?}\\
If you download a Biopython source code archive, it will include the
relevant version in both HTML and PDF formats. The latest published
version of this document (updated at each release) is online:
\begin{itemize}
\item \url{http://biopython.org/DIST/docs/tutorial/Tutorial.html}
\item \url{http://biopython.org/DIST/docs/tutorial/Tutorial.pdf}
\end{itemize}
\item \emph{What is wrong with my sequence comparisons?} \\
There was a major change in Biopython 1.65 making the \verb|Seq| and
\verb|MutableSeq| classes (and subclasses) use simple string-based
comparison which you can do explicitly with \verb|str(seq1) == str(seq2)|.
Older versions of Biopython would use instance-based comparison
for \verb|Seq| objects which you can do explicitly with
\verb|id(seq1) == id(seq2)|.
If you still need to support old versions of Biopython, use these
explicit forms to avoid problems. See Section~\ref{sec:seq-comparison}.
\item \emph{What file formats do} \verb|Bio.SeqIO| \emph{and} \verb|Bio.AlignIO| \emph{read and write?} \\
Check the built in docstrings (\texttt{from Bio import SeqIO}, then \texttt{help(SeqIO)}), or see \url{http://biopython.org/wiki/SeqIO} and \url{http://biopython.org/wiki/AlignIO} on the wiki for the latest listing.
\item \emph{Why won't the } \verb|Bio.SeqIO| \emph{and} \verb|Bio.AlignIO| \emph{functions} \verb|parse|\emph{,} \verb|read| \emph{and} \verb|write| \emph{take filenames? They insist on handles!} \\
You need Biopython 1.54 or later, or just use handles explicitly (see Section~\ref{sec:appendix-handles}).
It is especially important to remember to close output handles explicitly after writing your data.
\item \emph{Why won't the } \verb|Bio.SeqIO.write()| \emph{and} \verb|Bio.AlignIO.write()| \emph{functions accept a single record or alignment? They insist on a list or iterator!} \\
You need Biopython 1.54 or later, or just wrap the item with \verb|[...]| to create a list of one element.
\item \emph{Why doesn't} \verb|str(...)| \emph{give me the full sequence of a} \verb|Seq| \emph{object?} \\
You need Biopython 1.45 or later.
\item \emph{Why doesn't} \verb|Bio.Blast| \emph{work with the latest plain text NCBI blast output?} \\
The NCBI keep tweaking the plain text output from the BLAST tools, and keeping our parser up to date is/was an ongoing struggle.
If you aren't using the latest version of Biopython, you could try upgrading.
However, we (and the NCBI) recommend you use the XML output instead, which is designed to be read by a computer program.
\item \emph{Why has my script using} \verb|Bio.Entrez.efetch()| \emph{stopped working?} \\
This could be due to NCBI changes in February 2012 introducing EFetch 2.0.
First, they changed the default return modes - you probably want to add \verb|retmode="text"| to
your call.
Second, they are now stricter about how to provide a list of IDs -- Biopython 1.59 onwards
turns a list into a comma separated string automatically.
\item \emph{Why doesn't} \verb|Bio.Blast.NCBIWWW.qblast()| \emph{give the same results as the NCBI BLAST website?} \\
You need to specify the same options -- the NCBI often adjust the default settings on the website,
and they do not match the QBLAST defaults anymore. Check things like the gap penalties and expectation threshold.
\item \emph{Why can't I add} \verb|SeqRecord| \emph{objects together?} \\
You need Biopython 1.53 or later.
\item \emph{Why doesn't} \verb|Bio.SeqIO.index_db()| \emph{work? The module imports fine but there is no \texttt{index\_db} function!} \\
You need Biopython 1.57 or later (and a Python with SQLite3 support).
\item \emph{Where is the} \verb|MultipleSeqAlignment| \emph{object? The} \verb|Bio.Align| \emph{module imports fine but this class isn't there!} \\
You need Biopython 1.54 or later. Alternatively, the older \verb|Bio.Align.Generic.Alignment| class supports some of its functionality, but using this is now discouraged.
\item \emph{Why can't I run command line tools directly from the application wrappers?} \\
You need Biopython 1.55 or later. Alternatively, use the Python \verb|subprocess| module directly.
\item \emph{I looked in a directory for code, but I couldn't find the code that does something. Where's it hidden?} \\
One thing to know is that we put code in \verb|__init__.py| files. If you are not used to looking for code in this file this can be confusing. The reason we do this is to make the imports easier for users. For instance, instead of having to do a ``repetitive'' import like \verb|from Bio.GenBank import GenBank|, you can just use \verb|from Bio import GenBank|.
\item \emph{Why doesn't} \verb|Bio.Fasta| \emph{work?} \\
We deprecated the \verb|Bio.Fasta| module in Biopython 1.51 (August 2009) and removed it in Biopython 1.55 (August 2010). There is a brief example showing how to convert old code to use \verb|Bio.SeqIO| instead in the \href{https://github.com/biopython/biopython/blob/master/DEPRECATED.rst}{DEPRECATED.rst} file.
\end{enumerate}
\noindent For more general questions, the Python FAQ pages \url{https://docs.python.org/3/faq/index.html} may be useful.
|
