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Biopython Tutorial and Cookbook Je Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczynski Last Update { September 4, 2020 (Biopython 1.78) Contents 1 Introduction 9 0 [ /Filter 43 540 /Page 46 A Qt Console for Jupyter 0 R [�9 ͸�c�w7rlO�9w:K_�B��sZ�&y��u_�g�r�zx�6Y�I�Wo���3��:�HZ�s�U�?�:]}�u���C%:��b9��o��5ɒ�O�[⠿�'����,��*�L���*�0C�-�7NO��l�'+�P�D� b$Ow����RZ(i}�*?���f�10��ך;���ÑX� R •Concise chapter summaries, grouping logically related items, even if that does not match the order of introduc-tion. << 0 ] ] ,�`I�f�! 720 0 Jupyter Notebooks are a spin-off project from the IPython project, which used to have an IPython Notebook project itself. 0 These archives contain all the content in the documentation. /CS 0 /FlateDecode R 0 45 endobj endobj endobj /Type version 6.0, IPython stopped supporting compatibility with Python versions >> /CS /Filter ] 540 R 0 /PageLabels obj [ /Resources R [ 0 R /D 35 [ /S >> 540 0 /Parent ��|�����=��Dm�ED�2z,Ա F��ak�Ʋga�"�v�͐���z��%�v�5w� ����� ��8� �(��Ӟ�sw�#�;��,쬌Mp�;P?w�U�r�$��`�ӛ���T���t�9��1IrH#v�\R ^��!�3��r�Wz� � ҋ?�`��5�8_���D;=0ED0J�a}9���r�q�=oc������)��cӁ�"���'��}�~��'}�xK��'&�԰? 376 10 stream obj For more information, check the tips page, or look at examples in the IPython cookbook. stream There are other similar REPL shells for Python, for example, ptpython and bpython. ] 45 R At the command line, type ipython: 1. /Length >> 8 endobj obj /DeviceRGB 0 R stream /Parent /Filter R In []: X = np.eye(3) # 3x3 Identity Matrix Y = np.ones([3,3]) # 3x3 Matrix of ones print "X = " print X print "Y = " print Y Z = r_[X,Y] # concatenate y to x as rows print "\n Row Concatenated [X ; Y] : " print Z W = c_[X,Y] # concatenate y to x as columns print "\n Column Concatenated [X Y] : \n " print W Plotting In this class, we will use matplotlib.pyplot to plot signals and images. endstream /Resources ] /St /Length If you are looking for an IPython version compatible with Python 2.7, please use the IPython 5.x LTS release and refer to its documentation (LTS is … In 2014, Project Jupyter started as a spin-off project from IPython. 0 16 R /Transparency >> '��;ң�Å�ўJ�����ͣ.p�����p2�7�{��Ӟ]j)K�׿:���'#�/�Xa� 0 /Length /Transparency /Contents x��T�n�0$����Ar�,>$�����ؖ�ȥh�����#�+�'p�#r93K�t�?�u����5=�T�. 19 x��UMO�0����HK��|8GPIY����E\*TX << >> 1 IPython was originally developed by Fernando Perez in 2001 as an enhanced Python interpreter. /MediaBox You do not need to have any deep knowledge of Python to read this 0 obj How to Follow This Tutorial. x��WKoEn4�&-�#W�HI��= ʁȱ��Ilg�6�QbE�!$.�~0_�����s��c"U���6��XDÜ��YK�`��Ɍ�����6��q���7���U���|���k���@ݦl@����!h�%I+Ei�)='nsC�����LJ�U�t�o�Hw��Ie����=b�]]�s�;e'�` obj 0 /Type 21 9 >> obj /Page endobj The Portable Document Format, or PDF, is a file format that can be used to present and exchange documents reliably across operating systems. >> endobj [ 26 /Page x��T�n�@�ۤ� q�n��GPZZQ�I�U� P���‘����Yg�ظM*k�����7��ܠ�٫g%�_��I����I�n��t��+4�/����Ak4sl�=�)^�������/�>��r+�3����ebj)���w�Z�gm^��M���߯��juѤ��U R 23 /Contents /MediaBox endobj 22 ] stream endobj /Length >> obj 3 /Transparency 0 0 /Parent /Type done some work in the classic Python REPL. 7 486 ] Project Jupyter is a suite of software products used in interactive computing. 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To get the most out of this tutorial you should be familiar with programming — Python and pandas specifically. /Contents ј@f�Ȉ>au=�C��=�1}^Xw��`�gf���������#d��1�X�f�*�O��I;�̤z=��z �[٣�j�m^�Vt�]��fO�b��d��:A��2�E{%Ѝހ9���)�^7������z��\�U,Mj�m���l|��Y�͖6�� /Group /Page source A web based interface to IPython terminal in the form of IPython notebook was introduced in 2011. /Annots << stream [ /Page obj << 0 R /Group endobj is the long term support release). << /DeviceRGB 30 Some key features are described here. >> 0 0 R /S 0 >> endobj 28 of date, we welcome any report of inaccuracy, and Pull Requests that make R IPython is an interactive shell for the Python programming language that offers enhanced introspection, additional shell syntax, tab completion and rich history. About the Tutorial Python is a general-purpose interpreted, interactive, object-oriented, and high-level programming language. /Group This tutorial introduces the reader informally to the basic concepts and features of the Python language and system. /Parent Open document format for code, rich text, plots, images, video. To start ipython, open a command line terminal. 0 1 20 IPython is a Read-Evaluate-Print Loop shell for interactive Python development. R endstream << R What is IPython? 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But IPython can do much more than the standard prompt. >> The pdf version also gives page references. %PDF-1.4 1 0 << /Group ] Jupyter/IPython Notebook Quick Start Guide Documentation, Release 0.1 This document is a brief step-by-step tutorial on installing and running Jupyter (IPython) notebooks on local computer for new users who have no familiarity with python. 10 37 533 32 0 /Page 23 obj /Annots 0 /FlateDecode R 0 �9�gO�p��?o��ĵ���}�'��� �au�ʗ�?o@�yr��%��r��Ve���F�Մ�@���BvKL1;c�޹�љ �>$�e�ԁ���'UIG�Hd��Ÿ�l��}�F�k��-G��c6���^��"��L����,�� 29 Developer’s guide for third party tools and libraries. 47 27 There may be significant differences from the latest stable release. 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Python tutorial for beginners, who want to learn Python programming language from basic to advanced, Learn here free Python tutorial & also download Python tutorial pdf from here for easy-to-learn Python programming from basic to advanced. 39 << Anaconda is a Python distribution that is particularly popular for data analysis and scienti c computing Open source project developed by Continuum Analytics, Inc. • %history 457/7 # Line 7 from session number 457 • %history ~2/7 # Line 7 from 2 sessions ago • %history ~1/ # The whole previous session • %history ~8/1-~6/5 # From the 1st line 8 sessions ago until the 5th line of 6 38 720 0 << 52 Running scripts Editors ­­ Choose an editor which you can configure so that it indents with 4 spaces, not tab characters. << obj 50 IPython has many features for object in-trospection, system shell access, and its own special command system for adding functionality when x��TMO�@���ɟ�Q��W�{� ~��r1 Pԟ�v��BI5�fwf�ӷ��l�D���,s��>�q���Eք:�،)��Ud�(L_��k%ٙ�F�����C����C����|��:�1&��S�\��K�[m�V)e ?��|���z�e�!�T?.���t�4�:�'}�%����jЃ&\C�08E��-O�`��%礐��f}�E�Ĵ��*X��Z��6.�9��ojb^J ��-�FХ���:MH������n��(qq�J� ���Q����]j�1XB/S�.�KYM��uOףV�d����zO�B���"�*O�ۤ,!5}���̭��y"1O�鞼�2�.E\�G|m��/���R[ Jupyter/IPython Notebook Quick Start Guide¶ This document is a brief step-by-step tutorial on installing and running Jupyter (IPython) notebooks on local computer for new users who have no familiarity with python. 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