PPT-File input and output Genome 559: Introduction to Statistical and Computational Genomics

Prof William Stafford Noble Opening files The open command returns a file object lt filehandle gt openltfilenamegt ltaccess typegt Python can read write or append to a file. NHGRI strategic plan. What does the NIH think genomics should be for the next 10 years?. [Nature, Feb. 2011]. The Essence of Genomics. (according to NHGRI). Comprehensiveness. . Genomics . aims to generate complete data sets. Although relatively easy to define and measure for a genome sequence, attaining comprehensiveness can be more challenging for other targets (for example, functional genomic elements or the ‘proteome’). NHGRI strategic plan. What does the NIH think genomics should be for the next 10 years?. [Nature, Feb. 2011]. The Essence of Genomics. (according to NHGRI). Comprehensiveness. . Genomics . aims to generate complete data sets. Although relatively easy to define and measure for a genome sequence, attaining comprehensiveness can be more challenging for other targets (for example, functional genomic elements or the ‘proteome’). selection, . regulation, epigenomics, . disease. Manolis Kellis. MIT Computer Science & Artificial Intelligence Laboratory. Broad Institute of MIT and Harvard. Recombination breakpoints. Family Inheritance. Plan for the Day:. I/O (beyond . scanf. and . printf. ). Standard, String and File I/O. I/O in C. Input and output facilities provided by standard library . <. stdio.h. > . and not by the language. Prof. William Stafford Noble. A dictionary organizes linked information.. Examples:. - word and definition. - name and phone number. - name and DNA sequence. - username and password. If you know the first entry, you can quickly and easily get the second one.. Prof. William Stafford Noble. for. . loop review. block of code. for <element> in <object>:. <statement>. <statement>. . . .. <last statement>. . <element>. is a newly created variable name. You . Prof. William Stafford Noble. Stuff folks liked. Good pace. x3. Powerpoint. was easy to follow. x2. Really appreciate reading the program step by step. x2. Helpful to go over the sample problems at the beginning of class.. Albert Gatt Corpora and Statistical Methods Lecture 1 2 In this lecture Introduction to Natural Language Generation (NLG ) the use of corpora & statistical models in NLG Summarisation Single-document selection, . regulation, epigenomics, . disease. Manolis Kellis. MIT Computer Science & Artificial Intelligence Laboratory. Broad Institute of MIT and Harvard. Goal: A systems-level understanding of genomes and gene regulation:. “. User facility. providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative . energy. , . carbon cycling . & . bioremediation. .”. Opened in 1999. ~240 UC Employees. Genomics and Society Nature (2014) “ …disorders not readily explained by standard tests can sometimes be diagnosed through genome sequencing and analysis.” The Origin of “Genomics& Introduction. Data Input: . Three methods. 1. Assign data to variables through an assignment statement . 2. Input data from Keyboard . 3. Read data from a file stored in computer memory. Data Input . Dr. Kyung . Eun. Park. Summer . 2017 . Communicating with I/O Devices. Interactive Programming. Interactive program: . Reads input from . the console . Writes output to the console. Programming with a file. Bionano Genomics, San Diego, California, United States of America. Abstract. Pat Lynch, PhD. Background. Generating high-quality finished genomes replete with accurate identification of structural variation and high completion (minimal gaps) remains challenging using short read sequencing technologies alone. The .