101 Useful Linux Commands - Haydenjames.Io
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Modern Programming Languages CS508 Virtual University of Pakistan
Modern Programming Languages (CS508) VU Modern Programming Languages CS508 Virtual University of Pakistan Leaders in Education Technology 1 © Copyright Virtual University of Pakistan Modern Programming Languages (CS508) VU TABLE of CONTENTS Course Objectives...........................................................................................................................4 Introduction and Historical Background (Lecture 1-8)..............................................................5 Language Evaluation Criterion.....................................................................................................6 Language Evaluation Criterion...................................................................................................15 An Introduction to SNOBOL (Lecture 9-12).............................................................................32 Ada Programming Language: An Introduction (Lecture 13-17).............................................45 LISP Programming Language: An Introduction (Lecture 18-21)...........................................63 PROLOG - Programming in Logic (Lecture 22-26) .................................................................77 Java Programming Language (Lecture 27-30)..........................................................................92 C# Programming Language (Lecture 31-34) ...........................................................................111 PHP – Personal Home Page PHP: Hypertext Preprocessor (Lecture 35-37)........................129 Modern Programming Languages-JavaScript -
“Linux at the Command Line” Don Johnson of BU IS&T We’Ll Start with a Sign in Sheet
“Linux at the Command Line” Don Johnson of BU IS&T We’ll start with a sign in sheet. We’ll end with a class evaluation. We’ll cover as much as we can in the time allowed; if we don’t cover everything, you’ll pick it up as you continue working with Linux. This is a hands-on, lab class; ask questions at any time. Commands for you to type are in BOLD The Most Common O/S Used By BU Researchers When Working on a Server or Computer Cluster Linux is a Unix clone begun in 1991 and written from scratch by Linus Torvalds with assistance from a loosely-knit team of hackers across the Net. 64% of the world’s servers run some variant of Unix or Linux. The Android phone and the Kindle run Linux. a set of small Linux is an O/S core programs written by written by Linus Richard Stallman and Torvalds and others others. They are the AND GNU utilities. http://www.gnu.org/ Network: ssh, scp Shells: BASH, TCSH, clear, history, chsh, echo, set, setenv, xargs System Information: w, whoami, man, info, which, free, echo, date, cal, df, free Command Information: man, info Symbols: |, >, >>, <, ;, ~, ., .. Filters: grep, egrep, more, less, head, tail Hotkeys: <ctrl><c>, <ctrl><d> File System: ls, mkdir, cd, pwd, mv, touch, file, find, diff, cmp, du, chmod, find File Editors: gedit, nedit You need a “xterm” emulation – software that emulates an “X” terminal and that connects using the “SSH” Secure Shell protocol. ◦ Windows Use StarNet “X-Win32:” http://www.bu.edu/tech/support/desktop/ distribution/xwindows/xwin32/ ◦ Mac OS X “Terminal” is already installed Why? Darwin, the system on which Apple's Mac OS X is built, is a derivative of 4.4BSD-Lite2 and FreeBSD. -
Exercise I: Basic Unix for Manipulating NGS Data
Exercise I: Basic Unix for manipulating NGS data C. Hahn, July 2014 The purpose of this exercise is to practice manipulating NGS (Next Generation Sequencing) data using simple but incredibly powerful Unix commands. Try to solve the below tasks using your Unix skills. Do not hesitate to consult Google for help!! Hints for every task can be found on page 3 below. Possible solutions are suggested on page 4. 1. Download the testdata from https://www.dropbox.com/s/wcanmej6z03yfmt/testdata_1.tar?dl=0. Create a directory (exercise_1) in your home directory and copy the archive testdata.tar from ~/Downloads/ to this directory. 2. Decompress the archive. 3. Examine the content of the data files. For basic information on fastq format please visit: http://en.wikipedia.org/wiki/FASTQ_format. With this information try to interpret the content of your data files. Do you Know what all the lines represent? a) Which quality encoding (which offset) do these files use? b) What is the header of the third read in the file? Is this a single-end (forward) or a paired-end (reverse) read? c) What is the header of the last read in the file? Is this a forward or reverse read? 4. How many lines does the file have? 5. How many reads does the file contain? 6. How many single-end (“se” also referred to as forward reads) reads and how many paired-end (“pe” also reverse reads) reads does the file contain? 7. Extract all se/pe reads and write them to separate files testdata_1.fastq and testdata_2.fastq. -
Useful Commands in Linux and Other Tools for Quality Control
Useful commands in Linux and other tools for quality control Ignacio Aguilar INIA Uruguay 05-2018 Unix Basic Commands pwd show working directory ls list files in working directory ll as before but with more information mkdir d make a directory d cd d change to directory d Copy and moving commands To copy file cp /home/user/is . To copy file directory cp –r /home/folder . to move file aa into bb in folder test mv aa ./test/bb To delete rm yy delete the file yy rm –r xx delete the folder xx Redirections & pipe Redirection useful to read/write from file !! aa < bb program aa reads from file bb blupf90 < in aa > bb program aa write in file bb blupf90 < in > log Redirections & pipe “|” similar to redirection but instead to write to a file, passes content as input to other command tee copy standard input to standard output and save in a file echo copy stream to standard output Example: program blupf90 reads name of parameter file and writes output in terminal and in file log echo par.b90 | blupf90 | tee blup.log Other popular commands head file print first 10 lines list file page-by-page tail file print last 10 lines less file list file line-by-line or page-by-page wc –l file count lines grep text file find lines that contains text cat file1 fiel2 concatenate files sort sort file cut cuts specific columns join join lines of two files on specific columns paste paste lines of two file expand replace TAB with spaces uniq retain unique lines on a sorted file head / tail $ head pedigree.txt 1 0 0 2 0 0 3 0 0 4 0 0 5 0 0 6 0 0 7 0 0 8 0 0 9 0 0 10 -
Install and Run External Command Line Softwares
job monitor and control top: similar to windows task manager (space to refresh, q to exit) w: who is there ps: all running processes, PID, status, type ps -ef | grep yyin bg: move current process to background fg: move current process to foreground jobs: list running and suspended processes kill: kill processes kill pid (could find out using top or ps) 1 sort, cut, uniq, join, paste, sed, grep, awk, wc, diff, comm, cat All types of bioinformatics sequence analyses are essentially text processing. Unix Shell has the above commands that are very useful for processing texts and also allows the output from one command to be passed to another command as input using pipe (“|”). less cosmicRaw.txt | cut -f2,3,4,5,8,13 | awk '$5==22' | cut -f1 | sort -u | wc This makes the processing of files using Shell very convenient and very powerful: you do not need to write output to intermediate files or load all data into the memory. For example, combining different Unix commands for text processing is like passing an item through a manufacturing pipeline when you only care about the final product 2 Hands on example 1: cosmic mutation data - Go to UCSC genome browser website: http://genome.ucsc.edu/ - On the left, find the Downloads link - Click on Human - Click on Annotation database - Ctrl+f and then search “cosmic” - On “cosmic.txt.gz” right-click -> copy link address - Go to the terminal and wget the above link (middle click or Shift+Insert to paste what you copied) - Similarly, download the “cosmicRaw.txt.gz” file - Under your home, create a folder -
UNIX (Solaris/Linux) Quick Reference Card Logging in Directory Commands at the Login: Prompt, Enter Your Username
UNIX (Solaris/Linux) QUICK REFERENCE CARD Logging In Directory Commands At the Login: prompt, enter your username. At the Password: prompt, enter ls Lists files in current directory your system password. Linux is case-sensitive, so enter upper and lower case ls -l Long listing of files letters as required for your username, password and commands. ls -a List all files, including hidden files ls -lat Long listing of all files sorted by last Exiting or Logging Out modification time. ls wcp List all files matching the wildcard Enter logout and press <Enter> or type <Ctrl>-D. pattern Changing your Password ls dn List files in the directory dn tree List files in tree format Type passwd at the command prompt. Type in your old password, then your new cd dn Change current directory to dn password, then re-enter your new password for verification. If the new password cd pub Changes to subdirectory “pub” is verified, your password will be changed. Many systems age passwords; this cd .. Changes to next higher level directory forces users to change their passwords at predetermined intervals. (previous directory) cd / Changes to the root directory Changing your MS Network Password cd Changes to the users home directory cd /usr/xx Changes to the subdirectory “xx” in the Some servers maintain a second password exclusively for use with Microsoft windows directory “usr” networking, allowing you to mount your home directory as a Network Drive. mkdir dn Makes a new directory named dn Type smbpasswd at the command prompt. Type in your old SMB passwword, rmdir dn Removes the directory dn (the then your new password, then re-enter your new password for verification. -
Wildlife Management Activities and Practices
WILDLIFE MANAGEMENT ACTIVITIES AND PRACTICES COMPREHENSIVE WILDLIFE MANAGEMENT PLANNING GUIDELINES for the Edwards Plateau and Cross Timbers & Prairies Ecological Regions Revised April 2010 The following Texas Parks & Wildlife Department staff have contributed to this document: Mike Krueger, Technical Guidance Biologist – Lampasas Mike Reagan, Technical Guidance Biologist -- Wimberley Jim Dillard, Technical Guidance Biologist -- Mineral Wells (Retired) Kirby Brown, Private Lands and Habitat Program Director (Retired) Linda Campbell, Program Director, Private Lands & Public Hunting Program--Austin Linda McMurry, Private Lands and Public Hunting Program Assistant -- Austin With Additional Contributions From: Kevin Schwausch, Private Lands Biologist -- Burnet Terry Turney, Rare Species Biologist--San Marcos Trey Carpenter, Manager, Granger Wildlife Management Area Dale Prochaska, Private Lands Biologist – Kerr Wildlife Management Area Nathan Rains, Private Lands Biologist – Cleburne TABLE OF CONTENTS Comprehensive Wildlife Management Planning Guidelines Edwards Plateau and Cross Timbers & Prairies Ecological Regions Introduction Specific Habitat Management Practices HABITAT CONTROL EROSION CONTROL PREDATOR CONTROL PROVIDING SUPPLEMENTAL WATER PROVIDING SUPPLEMENTAL FOOD PROVIDING SUPPLEMENTAL SHELTER CENSUS APPENDICES APPENDIX A: General Habitat Management Considerations, Recommendations, and Intensity Levels APPENDIX B: Determining Qualification for Wildlife Management Use APPENDIX C: Wildlife Management Plan Overview APPENDIX D: Livestock -
GNU Coreutils Cheat Sheet (V1.00) Created by Peteris Krumins ([email protected], -- Good Coders Code, Great Coders Reuse)
GNU Coreutils Cheat Sheet (v1.00) Created by Peteris Krumins ([email protected], www.catonmat.net -- good coders code, great coders reuse) Utility Description Utility Description arch Print machine hardware name nproc Print the number of processors base64 Base64 encode/decode strings or files od Dump files in octal and other formats basename Strip directory and suffix from file names paste Merge lines of files cat Concatenate files and print on the standard output pathchk Check whether file names are valid or portable chcon Change SELinux context of file pinky Lightweight finger chgrp Change group ownership of files pr Convert text files for printing chmod Change permission modes of files printenv Print all or part of environment chown Change user and group ownership of files printf Format and print data chroot Run command or shell with special root directory ptx Permuted index for GNU, with keywords in their context cksum Print CRC checksum and byte counts pwd Print current directory comm Compare two sorted files line by line readlink Display value of a symbolic link cp Copy files realpath Print the resolved file name csplit Split a file into context-determined pieces rm Delete files cut Remove parts of lines of files rmdir Remove directories date Print or set the system date and time runcon Run command with specified security context dd Convert a file while copying it seq Print sequence of numbers to standard output df Summarize free disk space setuidgid Run a command with the UID and GID of a specified user dir Briefly list directory -
Constraints in Dynamic Symbolic Execution: Bitvectors Or Integers?
Constraints in Dynamic Symbolic Execution: Bitvectors or Integers? Timotej Kapus, Martin Nowack, and Cristian Cadar Imperial College London, UK ft.kapus,m.nowack,[email protected] Abstract. Dynamic symbolic execution is a technique that analyses programs by gathering mathematical constraints along execution paths. To achieve bit-level precision, one must use the theory of bitvectors. However, other theories might achieve higher performance, justifying in some cases the possible loss of precision. In this paper, we explore the impact of using the theory of integers on the precision and performance of dynamic symbolic execution of C programs. In particular, we compare an implementation of the symbolic executor KLEE using a partial solver based on the theory of integers, with a standard implementation of KLEE using a solver based on the theory of bitvectors, both employing the popular SMT solver Z3. To our surprise, our evaluation on a synthetic sort benchmark, the ECA set of Test-Comp 2019 benchmarks, and GNU Coreutils revealed that for most applications the integer solver did not lead to any loss of precision, but the overall performance difference was rarely significant. 1 Introduction Dynamic symbolic execution is a popular program analysis technique that aims to systematically explore all the paths in a program. It has been very successful in bug finding and test case generation [3, 4]. The research community and industry have produced many tools performing symbolic execution, such as CREST [5], FuzzBALL [9], KLEE [2], PEX [14], and SAGE [6], among others. To illustrate how dynamic symbolic execution works, consider the program shown in Figure 1a. -
Practical Linux Examples: Exercises 1
Practical Linux examples: Exercises 1. Login (ssh) to the machine that you are assigned for this workshop (assigned machines: https://cbsu.tc.cornell.edu/ww/machines.aspx?i=87 ). Prepare working directory, and copy data files into the working directory. (Replace “XXXXX” in the commands with your BioHPC User ID ) mkdir /workdir/XXXXX cd /workdir/XXXXX cp /shared_data/Linux_workshop2/* ./ 2. You are given a gzipped gff3 file. Inspect the content in the file. Linux functions: gunzip -c, head, tail, cut, less Inspect the first and last 100 lines of the file, using "head" and "tail" functions to retrieve first and last lines of the file; Retrieve line number 1001 to 2000 from the file and write these lines into a new file " mynew.gtf "; Inspect the columns 2,3,4 and 8 of lines 3901 to 4000, using "cut" function to specify the columns. Compare "cut" with "less -S" function. If you use "less" function, remember to exit "less" by pressing "q". gunzip -c human.gff3.gz | head -n 100 gunzip -c human.gff3.gz | tail -n 100 gunzip -c human.gff3.gz| head -n 2000 | tail -n 1000 > mynew.gtf gunzip -c human.gff3.gz| head -n 4000 | tail -n 100 | cut -f 2-5,8 gunzip -c human.gff3.gz| head -n 4000 | tail -n 100 | less -S 3. Count the number of genes listed in the file. Linux functions: awk, uniq Count the total number of lines in the file using "wc -l" function; Count the number of genes list in the file. First, you need to use "awk" to retrieve lines with the 3rd column value equals "gene", then count these lines with "wc -l"; Count the number for each of the feature categories (genes, exons, rRNA, miRNA, et al.) listed in this GFF3 file. -
Understanding Programming Languages
Understanding Programming Languages M. Ben-Ari Weizmann Institute of Science Originally published by John Wiley & Sons, Chichester, 1996. Copyright °c 2006 by M. Ben-Ari. You may download, display and print one copy for your personal use in non-commercial academic research and teaching. Instructors in non-commerical academic institutions may make one copy for each student in his/her class. All other rights reserved. In particular, posting this document on web sites is prohibited without the express permission of the author. Contents Preface xi I Introduction to Programming Languages 1 1 What Are Programming Languages? 2 1.1 The wrong question . 2 1.2 Imperative languages . 4 1.3 Data-oriented languages . 7 1.4 Object-oriented languages . 11 1.5 Non-imperative languages . 12 1.6 Standardization . 13 1.7 Computer architecture . 13 1.8 * Computability . 16 1.9 Exercises . 17 2 Elements of Programming Languages 18 2.1 Syntax . 18 2.2 * Semantics . 20 2.3 Data . 21 2.4 The assignment statement . 22 2.5 Type checking . 23 2.6 Control statements . 24 2.7 Subprograms . 24 2.8 Modules . 25 2.9 Exercises . 26 v Contents vi 3 Programming Environments 27 3.1 Editor . 28 3.2 Compiler . 28 3.3 Librarian . 30 3.4 Linker . 31 3.5 Loader . 32 3.6 Debugger . 32 3.7 Profiler . 33 3.8 Testing tools . 33 3.9 Configuration tools . 34 3.10 Interpreters . 34 3.11 The Java model . 35 3.12 Exercises . 37 II Essential Concepts 38 4 Elementary Data Types 39 4.1 Integer types . -
Standard TECO (Text Editor and Corrector)
Standard TECO TextEditor and Corrector for the VAX, PDP-11, PDP-10, and PDP-8 May 1990 This manual was updated for the online version only in May 1990. User’s Guide and Language Reference Manual TECO-32 Version 40 TECO-11 Version 40 TECO-10 Version 3 TECO-8 Version 7 This manual describes the TECO Text Editor and COrrector. It includes a description for the novice user and an in-depth discussion of all available commands for more advanced users. General permission to copy or modify, but not for profit, is hereby granted, provided that the copyright notice is included and reference made to the fact that reproduction privileges were granted by the TECO SIG. © Digital Equipment Corporation 1979, 1985, 1990 TECO SIG. All Rights Reserved. This document was prepared using DECdocument, Version 3.3-1b. Contents Preface ............................................................ xvii Introduction ........................................................ xix Preface to the May 1985 edition ...................................... xxiii Preface to the May 1990 edition ...................................... xxv 1 Basics of TECO 1.1 Using TECO ................................................ 1–1 1.2 Data Structure Fundamentals . ................................ 1–2 1.3 File Selection Commands ...................................... 1–3 1.3.1 Simplified File Selection .................................... 1–3 1.3.2 Input File Specification (ER command) . ....................... 1–4 1.3.3 Output File Specification (EW command) ...................... 1–4 1.3.4 Closing Files (EX command) ................................ 1–5 1.4 Input and Output Commands . ................................ 1–5 1.5 Pointer Positioning Commands . ................................ 1–5 1.6 Type-Out Commands . ........................................ 1–6 1.6.1 Immediate Inspection Commands [not in TECO-10] .............. 1–7 1.7 Text Modification Commands . ................................ 1–7 1.8 Search Commands .