Exercise I: Basic Unix for Manipulating NGS Data
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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 -
101 Useful Linux Commands - Haydenjames.Io
101 Useful Linux Commands - haydenjames.io Some of these commands require elevated permissions (sudo) to run. Enjoy! 1. Execute the previous command used: !! 2. Execute a previous command starting with a specific letter. Example: !s 3. Short way to copy or backup a file before you edit it. For example, copy nginx.conf cp nginx.conf{,.bak} 4. Toggle between current directory and last directory cd - 5. Move to parent (higher level) directory. Note the space! cd .. 6. Go to home directory cd ~ 7. Go to home directory cd $HOME 8. Go to home directory (when used alone) cd 9. Set permissions to 755. Corresponds to these permissions: (-rwx-r-x-r-x), arranged in this sequence: (owner-group-other) chmod 755 <filename> 10. Add execute permission to all users. chmod a+x <filename> 11. Changes ownership of a file or directory to . chown <username> 12. Make a backup copy of a file (named file.backup) cp <file> <file>.backup 13. Copy file1, use it to create file2 cp <file1> <file2> 14. Copy directory1 and all its contents (recursively) into directory2 cp -r <directory1> <directory2>/ 15. Display date date 16. Zero the sdb drive. You may want to use GParted to format the drive afterward. You need elevated permissions to run this (sudo). dd if=/dev/zero of=/dev/sdb 17. Display disk space usage df -h 18. Take detailed messages from OS and input to text file dmesg>dmesg.txt 19. Display a LOT of system information. I usually pipe output to less. You need elevated permissions to run this (sudo). -
“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. -
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. -
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 . -
Affirmative Action Plan FY2020
Affirmative Action Plan for the Recruitment, Hiring, Advancement, and Retention of Persons with Disabilities U.S. Environmental Protection Agency Fiscal Year 2020 To capture federal agencies’ affirmative action plans for persons with disabilities (PWD) and persons with targeted disabilities (PWTD), EEOC regulations (29 C.F.R. § 1614.203(e)) and MD-715 require agencies to describe how their plan will improve the recruitment, hiring, advancement, and retention of applicants and employees with disabilities. All agencies, regardless of size, must complete this Part of the MD-715 report. Section I: Efforts to Reach Regulatory Goals EEOC regulations (29 C.F.R. § 1614.203(d)(7)) require agencies to establish specific numerical goals for increasing the participation of persons with reportable and targeted disabilities in the federal government. 1. Using the goal of 12% as the benchmark, does your agency have a trigger involving PWD by grade level cluster in the permanent workforce? If “yes”, describe the trigger(s) in the text box. a. Cluster GS-1 to GS-10 (PWD) Yes No X b. Cluster GS-11 to SES (PWD) Yes X No Table B-4 Participation Rates for General Schedule Grades - Permanent PWD in GS-11 to SES cluster of the permanent workforce participate at 8.37% or 1085 PWD employees out of 12961 Total Workforce. 8.37% is lower than the expected 12% benchmark, indicating a trigger. 2. Using the goal of 2% as the benchmark, does your agency have a trigger involving PWTD by grade level cluster in the permanent workforce? If “yes”, describe the trigger(s) in the text box. -
Unix Commands January 2003 Unix
Unix Commands Unix January 2003 This quick reference lists commands, including a syntax diagram 2. Commands and brief description. […] indicates an optional part of the 2.1. Command-line Special Characters command. For more detail, use: Quotes and Escape man command Join Words "…" Use man tcsh for the command language. Suppress Filename, Variable Substitution '…' Escape Character \ 1. Files Separation, Continuation 1.1. Filename Substitution Command Separation ; Wild Cards ? * Command-Line Continuation (at end of line) \ Character Class (c is any single character) [c…] 2.2. I/O Redirection and Pipes Range [c-c] Home Directory ~ Standard Output > Home Directory of Another User ~user (overwrite if exists) >! List Files in Current Directory ls [-l] Appending to Standard Output >> List Hidden Files ls -[l]a Standard Input < Standard Error and Output >& 1.2. File Manipulation Standard Error Separately Display File Contents cat filename ( command > output ) >& errorfile Copy cp source destination Pipes/ Pipelines command | filter [ | filter] Move (Rename) mv oldname newname Filters Remove (Delete) rm filename Word/Line Count wc [-l] Create or Modify file pico filename Last n Lines tail [-n] Sort lines sort [-n] 1.3. File Properties Multicolumn Output pr -t Seeing Permissions filename ls -l List Spelling Errors ispell Changing Permissions chmod nnn filename chmod c=p…[,c=p…] filename 2.3. Searching with grep n, a digit from 0 to 7, sets the access level for the user grep Command grep "pattern" filename (owner), group, and others (public), respectively. c is one of: command | grep "pattern" u–user; g–group, o–others, or a–all. p is one of: r–read Search Patterns access, w–write access, or x–execute access. -
Uniqlaser Spa Policies
UNIQLASER SPA POLICIES RESCHEDULING/CANCELLATION POLICY- If you need to reschedule or cancel, please contact us 24 hours in advance of your scheduled time. All rescheduling/cancellations with less than 24 hours' notice are subject to a $20 fee, or a deduction to your gift certificate. This courtesy enables us to compensate our employees for their time, and maintains a higher availability of our time for you as well as others. By scheduling an appointment, you are agreeing to our rescheduling/cancellation policy. Patients arriving more than 5 minutes late may result in a shortened appointment or a cancellation if there is not enough time to complete the procedure. If your appointment is rescheduled or cancelled due to late arrival you will be charged the $20 cancellation fee. CHILD CARE- Unfortunately, we do not offer child care services in our facilities and children are not permitted in the spa. We provide a spa environment and for the enjoyment of our clients as well as for the safety of children we must enforce this policy. We appreciate your understanding and apologize for any inconvenience. PAYMENT-We require payment in full on the day of your procedure unless other arrangements are discussed. We conveniently accept Cash, Visa, MasterCard, American Express, Discover Card and Care Credit. REFUND-If you no longer wish to complete a package series, any remaining funds may be transferred towards another service. Remaining balance will not include the price of the free treatment in the package. No cash or charge refunds will be given. PRICES &PROMOTIONS-We are committed to continuously expanding our services to ensure we bring you the latest and greatest technology.