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Introduction to UNIX Text Processing Harendra Guturu 11 Oct 2013

Introduction to UNIX Text Processing Harendra Guturu 11 Oct 2013 Thank you to Cory McLean, Gus Katsiapis , Aaron Wenger, & Jim Notwell . Stanford UNIX resources. Host: cardinal.stanford.edu

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Introduction to UNIX Text Processing Harendra Guturu 11 Oct 2013

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  1. Introduction to UNIX Text Processing HarendraGuturu 11 Oct 2013 Thank you to Cory McLean, Gus Katsiapis, Aaron Wenger, & Jim Notwell.

  2. Stanford UNIX resources • Host: cardinal.stanford.edu • To connect from Unix/Linux/Mac:Open a terminal:sshuser@myth.stanford.edusshuser@cardinal.stanford.edusshuser@corn.stanford.edu • To connect from Windows: • SecureCRT/SecureFX (software.stanford.edu) • PuTTy (http://goo.gl/s0itD)

  3. Many useful text processing UNIX commands • awkbzcat cat column cut grep head join sedsort tail tee truniqwczcat … • UNIX commands work together via text streams. • Example usage and others available at http://tldp.org/LDP/abs/html/textproc.htmlhttp://en.wikipedia.org/wiki/Cat_%28Unix%29#Other

  4. Huge suite of tools

  5. Knowing UNIX commands eliminates having to reinvent the wheel • For homework #1 last year, to perform a simple file sort, submissions used: • 35 lines of Python • 19 lines of Perl • 73 lines of Java • 1 line of UNIX commands

  6. Anatomy of a UNIX command command [options] [FILE1] [FILE2] • options: -n 1 -g -c = -n1 -gc • output is directed to “standard output” (stdout) • if no input file is specified, input comes from “standard input” (stdin) • “-” also means stdin in a file list

  7. The real power of UNIX commands comes from combinations through piping (“|”) • Pipes are used to pass the output of one program (stdout) as the input (stdin) to another • Pipe character is <Shift>-\ grep “CS273a” grades.txt | sort -k 2,2gr | uniq Find all lines in the file that have “CS273a” in them somewhere Sort those lines by second column, in numerical order, highest to lowest Remove duplicates and print to standard output

  8. Output redirection (>, >>) • Instead of writing everything to standard output, we can write (>)or append (>>) to a file grep “CS273a” allClasses.txt > CS273aInfo.txt cat addlInfo.txt >> CS273aInfo.txt

  9. http://genomewiki.ucsc.edu/index.php/Kent_source_utilities UCSC KENT Source utilities

  10. /afs/ir/class/cs273a/bin/@sys/ • Many C programs in this directory that do manipulation of sequences or chromosome ranges • Run programs with no arguments to see help message overlapSelect [OPTION]… selectFileinFileoutFile Many useful options to alter how overlaps computed selectFile inFile Output is all inFile elements that overlap any selectFile elements outFile

  11. Kent Source and Mysql • Linux + Mac Binaries • http://hgdownload.soe.ucsc.edu/admin/exe/ • Using MySQL on browser • http://genome.ucsc.edu/goldenPath/help/mysql.html

  12. Interacting with UCSC Genome Browser MySQL Tables • Galaxy (a GUI to make SQL commands easy) • http://main.g2.bx.psu.edu/ • Direct interaction with the tables: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A –Ne “<STMT>“ e.g. mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A –Ne \ “select count(*) from hg18.knownGene“; +-------+ | 66803 | +-------+ http://dev.mysql.com/doc/refman/5.1/en/tutorial.html

  13. Stop for Practice Exercise

  14. Exercise From Class ## inspect your data head 50kbx5kbWindows.txt                       # Gets top 10 lines column -t 50kbx5kbWindows.txt  | head          # Spaces the columns for nice viewing and then shows top 10 lines ## NOTE: Don't process output from column since the pretty output usually is mangled in terms of field separators ## get the desired fields  cat 50kbx5kbWindows.txt | cut -f1,4 | sort -k1,1 -0 50kbx5kbWindows.cut.txt ## data verifications md5sum 50kbx5kbWindows.cut.txt 50kbx5kbWindows.awk.txt ## sort the bed file by name cat mm9.50kbx5kbWindows.bed | sort -k4,4 > mm9.50kbx5kbWindows.sort.bed ## NOTE: cat fileName | sort -k4,4 > fileName ## Will kill the file, but ## cat fileName | sort -k4,4 -o fileName ## Will not ## select windows overlapping a p300 peak, join on the name, sort to find the most ## enriched windows, clean, and take the top 20 overlapSelect mm9.wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1.bed mm9.50kbx5kbWindows.sort.bed stdout | join -t$'\t' -1 4 -2 1 - 50kbx5kbWindows.cut.txt | sort -k5,5 -gr | awk '{print $2"\t"$3"\t"$4"\t"$5}' | head -20 > top20.bed ## remove the temporary files rm 50kbx5kbWindows.cut.txt mm9.50kbx5kbWindows.sort.bed

  15. Other operations with bash/shell • http://www.catonmat.net/blog/set-operations-in-unix-shell/ • Bash noclobber • $ set -o noclobber • $ echo "Can we overwrite it again?" >file.txt • -bash: file.txt: cannot overwrite existing file • $ echo "Can we overwrite it again?" >| file.txt • Bash Dual pipes (tricky, be careful) • sort <(cat file1) <(cat file2)

  16. Specific unix commands

  17. man, whatis, apropos • UNIX program that invokes the manual written for a particular program • man sort • Shows all info about the program sort • Hit <space> to scroll down, “q” to exit • whatis sort • Shows short description of all programs that have “sort” in their names • apropos sort • Shows all programs that have “sort” in their names or short descriptions

  18. cat • Concatenates files and prints them to standard output • cat [OPTION] [FILE]… • Variants for compressed input files:zcat (.gz files)bzcat (.bz2 files) A B C D 1 2 3 A B C D 1 2 3

  19. head, tail • head: first ten linestail: last ten lines • -n option: number of lines • For tail, -n+K means line K to the end. • head –n5 : first five lines • tail –n73 : last 73 lines • tail –n+10 | head –n 5 : lines 10-14

  20. cut • Prints selected parts of lines from each file to standard output • cut [OPTION]… [FILE]… • -d Choose delimiter between columns (default TAB) • -f Fields to print-f1,7 : fields 1 and 7-f1-4,7,11-13: fields 1,2,3,4,7,11,12,13

  21. cut example file.txt CS a CS.273.a CS CS 273 a CS.273.a CS 273 a cut –f1,3 file.txt =cat file.txt | cut –f1,3 CS 273 a CS.a CS 273 a cut –d ‘.’ –f1,3 file.txt In general, you should make sure your file columns are all delimited with the same character(s) before applying cut!

  22. wc • Print line, word, and character (byte) counts for each file, and totals of each if more than one file specified • wc [OPTION]… [FILE]… • -l Print only line counts

  23. sort • Sorts lines in a delimited file (default: tab) • -k m,n sorts by columns m to n (1-based) • -g sorts by general numerical value (can handle scientific format) • -r sorts in descending order • sort -k1,1gr -k2,3 • Sort on field 1 numerically (high to low because of r). • Break ties on field 2 alphabetically. • Break further ties on field 3 alphabetically.

  24. uniq • Discard all but one of successive identical lines from input and print to standard output • -d Only print duplicate lines • -i Ignore case in comparison • -u Only print unique lines

  25. uniq example file.txt CS 273a TA: Cory McLean CS 273a CS 273a CS 273a TA: Cory McLean CS 273a uniq file.txt TA: Cory McLean CS 273a uniq –u file.txt uniq –d file.txt CS 273a In general, you probably want to make sure your file is sorted before applying uniq!

  26. grep • Search for lines that contain a work or match a regular expression • grep [options] PATTERN [FILE…] • -i ignore case • -v Output lines that do not match • -E regular expressions • -f <FILE>: patterns from a file (1 per line)

  27. grep example grep -E “^CS[[:space:]]+273$” file Then have one or more spaces (or tabs) For lines that start with CS And end with 273 Search through “file” file CS 273a CS273 CS 273 cs 273 CS 273 CS 273 CS 273

  28. tr • Translate or delete characters from standard input to standard output • tr [OPTION]… SET1 [SET2] • -d Delete chars in SET1, don’t translate cat file.txt | tr ‘\n’ ‘,’ file.txt This is an Example. This,is an,Example.,

  29. sed: stream editor • Most common use is a string replace. • sed –e “s/SEARCH/REPLACE/g” cat file.txt | sed –e “s/is/EEE/g” file.txt ThEEE EEE an Example. This is an Example.

  30. join • Join lines of two files on a common field • join [OPTION]… FILE1 FILE2 • -1 Specify which column of FILE1 to join on • -2 Specify which column of FILE2 to join on • Important: FILE1 and FILE2 must alreadybe sorted on their join fields!

  31. join example file1.txt file2.txt Bejerano CS273a Villeneuve DB210 Batzoglou DB273a CS273a Comp Tour Hum Gen. CS229 Machine Learning DB210 Devel. Biol. join -1 2 -2 1 file1.txt file2.txt CS273a Bejerano Comp Tour Hum Gen. DB210 Villeneuve Devel. Biol.

  32. SHELL SCripting

  33. Common shells • Two common shells: bash and tcsh • Run ps to see which you are using.

  34. Multiple UNIX commands can be combined into a single shell script. Means die on error. script.sh script.csh #!/bin/bash set -beEu -o pipefail cat $1 $2 > tmp.txt paste tmp.txt $3 > $4 export A=“Value” #!/bin/tcsh -e cat $1 $2 > tmp.txt paste tmp.txt $3 > $4 setenv A “Value” Command prompt % ./script.sh file1.txt file2.txt file3.txt out.txt % ./script.csh file1.txt file2.txt file3.txt out.txt Scripts must first be set to be executable: % chmod u+x script.sh script.csh http://www.faqs.org/docs/bashman/bashref_toc.html http://www.the4cs.com/~corin/acm/tutorial/unix/tcsh-help.html

  35. for loop # BASH for loop to print 1,2,3 on separate lines for i in `seq 1 3` do echo ${i} done # TCSH for loop to print 1,2,3 on separate lines foreachi ( `seq 1 3` ) echo ${i} end Special quote character, usually left of “1” on keyboard that indicates we should execute the command within the quotes

  36. SCRIPTING languages

  37. awk • A quick-and-easy shell scripting language • http://www.grymoire.com/Unix/Awk.html • Treats each line of a file as a record, and splits fields by whitespace • Fields referenced as $1, $2, $3, … ($0 is entire line)

  38. Anatomy of an awk script. awk ‘BEGIN {…} {…} END {…}’ before first line once per line after last line

  39. awk example • Output the lines where column 3 is less than column 5 in a comma-delimited file. Output a summary line at the end. awk -F',‘'BEGIN{ct=0;}{ if ($3 < $5) { print $0; ct=ct+1; } }END { print "TOTAL LINES: " ct; }'

  40. Useful things from awk • Make sure fields are delimited with tabs (to be used by cut, sort, join, etc. awk ‘{print $1 “\t” $2 “\t” $3}’ whiteDelim.txt > tabDelim.txt • Good string processing using substr, index, length functions awk ‘{print substr($1, 1, 10)}’ longNames.txt > shortNames.txt Start position Length String to manipulate substr(“helloworld”, 4, 3) = “low” index(“helloworld”, “low”) = 4 length(“helloworld”) = 10 index(“helloworld”, “notpresent”) = 0

  41. Python • A scripting language with many useful constructs • Easier to read than Perl • http://wiki.python.org/moin/BeginnersGuide • http://docs.python.org/tutorial/index.html • Call a python program from the command line: python myProg.py

  42. Number types • Numbers: int, float >>> f = 4.7 >>> i = int(f) >>> j = round(f) >>> i 4 >>> j 5.0 >>> i*j 20.0 >>> 2**i 16

  43. Strings >>> dir(“”) […, 'capitalize', 'center', 'count', 'decode', 'encode', 'endswith', 'expandtabs', 'find', 'index', 'isalnum', 'isalpha', 'isdigit', 'islower', 'isspace', 'istitle', 'isupper', 'join', 'ljust', 'lower', 'lstrip', 'replace', 'rfind', 'rindex', 'rjust', 'rstrip', 'split', 'splitlines', 'startswith', 'strip', 'swapcase', 'title', 'translate', 'upper', 'zfill'] >>> s = “hi how are you?” >>> len(s) 15 >>> s[5:10] ‘w are’ >>> s.find(“how”) 3 >>> s.find(“CS273”) -1 >>> s.split(“ “) [‘hi’, ‘how’, ‘are’, ‘you?’] >>> s.startswith(“hi”) True >>> s.replace(“hi”, “hey buddy,”) ‘hey buddy, how are you?’ >>> “ extraBlanks ”.strip() ‘extraBlanks’

  44. Lists • A container that holds zero or more objects in sequential order >>> dir([]) […, 'append', 'count', 'extend', 'index', 'insert', 'pop', 'remove', 'reverse', 'sort'] >>> myList = [“hi”, “how”, “are”, “you?”] >>> myList[0] ‘hi’ >>> len(myList) 4 >>> for word in myList: print word[0:2] hi ho ar yo >>> nums = [1,2,3,4] >>> squares = [n*n for n in nums] >>> squares [1, 4, 9, 16]

  45. Dictionaries • A container like a list, except key can be anything (instead of a non-negative integer) >>> dir({}) […, clear', 'copy', 'fromkeys', 'get', 'has_key', 'items', 'iteritems', 'iterkeys', 'itervalues', 'keys', 'pop', 'popitem', 'setdefault', 'update', 'values'] >>> fruits = {“apple”: True, “banana”: True} >>> fruits[“apple”] True >>> fruits.get(“apple”, “Not a fruit!”) True >>> fruits.get(“carrot”, “Not a fruit!”) ‘Not a fruit!’ >>> fruits.items() [('apple', True), ('banana', True)]

  46. Reading from files file.txt >>> openFile = open(“file.txt”, “r”) >>> allLines = openFile.readlines() >>> openFile.close() >>> allLines [‘Hello, world!\n’, ‘This is a file-reading\n’, ‘\texample.\n’] Hello, world! This is a file-reading example.

  47. Writing to files >>> writer = open(“file2.txt”, “w”) >>> writer.write(“Hello again.\n”) >>> name = “Cory” >>> writer.write(“My name is %s, what’s yours?\n” % name) >>> writer.close() file2.txt Hello again. My name is Cory, what’s yours?

  48. Creating functions def compareParameters(param1, param2): if param1 < param2: return -1 elif param1 > param2: return 1 else: return 0 def factorial(n): if n < 0: return None elif n == 0: return 1 else: retval = 1 num = 1 while num <= n: retval = retval*num num = num + 1 return retval

  49. Example program Example.py #!/usr/bin/env python import sys # Required to read arguments from command line if len(sys.argv) != 3: print “Wrong number of arguments supplied to Example.py” sys.exit(1) inFile = open(sys.argv[1], “r”) allLines = inFile.readlines() inFile.close() outFile = open(sys.argv[2], “w”) for line in allLines: outFile.write(line) outFile.close()

  50. Example program #!/usr/bin/env python import sys # Required to read arguments from command line if len(sys.argv) != 3: print “Wrong number of arguments supplied to Example.py” sys.exit(1) inFile = open(sys.argv[1], “r”) allLines = inFile.readlines() inFile.close() outFile = open(sys.argv[2], “w”) for line in allLines: outFile.write(line) outFile.close() python Example.py file1 file2 sys.argv = [‘Example.py’, ‘file1’, ‘file2’]

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