New User Special Price Expires in

Let's log you in.

Sign in with Facebook


Don't have a StudySoup account? Create one here!


Create a StudySoup account

Be part of our community, it's free to join!

Sign up with Facebook


Create your account
By creating an account you agree to StudySoup's terms and conditions and privacy policy

Already have a StudySoup account? Login here


by: Mrs. Frederic Hansen


Mrs. Frederic Hansen
GPA 3.91


Almost Ready


These notes were just uploaded, and will be ready to view shortly.

Purchase these notes here, or revisit this page.

Either way, we'll remind you when they're ready :)

Preview These Notes for FREE

Get a free preview of these Notes, just enter your email below.

Unlock Preview
Unlock Preview

Preview these materials now for free

Why put in your email? Get access to more of this material and other relevant free materials for your school

View Preview

About this Document

Class Notes
25 ?




Popular in Course

Popular in BioInformatics

This 4 page Class Notes was uploaded by Mrs. Frederic Hansen on Sunday September 27, 2015. The Class Notes belongs to BCB 444 at Iowa State University taught by Staff in Fall. Since its upload, it has received 51 views. For similar materials see /class/214473/bcb-444-iowa-state-university in BioInformatics at Iowa State University.

Similar to BCB 444 at ISU

Popular in BioInformatics




Report this Material


What is Karma?


Karma is the currency of StudySoup.

You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!

Date Created: 09/27/15
Introduction to Perl amp Bioperl I Basic Perl Programming Xuefeng Zhao L H Baker Center ISU ECE 444544X Objectives Get an overview of basic Perl programming Write simple perl scripts to manipulate DNARNA sequences Outline Perl lnstall PerlBloperl on WlnooWs Purl a Hello perl sonpt ta Types vanaoles and Bulltclrl Functlons Control structures Baslo l Subroutlnes amp Functh More stnng Manlpulatlon Why Perl Perl Practlcal Extractlon and Report Language Easvto learn Good forstrlrlg rnanlpulatlon and Flle lo Open source forall o A lot of Blolrlforrnatlcs tools avallable Install PerlBioperl Ref lnstall Note on WWW ploperl org 1 UrllxLlrlux Preelnstalled 2 Mat nttp WWW rnacperl org 3 WlnooWs DoWnloao tne current ActlvEPErl trorn VWWV actlvegerl corn Tne WlnooWs lnstaller package rlle ls AmlvEPErlr E E El leM SWlnSZnXEEnl ZZZEIE rnsl e lnstal ng tne oeraultvalues by duublecllcklngtne rnsl fllE uslng c ell as tne Perl norne m TD lnstall GD prn FEW W513 WEBB WW e To lnstall alopell pprngtrep aoo alopell ntto blqurl orgolst pprngtsearcn plopell l bluPEYl ll 2 3 blulnlurmatlcstuul klts bluPEYl ll 2 ll non a A a lePEVH a ll ol aloPelll a PPMSArchlve pprngtlnstall a Successfullvlnstalled Eluperlrl Averslon l 4 ln ActlvEPErl 5 E 6 EM Run a Hello Perl script DoWnloao all Perl scnpts ror to vuurUSE dlSK and run ne perl nell tne class rrorn WWW ololrronnatlcs lastate eouElElsl llo pl TD run r o pl TD run ello pl Scllvt Halls pl lusrlucalblnpen nellu perl scrlpt use strlct prlnt Hellu lSUrECESlVl X Easl syntax l tne rlrst l llne lnolcates tne locanon or park useo ror UnlxLlrlux cs 2 Freeronn casesensltlve a Eacn staternentenos Wltn a sernlcolon l A A cornrnentllne starts Wltn a pound slgn 3 you nave to comment llne by Data type Variables and Built in functions Data Tvpes i Scalar string and number 2 Arrav listarravs arravand associative arravsthash vanab es i Scalarvarlables start Witha Ex DNAstri riurnNT 2 Arrav startWi Ex narne 3 Hash Startvvlth Ex uuRestncteEnzvrn Some Perl bulltnll39l runctions length substr index rll39ldex sort push pop open close die exit print Scalar variables number and string Nurnber nurnvarEgtltPREssloNi suunter2ni Tm 75 string variables strVarEXPREssloNi uslng single gubtet i nu variable Expanslun takes place strl lsurbcbsl i str5uppurt NlHVNSF str5uppurt ms NlHVNSF uslng duuble quutef i a variable Expanslun takes place 52 entered characters needstu be ese strl arnes iuvva str2 unbcbsli arnesi iuvva X str uslng backstlcllt i the variable is assigned the return values rrbrn the cumrnarid Operators and Functions for Scalar variables Arithmetic Operaturs t 7 i quotn Nutatlun Euunter sen euunter euunterli euunter unterr ter uunter Euunternli cuun c DNA and RNA EhumpsrRlNe Ehupastrl Hash Hash n axed bv strings Brace fur kev bereent sign rbr entire arrav assign 4 elernents tn the arrav AAllsFAlagt Aixclv G xhisgt Hx Pnegt r aa7glvAAlislclvii strDateNuW date t strDateNuW Mun DEEIBZEIEIE Array Arrav NTlls i i asslgnA elements tn the array included in i rit72 a NTllstl tne arrav ingex starts n the index number is include in 1 last ldx WTllst last ldx 3 riumele saiarNTlisti numielement 4 ControlStructures IF ELSIF ESE statern ents statements statern entsi ControlStructureslF ELSIF ESE if m7n1 eq A QuirkMt at A euunter eisif m7nt eq T inumjg T eeunter eisif m7nt eq G Hum76 3 eeunter eisif m7nt eq C num7c C eeunter eiseinum7errprg errur Loop Structures WHILEDO WLE FOR rWHiLE Lump Whiie unditiun st mEnfS r r DOVWHiLE Lump dB at East EINEE Deni statement Whiieurrdmun 7 FOR Lump FurUmtiai vaiues test increment statement i Tvvu epntrpi statements tpr ippp Deeiare tnat tnrs is tne iast statement in tne iuup Start a nevviteratiun prtne iuup GCcounterp Wnte a peri senpttp epunt 3c untentin a DNA sequence Basic IO read and wnte Ou12FieFASTAp Output the DNA sequence to a le in FASTA format The FASTA format description is nttp Ungfnbiast gbf deducsfasta irtmi Subroutine amp Functions i um r n r r 2 Hunter eaiisup amprs used perpretne sup name 3 Arguments are passed in tne subruutine by a speciai array demu eaiis subruutine s msgs eainng rrpm putsrue x a S getemswg a print gimsg sup getmsg i m7msg 7M Arguments are iis ted in pnnt m7msg n gimsg eiiu rrpm sup x tne ginbai variabie is updated hereiiii Sample issue Antibugging all variables must be declared before being used 5e strict at give Warning mSg Wm it a little bit more info than use Warnings 5 use draghostre it Limit the scope ofvariables rhyo lexical scope visible ll l the scope orthe current block that defines it only local does hot create a private variable but let the global variable has a temp value and be restored to the old values when the variable is o tofscope debugging 1 print out or comment out 2 run perl debugger perl d your scripth dbgt h dbgtn next step dbgt x yourvar to exam the value More String Manipulationsplit match amp regular expression Ref Ch7 by Michael Moorhouse and Paul Barry A T 3 3 2 NTstr Substitute t NTS NTst Translatan charamerrbyrcharacter tr n latiu NTSt ATG CAAAAAAAN NTstr e trATGCTACG r summary Data Types Variables and Operatluns Cuntrul Strumures Basic lO Subruutines StFuriEtlDriS Mare String Manlpulatlun Debug


Buy Material

Are you sure you want to buy this material for

25 Karma

Buy Material

BOOM! Enjoy Your Free Notes!

We've added these Notes to your profile, click here to view them now.


You're already Subscribed!

Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'

Why people love StudySoup

Bentley McCaw University of Florida

"I was shooting for a perfect 4.0 GPA this semester. Having StudySoup as a study aid was critical to helping me achieve my goal...and I nailed it!"

Amaris Trozzo George Washington University

"I made $350 in just two days after posting my first study guide."

Jim McGreen Ohio University

"Knowing I can count on the Elite Notetaker in my class allows me to focus on what the professor is saying instead of just scribbling notes the whole time and falling behind."

Parker Thompson 500 Startups

"It's a great way for students to improve their educational experience and it seemed like a product that everybody wants, so all the people participating are winning."

Become an Elite Notetaker and start selling your notes online!

Refund Policy


All subscriptions to StudySoup are paid in full at the time of subscribing. To change your credit card information or to cancel your subscription, go to "Edit Settings". All credit card information will be available there. If you should decide to cancel your subscription, it will continue to be valid until the next payment period, as all payments for the current period were made in advance. For special circumstances, please email


StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.