Varia

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(No Transcript)
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Les 3 (theorie oefeningen)

• Varia
• http//biochema.rug.ac.be/
• Herhaling
• Demos (sequence retrieva, dotplot, pairwise
  alignment SW) tijdens les
• Installatie
• Windows versus Linux
• Perl
• Herhaling
• Array/Hashes/FileIO
• Oefeningen

3
Overview

• Fr 4/10 Introduction History, Database
  Biology, Sequence Formats
• Fr 11/10 Pairwise comparison, scoring, matrices
• Do 17/10 B10 Theorie Herhaling (Demo) Perl
  Herhaling Oefeningen
• Fr 18/10 Multiple alignment, Basic and advanced
  Database Searching
• Do geen practicum / Oefeningen
• Fr 25/10 geen les
• Do geen practicum / Oefeningen
• Fr 1/11 geen les
• Fr 8/11 Phylogenetics, Gene prediction, junk
  mining (RNA prediction)
• Fr 15/11 geen les
• Fr 22/11 Protein structure, classification and
  engineering

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Genetic Code Matrix
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Other similarity scoring matrices might be
constructed from any property of amino acids
that can be quantified - partition coefficients
between hydrophobic and hydrophilic phases -
charge - molecular volume Unfortunately
,
Overview
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Principles of Scoring Matrix Construction

• 1978 1991
• A 100 100
• C 20 44
• D 106 86
• E 102 77
• F 41 51
• G 49 50
• H 66 91
• I 96 103
• K 56 72
• L 40 54
• M 94 93
• N 134 104
• P 56 58
• Q 93 84
• R 65 83
• S 120 117
• T 97 107
• V 74 98

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Which matrix should I use?

• When comparing sequences that were not known in
  advance to be related, for example when database
  scanning
• default scoring matrix used is the BLOSUM62
  matrix
• if one is restricted to using only PAM scoring
  matrices, then the PAM120 is recommended for
  general protein similarity searches
• When using a local alignment method, Altschul
  suggests that three matrices should ideally be
  used PAM40, PAM120 and PAM250, the lower PAM
  matrices will tend to find short alignments of
  highly similar sequences, while higher PAM
  matrices will find longer, weaker local
  alignments.

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Overview

• C K H V F C R V C I
• --------------------
• C 5 3 3 3 2 2 1 1 1 0
• K 4 4 3 3 2 1 1 1 0 0
• K 3 4 3 3 2 1 1 1 0 0
• C 4 3 3 3 2 2 1 1 1 0
• F 3 2 2 2 3 1 1 1 0 0
• C 4 2 2 2 2 2 1 1 1 0
• K 2 3 2 2 2 1 1 1 0 0
• C 2 1 1 1 1 2 1 0 1 0
• V 0 0 0 1 0 0 0 1 0 0

• C K H V F C R V C I
• C K K C F C - K C V
• C K H V F C R V C I
• C K K C F C K - C V
• C - K H V F C R V C I
• C K K C - F C - K C V
• C K H - V F C R V C I
• C K K C - F C - K C V

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Overview

• C K H V F C R V C I
• --------------------
• C 5 3 3 3 2 2 1 1 1 0
• K 4 4 3 3 2 1 1 1 0 0
• K 3 4 3 3 2 1 1 1 0 0
• C 4 3 3 3 2 2 1 1 1 0
• F 3 2 2 2 3 1 1 1 0 0
• C 4 2 2 2 2 2 1 1 1 0
• K 2 3 2 2 2 1 1 1 0 0
• C 2 1 1 1 1 2 1 0 1 0
• V 0 0 0 1 0 0 0 1 0 0

• C K H V F C R V C I
• C K K C F C - K C V
• C K H V F C R V C I
• C K K C F C K - C V
• C - K H V F C R V C I
• C K K C - F C - K C V
• C K H - V F C R V C I
• C K K C - F C - K C V

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Get Sequences

• Entrez
• Simple
• ZK822 (genomic)
• ZK822.4 (gene)
• Limits Details
• Eg. all ion channels, complete CDS
• Batch-Entrez
• SRS Sequence Retrieval System
• Swissport

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SQL structured query language

• SQL is very powerful because it consists of only
  4 statements, sometimes referred to as CRUD
• 1) Create - INSERT - to store new data
• 2) Read - SELECT - to retrieve data
• 3) Update - UPDATE - to change or modify data.
• 4) Delete - DELETE - delete or remove data
• Select from table where .

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• Select from table where . (http//sqlcourse2.co
  m/select2.html)
• ((ion channelAll Fields AND "homo
  sapiens"Organism) AND ((((((1900MDAT
  3000MDAT) NOT gbdiv_estPROP) AND ((1900MDAT
  3000MDAT) NOT gbdiv_stsPROP)) AND
  ((1900MDAT 3000MDAT) NOT gbdiv_gssPROP))
  AND ((1900MDAT 3000MDAT) NOT
  gbdiv_htgPROP)) AND ((1900MDAT 3000MDAT)
  NOT gbdiv_patPROP)))

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Get Sequences

• Entrez
• Simple
• ZK822 (genomic)
• ZK822.4 (gene)
• Limits Details
• Eg. all ion channels, complete CDS
• Batch-Entrez
• SRS Sequence Retrieval System
• Swissport

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• Perform multiple alignment
• Blosum62 12 -2
• Change gap opening and extenion to get correct
  alignment
• Goal Align two similar proteins

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Extensions to basic dynamic programming method
Overview

• use similarity function in initialization step -gt
  scoring tables
• use gap penalties
• constant gap penalty for gap gt 1
• gap penalty proportional to gap size
• one penalty for starting a gap (gap opening
  penalty)
• different (lower) penalty for adding to a gap
  (gap extension penalty)

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Sequence comparison with dot matrices
Dot matrices

• Goal Graphically display regions of similarity
  between two sequences (e.g., domains in common
  between two proteins of suspected similar
  function)
• Extremely USEFULL !!
• Remember DNA is double stranded (plot again RCC)

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Overview
18
Overview

• Window size changes with goal of analysis
• size of average exon
• size of average protein structural element
• size of gene promoter
• size of enzyme active site

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• Dotmatrix

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Les 3 (theorie oefeningen)

• Varia
• http//biochema.rug.ac.be/
• Herhaling
• Demos (sequence retrieva, dotplot, pairwise
  alignment SW) tijdens les
• Installatie
• Windows versus Linux
• Perl
• Herhaling
• Array/Hashes/FileIO
• Oefeningen

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Perl installation

• Perl
• Perl is available for various operating systems.
  To download Perl and install it on your computer,
  have a look at the following resources
• www.perl.com (O'Reilly).
• Downloading Perl Software
• ActiveState. ActivePerl for Windows, as well as
  for Linux and Solaris.
• ActivePerl binary packages.
• CPAN
• PHPTriad
• bevat Apache/PHP en MySQL http//sourceforge.net/
  projects/phptriad

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BioPerl installation

• Bioperl
• Download bioperl bioperl-1.0.2.zip van
  http//bioperl.org/Core/Latest/
• perl Makefile.PL
• (n)make (oftwel nmake, download van microsoft
  http//download.microsoft.com/download/vc15/Patch/
  1.52/W95/EN-US/Nmake15.exe)
• (n)make install
• Voor bundle-bioperl
• Download bundle from cpan http//search.cpan.org/a
  uthor/CRAFFI/Bundle-BioPerl-2.03/BioPerl.pm
• perl Makefile.PL
• (n)make (oftwel nmake, download van microsoft
  http//download.microsoft.com/download/vc15/Patch/
  1.52/W95/EN-US/Nmake15.exe)
• (n)make install
• DBI en DBDMysql met PPM (perl package manager
  van ActivePerl)

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What is Perl ?

• Perl is a High-level Scripting language
• Faster than sh or csh, slower than C
• No need for sed, awk, tr, wc, cut,
• Compiles at run-time
• Perl is a computer language that is
• Interpreted
• Loosely typed
• String/text oriented
• Capable of using multiple syntax formats
• In Perl, theres more than one way to do it

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Why use Perl for bioinformatics ?

• Ease of use by novice programmers
• Fast software prototyping
• Flexible language
• Compact code
• Powerfull pattern matching via regular
  expressions (Best Regular Expressions on Earth)
• Availability of Perl modules for Bioinformatics
  and Internet.
• Available for Unix, PC, Mac
• Portability, Best for CGI-programming.
• Open Source easy to extend and custumize
• No licensing fees
• Some tasks are still better done with other
  languages (heavy computations / graphics).
• With perl you can write simple programs fast, but
  on the other hand it is also suitable for large
  and complex programs. (yet, it is not adequate
  for very large projects).

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What bioinformatics tasks are suited to Perl ?

• Sequence manipulation and analysis
• Parsing results of sequence analysis programs
  (Blast, Genscan, Hmmer etc)
• Parsing database (eg Genbank) files
• Obtaining multiple database entries over the
  internet

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General Remarks

• Perl is mostly a free format language add
  spaces, tabs or new lines wherever you want.
• For clarity, it is recommended to write each
  statement in a separate line, and use indentation
  in nested structures.
• Comments Anything from the sign to the end of
  the line is a comment. (There are no multi-line
  comments).
• A perl program consists of all of the Perl
  statements of the file taken collectively as one
  big routine to execute.

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How does the real perl program look like
!/usr/local/bin/perl print Hello everyone\n
Mandatory first line !
How to run it
1. Save the text of your code as a file --
program.pl 2. Execute it perl program.pl
Hello everyone
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22 ?

- indicates a variable
a 2 b 2 c a b

- ends every command

- assigns a value to a variable
or
c 2 2
or
c 2 2
or
c 2 / 2
or
24 lt-gt 24 16
c 2 4
or
c 1.35 2 - 3 / (0.12 1)
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Ok, c is 4. How do we know it?
c 4 print c
print command

- bracket output expression
print Hello \n
\n
- print a end-of-the-line character (equivalent
to pressing Enter)
Strings concatenation
print Hello everyone\n print Hello .
everyone . \n
Expressions and strings together
2 2 4
print 2 2 . (22) . \n
expression
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Loops and cycles (for statement)
Output all the numbers from 1 to 100 for (n1
nlt100 n1) print n \n
1. Initialization
for ( n1 )
2. Increment
for ( n1 )
3. Termination (do until the criteria is
satisfied)
for ( nlt100 )
4. Body of the loop - command inside curly
brackets
for ( )
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FOR IF -- all the even numbers from 1 to 100
for (n1 nlt100 n1) if ((n 2) 0)
print n
Note a b -- Modulus -- Remainder
when a is divided by b
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Text Processing Functions

• The substr function
• Definition
• The substr function extracts a substring out of a
  string and returns it. The function receives 3
  arguments a string value, a position on the
  string (starting to count from 0) and a length.
• Example
• a "university"
• k substr (a, 3, 5)
• k is now "versi" a remains unchanged.
• If length is omitted, everything to the end of
  the string is returned.

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• !/usr/local/bin/perl
• use strict
• use warnings
• my (sp_file, line, id, ac, de)
• sp_file "sp.txt"
• open (SP, sp_file) die "cannot open
  \"sp_file\" !"
• while (line ltSPgt)
• chomp (line)
• my field substr (line, 0, 2)
• my value substr (line, 5)
• if (field eq "ID")
• id value
• if (field eq "AC")
• ac value

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Text Processing Functions

• The split function
• The split function splits a string to a list of
  substrings according to the positions of a given
  delimiter. The delimiter is written as a pattern
  enclosed by slashes /PATTERN/. Examples
• string "programmingcourseforbioinformatic
  s"
• _at_list split (//, string)
• _at_list is now ("programming", "course", "for",
  "bioinformatics") string remains unchanged.
• string "protein kinase C\t450 Kilodaltons\t120
  Kilobases"
• _at_list split (/\t/, string) \t indicates tab
  
• _at_list is now ("protein kinase C", "450
  Kilodaltons", "120 Kilobases")

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Text Processing Functions

• The join function
• The join function does the opposite of split. It
  receives a delimiter and a list of strings, and
  joins the strings into a single string, such that
  they are separated by the delimiter.
• Note that the delimiter is written inside quotes.
  
• Examples
• _at_list ("programming", "course", "for",
  "bioinformatics")
• string join ("", _at_list)
• string is now "programmingcourseforbioinf
  ormatics"
• name "protein kinase C" mol_weight "450
  Kilodaltons" seq_length "120 Kilobases"
• string join ("\t", name, mol_weight,
  seq_length)
• string is now "protein kinase C\t450
  Kilodaltons\t120 Kilobases"

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Regular Expressions

• Match to a sequence of characters
• The EcoRI restriction enzyme cuts at the
  consensus sequence GAATTC.
• To find out whether a sequence contains a
  restriction site for EcoR1, write
• if (sequence /GAATTC/)
• ...

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Regular Expressions

• Match to a character class
• Example
• The BstYI restriction enzyme cuts at the
  consensus sequence rGATCy, namely A or G in the
  first position, then GATC, and then T or C. To
  find out whether a sequence contains a
  restriction site for BstYI, write
• if (sequence /AGGATCTC/) ... This
  will match all of AGATCT, GGATCT, AGATCC, GGATCC.
  
• Definition
• When a list of characters is enclosed in square
  brackets , one and only one of these characters
  must be present at the corresponding position of
  the string in order for the pattern to match. You
  may specify a range of characters using a hyphen
  -.
• A caret at the front of the list negates the
  character class.
• Examples
• if (string /AGTC/) ... matches any
  nucleotide
• if (string /a-z/) ... matches any
  lowercase letter
• if (string /chromosome1-6/) ...
  matches chromosome1, chromosome2 ... chromosome6
• if (string /xyzXYZ/) ... matches any
  character except x, X, y, Y, z, Z

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• We would like to find out whether the concensus
  sequence is contained (somewhere) in a given
  sequence a.
• Without quantifiers
• if (a /ACCCCAGAGAGGTGT/) ...
• With quantifiers
• if (a /AC4AG3(GT)2/) ...

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Regular Expressions

• Case-insensitive pattern matching
• To achieve a case-insensitive pattern matching,
  add the i modifier after the closing slash of the
  regular expression.
• Example
• When searching for HTML tags, we preferably do a
  case-insensitive search. e.g. if (doc
  /ltTABLE.gt/i)
• This would match ltTABLE...gt, lttablegt, ltTAblEgt,
  etc.

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Alternation

• Alternation allows matching any one of several
  subexpressions. The alternative subexpressions
  are separated by vertical bar(s) .
• Example 1
• extract all lines including either human, rat or
  mouse proteins
• if (line /HUMANRATMOUSE/) match line
  against either HUMAN, RAT or MOUSE
• Example 2
• In the same file, let us now restrict our search
  only for the ACM1 receptors in either human, rat
  or mouse. if (line /ACM1_(HUMANRATMOUSE)/)
  we enclosed the alternative subexpressions
  in parentheses (HUMANRATMOUSE) and added the
  receptor name prefix ACM1_ before them.

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Anchoring a pattern to the beginning or end of a
string

• To force matching of your pattern to the
  beginning of the string, write a caret as the
  first character of the regular expression.
• To force the matching to the end of the string,
  write a dollar sign as the last character of
  the regular expression.
• To print the "description" line, which starts
  with DE, we write
• !/usr/local/bin/perl
• my sp_file "sources/sp_entry"
• open (SP, sp_file) die "cannot open
  \"sp_file\" !"
• while (my line ltSPgt)
• if (line /DE/)
• print line
• Result
• DE MUSCARINIC ACETYLCHOLINE RECEPTOR M1.
• Note if we omitted the caret from the regular
  expression
• if (line /DE/)

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Regex

• OReilly book Mastering regular expressions (2nd
  edition)
• Regular Expressions Tutorial

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Substitutions
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Translations
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GC

• sub gc_content
• my seq shift
• print "\seq",seq
• my win shift
• print "length ",length(seq),"\n"
• for (my i 0 i lt length(seq) - win i)
• my segment substr(seq,i,win)
• my gc_count segment tr/GCgc/GCgc/
• print i1,"\t",segment,"\t",gc_count,"\n"

46
Les 3 (theorie oefeningen)

• Varia
• http//biochema.rug.ac.be/
• Herhaling
• Demos (sequence retrieva, dotplot, pairwise
  alignment SW) tijdens les
• Installatie
• Windows versus Linux
• Perl
• Herhaling
• Array/FileIO/Hashes
• Oefeningen

47
Arrays

• Definitions
• A scalar variable contains a scalar value one
  number or one string. A string might contain many
  words, but Perl regards it as one unit.
• An array variable contains a list of scalar data
  a list of numbers or a list of strings or a mixed
  list of numbers and strings. The order of
  elements in the list matters.
• Syntax
• Array variable names start with an _at_ sign.
• You may use in the same program a variable named
  var and another variable named _at_var, and they
  will mean two different, unrelated things.
• Example
• Assume we have a list of numbers which were
  obtained as a result of some measurement. We can
  store this list in an array variable as the
  following
• _at_msr (3, 2, 5, 9, 7, 13, 16)

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The foreach construct

• The foreach construct iterates over a list of
  scalar values (e.g. that are contained in an
  array) and executes a block of code for each of
  the values.
• Example
• foreach i (_at_some_array)
• statement_1
• statement_2
• statement_3
• Each element in _at_some_array is aliased to the
  variable i in turn, and the block of code inside
  the curly brackets is executed once for each
  element.
• The variable i (or give it any other name you
  wish) is local to the foreach loop and regains
  its former value upon exiting of the loop.
• Remark _

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Binary assignment operators

• A short hand for
• k k - 2
• is
• k - 2
• Similarly, you may use
• k 2 same as k k 2
• k 2 same as k k 2
• k / 2 same as k k / 2
• or even
• k . "some string" same as k k . "some
  string" These are called binary assignment
  operators, and are very useful in iterative
  (looping) constructs.

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Examples for using the foreach construct - cont.

• Calculate sum of all array elements
• !/usr/local/bin/perl
• _at_msr (3, 2, 5, 9, 7, 13, 16)
• sum 0
• foreach i (_at_msr)
• sum i
• print "sum is sum\n"

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Accessing individual array elements

• Individual array elements may be accessed by
  indicating their position in the list (their
  index).
• Example
• _at_msr (3, 2, 5, 9, 7, 13, 16)
• index value 0 3 1 2 2 5 3 9 4 7 5 13 6 16
• First element msr0 (here has the value of 3),
• Third element msr2 (here has the value of 5),
• and so on.

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The sort function

• The sort function receives a list of variables
  (or an array) and returns the sorted list.
• _at_array2 sort (_at_array1)
• !/usr/local/bin/perl
• _at_countries ("Israel", "Norway", "France",
  "Argentina")
• _at_sorted_countries sort ( _at_countries)
• print "ORIG _at_countries\n", "SORTED
  _at_sorted_countries\n"
• Output
• ORIG Israel Norway France Argentina
• SORTED Argentina France Israel Norway
• !/usr/local/bin/perl
• _at_numbers (1 ,2, 4, 16, 18, 32, 64)
• _at_sorted_num sort (_at_numbers)
• print "ORIG _at_numbers \n", "SORTED _at_sorted_num
  \n"
• Output
• ORIG 1 2 4 16 18 32 64
• SORTED 1 16 18 2 32 4 64

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The push and shift functions

• The push function adds a variable or a list of
  variables to the end of a given array.
• Example
• a 5
• b 7
• _at_array ("David", "John", "Gadi")
• push (_at_array, a, b)
• _at_array is now ("David", "John", "Gadi", 5, 7)
• The shift function removes the first element of a
  given array and returns this element.
• Example
• _at_array ("David", "John", "Gadi")
• k shift (_at_array)
• _at_array is now ("John", "Gadi") k is now
  "David"
• Note that after both the push and shift
  operations the given array _at_array is changed!

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How can I know the length of a given array?

• You have three options
• Assing the array variable into a scalar variable,
  as in the previous slide. This is not
  recommended, because the code is confusing.
• Use the scalar function. Example
• x scalar (_at_array) x now contains the
  number of elements in _at_array.
• Use the special variable array_name to get the
  index value of the last element of _at_array_name.
  Example
• _at_fruits ("apple", "orange", "banana", "melon")
  
• a fruits
• a is now 3
• b fruits 1
• b is now 4, i.e. the no. of elements in
  _at_fruits.

55
File input / output

• Opening a filehandle
• In order to use a filehandle other than STDIN,
  STDOUT and STDERR, the filehandle needs to be
  opened. The open function opens a file or device
  and associates it with a filehandle.
• It returns 1 upon success and undef otherwise.
• Examples
• open a filehandle for reading open
  (SOURCE_FILE, "filename")
• or open (SOURCE_FILE, "ltfilename")
• open a filehandle for writing open
  (RESULT_FILE, "gtfilename")
• open a filehandle for appending open (LOGFILE,
  "gtgtfilename"

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File input / output

• Closing a filehandle
• When you are finished with a filehandle, you may
  close it with the close function. The close
  function closes the file or device associated
  with the filehandle.
• Example
• close (MY_FILE_HANDLE) Filehandles are
  automatically closed when the program exits, or
  when the filehandle is reopened.

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File input / output

• The die function
• Sometimes the open function fails. For example,
  opening a file for input might fail because the
  file does not exist, and opening a file for
  output might fail because the file does not have
  a write permission. A perl program will
  nevertheless use the filehandle, and will not
  warn you that all input and output activities are
  actually meaningless.
• Therefore, it is recommended to explicitly check
  the result of the open command, and if it fails
  to print an error message and exit the program.
• This is easily done using the die function.
• Example
• my k open (FILEHANDLE, "filename") unless
  (k) die ("cannot open file filename !")
  in case file "filename" cannot be opened, the
  argument of die will be printed on the screen
  and the program will exit. ! is a special
  variable that contains the respective error
  message sent by the operating system.. A short
  hand
• open (FILEHANDLE, "filename") die "cannot open
  file filename !"

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Using filehandles for writing

• Example
• !/usr/local/bin/perl use strict
• use warnings
• open (OUTF, "gtout_file") die "cannot open
  out_file !" open (LOGF, "gtgtlog_file") die
  "cannot open log_file !"
• print OUTF "Here is my program output\n"
• print LOGF "First task of my program
  completed\n"
• print "Nice, isn't it?\n" will be printed on
  the screen close (OUTF)
• close (LOGF)

59
Using filehandles for reading (1/3)

• !/usr/local/bin/perl
• use strict
• use warnings
• my infile "CEACAM3.txt"
• my (line1, line2, line3)
• open (FH, infile) die "cannot open
  \"infile\" !"
• line1 ltFHgt read first line
• print line1 proccess line (here we only
  print it)
• line2 ltFHgt read next line
• print line2 proccess line (here we only
  print it)
• line3 ltFHgt read next line
• print line3 proccess line (here we only
  print it)
• close (FH)

60
Using filehandles for reading (2/3)

• When ltFILEHANDLEgt is assigned into an array
  variable, all lines up to the end of the file are
  read at once. Each line becomes a separate
  element of the array.
• !/usr/local/bin/perl
• use strict
• use warnings
• my infile "CEACAM3.txt"
• open (FH, infile) die "cannot open
  \"infile\" !"
• my _at_lines ltFHgt
• chomp (_at_lines) chomp each element of _at_lines
• close (FH)
• to process the lines you might wish to iterate
• over the _at_lines array with a foreach loop
• my line
• foreach line (_at_lines)
• process line. here we just print it.
• print "line\n"

61
Using filehandles for reading (3/3)

• Using a while loop, read one line at a time and
  assign it into a scalar variable, as long as the
  variable is not an empty string (which will
  happen at end-of-file).
• Note that a blank line read from the file will
  not result in an empty string, since it still
  contains the terminating \n.
• !/usr/local/bin/perl
• use strict
• use warnings
• my infile "CEACAM3.txt"
• open (FH, infile) die "cannot open
  \"infile\" !"
• my line or, in one line
• while (line ltFHgt) while (my line
  ltFHgt)
• chomp (line)
• print "line\n" process line. here we just
  print it.
• close (FH)

62
Hashes

• Definition
• A hash variable contains a collection of
  key/value pairs, arranged such that you can
  easily use any key to find its associated value.
  The order of the key/value pairs in the hash is
  not important.
• Hashes are also called associative arrays.
• Hash variable names start with a sign.
• You may use in the same program a variable named
  var and another variable named _at_var, and a third
  variable named var, and they will mean three
  different, unrelated things.

63
A Hash Is a Lookup Table

• A hash is a lookup table.
• We use a key to find an associated value. my
  translate
• translate'atg' 'M'
• translate'taa' ''
• translate'ctt' 'K' oops
• translate'ctt' 'L' fixed
• print translate'atg'
• Getting All Keys
• keys translate
• Removing Key, Value Pairs
• delete translate'taa' keys translate
• Initializing From a List
• translate ( 'atg' gt 'M', 'taa' gt '', 'ctt'
  gt 'L', 'cct' gt 'P', )

64

• AA1 ("TGT" gt "Cys",
• "TGC" gt "Cys",
• "GAT" gt "Asp",
• "GAC" gt "Asp",
• "GAA" gt "Glu",
• "GAG" gt "Glu",
• "TTT" gt "Phe")

65

• Accessing individual hash elements
• Whereas array elements are accessed by their
  (numerical) index, hash elements (values) are
  accessed by their keys.
• Example
• !/usr/local/bin/perl
• use strict
• use warnings
• my (prices, s, t)
• prices ("shirt" gt 45,
• "pullover" gt 90,
• "trousers" gt 120,
• "socks" gt 15)
• s prices"shirt"
• t prices"trousers"

66

• Adding an element to a hash
• Simply assign a value to a hash individual
  element, e.g. prices"coat" 250
• coat, 250 will be added to the prices hash
• Deleting an element from a hash
• use the delete function, e.g. delete
  prices"coat"
• Checking whether a hash is empty
• if (hash_name) will be false if hash is
  empty .......
• Using a Hash for Counting
• number_of_nuc"g"
• Using a Hash for Eliminating Duplicates
• genbankaccession 1In this case, the keys
  in the hash are what's important. The values may
  be irrelevant.

67
The keys function

• The keys function yields a list of all the
  current keys in a given hash.
• Example
• !/usr/local/bin/perl
• use strict
• use warnings
• my prices ("shirt" gt 45, "pullover" gt 90,
  "trousers" gt 120, "socks" gt 15)
• my _at_items keys (prices)
• print "ITEMS _at_items\n"
• Result ITEMS pullover shirt socks trousers

68
Iterating over all hash elements using the keys
function

• Example - printing all keys and values of the
  prices hash
• my _at_items_list keys (prices)
• foreach item (_at_items_list)
• print "item pricesitem NIS\n"
• or, shorter
• foreach item (keys (prices))
• print "item pricesitem NIS\n"
• Result pullover 90 NIS shirt 45 NIS socks
  15 NIS trousers 120 NIS

69
The values function

• The values function yields a list of all the
  current values in a given hash.
• Example
• !/usr/local/bin/perl
• use strict
• use warnings
• my prices ("shirt" gt 45, "pullover" gt 90,
  "trousers" gt 120, "socks" gt 15)
• my _at_EURO values (prices)
• print "PRICES _at_EURO\n"
• Result PRICES 90 45 15 120

70
Oefeningen http//biochema.rug.ac.be/

• Which genes are involved in the PRADER-WILLI
  SYNDROME ?
• How may different human PDE (phosphodiesterases)
  are available in Genbank ?
• How big is the anthrax genome and how many genes
  are present ?
• Which of the 4 sequences (seq1/2/3/4)
• Contains a hexokinases signature
  (LIVM-G-F-TN-F-S-FY-P-x(5)-LIVM-DNST-x(3
  )-LIVM- x(2)-W-T-K-x-LF)
• How many of them?
• Where (hint) ?
• Write program (random.pl) to generate 10 random
  sequences of 1000 bp and write them to a file in
  fasta format
• Find the answer in ultimate-sequence.txt
• (hint use AA1 to perform translation(s))
• What is the restriction enzyme which the longest
  recognition site ?

71

• gtSEQ1
• MGNLFENCTHRYSFEYIYENCTNTTNQCGLIRNVASSIDVFHWLDVYIST
  TIFVISGILNFYCLFIALYT YYFLDNETRKHYVFVLSRFLSSILVIISL
  LVLESTLFSESLSPTFAYYAVAFSIYDFSMDTLFFSYIMIS
  LITYFGVVHYNFYRRHVSLRSLYIILISMWTFSLAIAIPLGLYEAASNSQ
  GPIKCDLSYCGKVVEWITCS LQGCDSFYNANELLVQSIISSVETLVGSL
  VFLTDPLINIFFDKNISKMVKLQLTLGKWFIALYRFLFQMT
  NIFENCSTHYSFEKNLQKCVNASNPCQLLQKMNTAHSLMIWMGFYIPSAM
  CFLAVLVDTYCLLVTISILK SLKKQSRKQYIFVVVRLSAAILIALCIII
  IQSTYFIDIPFRDTFAFFAVLFIIYDFSILSLLGSFTGVAM
  MTYFGVMRPLVYRDKFTLKTIYIIAFAIVLFSVCVAIPFGLFQAADEIDG
  PIKCDSESCELIVKWLLFCI ACLILMGCTGTLLFVTVSLHWHSYKSKKM
  GNVSSSAFNHGKSRLTWTTTILVILCCVELIPTGLLAAFGK
  SESISDDCYDFYNANSLIFPAIVSSLETFLGSITFLLDPIINFSFDKRIS
  KVFSSQVSMFSIFFCGKR
• gtSEQ2
• MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE
  MDRGLRLETH EEASVKMLPT YVRSTPEGSE VGDFLSLDLG
  GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
  MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID
  KGILLNWTKG FKASGAEGNN VVGLLRDAIK RRGDFEMDVV
  AMVNDTVATM ISCYYEDHQC EVGMIVGTGC NACYMEEMQN
  VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES
  SANPGQQLYE KLIGGKYMGE LVRLVLLRLV DENLLFHGEA
  SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS
  TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED
  VMRITVGVDG SVYKLHPSFK ERFHASVRRL TPSCEITFIE
  SEEGSGRGAA LVSAVACKKA CMLGQ
• gtSEQ3
• MESDSFEDFLKGEDFSNYSYSSDLPPFLLDAAPCEPESLEINKYFVVIIY
  VLVFLLSLLGNSLVMLVILY SRVGRSVTDVYLLNLALADLLFALTLPIW
  AASKVTGWIFGTFLCKVVSLLKEVNFYSGILLLACISVDRY
  LAIVHATRTLTQKRYLVKFICLSIWGLSLLLALPVLIFRKTIYPPYVSPV
  CYEDMGNNTANWRMLLRILP QSFGFIVPLLIMLFCYGFTLRTLFKAHMG
  QKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTWVIQET
  CERRNDIDRALEATEILGILHSCLNPLIYAFIGQKFRHGLLKILAIHGLI
  SKDSLPKDSRPSFVGSSSGH TSTTL
• gtSEQ4
• MEANFQQAVK KLVNDFEYPT ESLREAVKEF DELRQKGLQK
  NGEVLAMAPA FISTLPTGAE TGDFLALDFG GTNLRVCWIQ
  LLGDGKYEMK HSKSVLPREC VRNESVKPII DFMSDHVELF
  IKEHFPSKFG CPEEEYLPMG FTFSYPANQV SITESYLLRW
  TKGLNIPEAI NKDFAQFLTE GFKARNLPIR IEAVINDTVG
  TLVTRAYTSK ESDTFMGIIF GTGTNGAYVE QMNQIPKLAG
  KCTGDHMLIN MEWGATDFSC LHSTRYDLLL DHDTPNAGRQ
  IFEKRVGGMY LGELFRRALF HLIKVYNFNE GIFPPSITDA
  WSLETSVLSR MMVERSAENV RNVLSTFKFR FRSDEEALYL
  WDAAHAIGRR AARMSAVPIA SLYLSTGRAG KKSDVGVDGS
  LVEHYPHFVD MLREALRELI GDNEKLISIG IAKDGSGIGA
  ALCALQAVKE KKGLA MEANFQQAVK KLVNDFEYPT ESLREAVKEF
  DELRQKGLQK NGEVLAMAPA FISTLPTGAE TGDFLALDFG
  GTNLRVCWIQ LLGDGKYEMK HSKSVLPREC VRNESVKPII
  DFMSDHVELF IKEHFPSKFG CPEEEYLPMG FTFSYPANQV
  SITESYLLRW TKGLNIPEAI NKDFAQFLTE GFKARNLPIR
  IEAVINDTVG TLVTRAYTSK ESDTFMGIIF GTGTNGAYVE
  QMNQIPKLAG KCTGDHMLIN MEWGATDFSC LHSTRYDLLL
  DHDTPNAGRQ IFEKRVGGMY LGELFRRALF HLIKVYNFNE
  GIFPPSITDA WSLETSVLSR MMVERSAENV RNVLSTFKFR
  FRSDEEALYL WDAAHAIGRR AARMSAVPIA SLYLSTGRAG
  KKSDVGVDGS LVEHYPHFVD MLREALRELI GDNEKLISIG
  IAKDGSGIGA ALCALQAVKE KKGLA

72

• gtultimate-sequence
• ACTCGTTATGATATTTTTTTTGAACGTGAAAATACTTTTCGTGCTATGGA
  AGGACTCGTTATCGTGAAGTTGAACGTTCTGAATGTATGCCTCTTGAAAT
  GGAAAATACTCATTGTTTATCTGAAATTTGAATGGGAATTTTATCTACAA
  TGTTTTATTCTTACAGAACATTAAATTGTGTTATGTTTCATTTCACATTT
  TAGTAGTTTTTTCAGTGAAAGCTTGAAAACCACCAAGAAGAAAAGCTGGT
  ATGCGTAGCTATGTATATATAAAATTAGATTTTCCACAAAAAATGATCTG
  ATAAACCTTCTCTGTTGGCTCCAAGTATAAGTACGAAAAGAAATACGTTC
  CCAAGAATTAGCTTCATGAGTAAGAAGAAAAGCTGGTATGCGTAGCTATG
  TATATATAAAATTAGATTTTCCACAAAAAATGATCTGATAA

73

• my AA1 (
• 'UUU','F',
• 'UUC','F',
• 'UUA','L',
• 'UUG','L',
• 'UCU','S',
• 'UCC','S',
• 'UCA','S',
• 'UCG','S',
• 'UAU','Y',
• 'UAC','Y',
• 'UAA','',
• 'UAG','',
• 'UGU','C',
• 'UGC','C',
• 'UGA','',
• 'UGG','W',
• 'CUU','L',