生物資訊程式語言應用 Part 3

生物資訊程式語言應用 Part 3 Perl Language

Outline • Introduction. • Installation. • Background knowledge in Perl. • Data type. • Control structure. • Regular expression. • Overall practice.

Introduction • Perl is free software. • Larry Wall (He is a linguist). • The history of Perl language. • 1987- Perl 1.0. • 1994 - Perl 5 (contain OOP). • OOP (object oriented programming) 物件導向程式語言 • Perl 5.8.0 – support unicode. • 2003 – Perl 6. • Now. • Characteristic. • The script language base on C language (具跨平台的特性).

Installation • Perl is the default language in any distribution of Linux. • Perl can be executed and worked by the ActivePerl package in windows platform. • http://www.activestate.com/activeperl/ • How to edit Perl program? • Notepad in windows, UltraEdit and any text editor.

Installation cont. • Practice. • Download ActivePerl software file. • Install ActivePerl.

Background knowledge • Data type in Perl. • Control structure in Perl. • Regular expression in Perl.

Data type in Perl • Like English • Scalar (純量變數) – 比喻單件事物. • 數字常數 $x = 5; • 字串常數 $y = “Hello” ; • The special expression of Perl. • Print “Hello” . ”World” ; (Hello World). • Print “Hello” * 2 ; (HelloHello). • 字串與數字間的轉換 • $x = 123; $y = “456”; • Print $x + $y ; (數字) • Print $x . $y ;(字串)

Data type in Perl cont. • Practice. • Using scalar. • Special expression. • 字串與數字間的轉換.

Data type in Perl cont. • Array (陣列). • The definition of Array in Perl. • @student=("9154610","9154611",”9154612”); • my @student; • $student[0] ="9154610“; $student[1] =“9154611“; $student[2] =“9154611”; • Array 單數的取用. • print $student[0],"\n"; • print "$student[1]\n"; • print $student[2]."\n"; • Array 複數的取用. • print @student,“\n”; (全部一起print出來) • 以單數取用方式print出複數資料 (in control structure chapter).

Data type in Perl cont. • Practice. • Using array (definition). • 單數取用. • 複數取用.

Data type in Perl cont. • Hash (雜湊). • $純量 = 單一 = 單數 • @陣列 = 串列 = 複數 • %雜湊 = 串列 = 複數 • 定義陣列 = 類似ip • @student=("9154610","9154611",”9154612”); • 定義雜湊 = 類似dns • %students = ("Peter"=>"9154610" , "Mary"=>"9154611" , "Cathy"=>"9154612");

Data type in Perl cont. • Hash (雜湊). • 定義雜湊 = 類似dns • %students = ("Peter"=>"9154610" , "Mary"=>"9154611" , "Cathy"=>"9154612"); • Hash 單數的取用. • print $students{"Peter"},"\n"; • print $students{"Mary"},"\n"; • print $students{"Cathy"},"\n"; • Hash 複數的取用. • print %students,"\n"; • 以單數取用方式print出複數資料 (in control structure chapter).

Data type in Perl cont. • Practice. • Using hash (definition). • 單數取用. • 複數取用.

Control structure in Perl • If statement (陳述式). • For loop (迴圏). • Foreach loop (迴圏). • While loop (迴圏).

Control structure in Perl cont. • If statement (陳述式). If 條件判斷 If 條件成立則執行若If 條件不成立則執行 (else statement可有可無)

Control structure in Perl cont. • Practice. • If statement. • If - else statement.

Control structure in Perl cont. • For loop (迴圏). $#array : 取得array的大小 $i++ : 等同於 $i = $i + 1; $sum += $i : 等同於 $sum = $sum + $i;

Control structure in Perl cont. • Practice. • For loop 迴圏. • 以array單數取用方式print出array複數資料. • 以hash單數取用方式print出hash複數資料.

Control structure in Perl cont. • Foreach loop (迴圏). • Like for loop. For loop Foreach loop

Control structure in Perl cont. • Practice. • Foreach loop (迴圏). • 以array單數取用方式print出array複數資料. • 以hash單數取用方式print出hash複數資料.

Control structure in Perl cont. • While loop (迴圏). While 判斷式

Control structure in Perl cont. • Practice. • While loop (迴圏). • 1+2+…+100.

Regular expression in Perl • 樣式 (pattern) 的表達. • 繫結符號 =~. • =~可用來將右邊的樣式比對左邊的字串純量，成功傳回1，失敗傳回0. • 表否定則可改用!~ • 通常搭配判斷式使用.

Regular expression in Perl cont. • 比對. • $` : 代表字串中比對成功之前的部分. • $& : 代表字串中比對成功的部分. • $‘ : 代表字串中比對成功之後的部分.

Regular expression in Perl cont. • 字元取代. • $var =~ tr/xxx/yyy/ • 把變數 $var 內的 xxx 字元都逐一代換成 yyy 字元 • 字串取代. • $var =~ s/xxx/yyy/ • 把變數 $var 內的第一個 xxx 子字串整個代換成 yyy 子字串 • $var =~ s/xxx/yyy/ig • I : 忽略大小寫 • g : 取代 $var 字串內所有符合的子字串

Regular expression in Perl cont. • Practice. • 比對. • 字元取代. • 字串取代.

生物資訊程式語言應用 Part 3