2 Perl What is Perl http www perl

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2. Perl – What is Perl ? http: //www. perl. org • Practical Extraction

2. Perl – What is Perl ? http: //www. perl. org • Practical Extraction and Report Language • Interpreted Language – Optimized for String Manipulation and File I/O – Full support for Regular Expressions

2. Perl – Running Perl Scripts – Download Active. Perl from Active. State –

2. Perl – Running Perl Scripts – Download Active. Perl from Active. State – Just run the script from a 'Command Prompt' window or a ‘Terminal' – Put the following in the first line of your script #!/usr/bin/perl or #!C: /Strawberry/perl/bin/perl. exe – Run the script perl script_name. pl

2. Perl – Basic Syntax • Statements end with semicolon ‘; ’ • Comments

2. Perl – Basic Syntax • Statements end with semicolon ‘; ’ • Comments start with ‘#’ – Only single line comments • Variables – You don’t have to declare a variable before you access it – You don't have to declare a variable's type

2. Perl – Scalars and Identifiers • Identifiers – A variable name – Case

2. Perl – Scalars and Identifiers • Identifiers – A variable name – Case sensitive • Scalar – A single value (string or numerical) – Accessed by prefixing an identifier with '$' – Assignment with '=' $scalar = expression

2. Perl – Strings • Quoting Strings $output='Hellon. World!'; print $output; – With '

2. Perl – Strings • Quoting Strings $output='Hellon. World!'; print $output; – With ' (apostrophe) • Everything is interpreted literally – With " (double quotes) $output="Hellon. World!"; print $output; • Variables get expanded – With ` (backtick) • The text is executed as a separate process, and the output of the command is returned as the value of the string print `java -version`;

2. Perl – Comparison Operators String Operation Arithmetic lt less than < gt greater

2. Perl – Comparison Operators String Operation Arithmetic lt less than < gt greater than > eq equal to == le less than or equal to <= ge greater than or equal to >= ne not equal to != cmp compare, return 1, 0, -1 <=> 0 1 2 3 4 5 6 7 8 9 符号 A B C … X Y Z a b c … x y z 由小到大

2. Perl – Logical Operators Operator Operation ||, or logical or &&, and logical

2. Perl – Logical Operators Operator Operation ||, or logical or &&, and logical and !, not logical not xor logical xor a xor b = (a' and b) or (a and b')（a'为非a）

2. Perl – String Operators Operator Operation . string concatenation x string repetition .

2. Perl – String Operators Operator Operation . string concatenation x string repetition . = concatenation and assignment $string 1 = "potato"; $string 2 = "head"; $newstring = $string 1. $string 2; #"potatohead" $newerstring = $string 1 x 2; #"potato" $string 1. = $string 2; #"potatohead"

2. Perl – Perl Functions • Perl functions are identified by their unique names

2. Perl – Perl Functions • Perl functions are identified by their unique names (print, chop, close, etc) • Function arguments are supplied as a comma separated list in parenthesis. – The commas are necessary – The parentheses are often not – Be careful! You can write some nasty and unreadable code this way!

2. Perl - Arrays • A named list – Dynamically allocated, can be saved

2. Perl - Arrays • A named list – Dynamically allocated, can be saved – Zero-indexed – Shares list operations, and adds to them • Array Operators – @: reference to the array (or a portion of it, with []) – $: reference to an element (used with []) – Eg. @arr = ("A", "T", "C", "G"); print $arr[2]; print @arr[1, 3]; print @arr; print "@arr"; $x = @arr; 返回@arr中元素的个数

指令：shift 语法：shift(@array) 说明：将数组@array的第一个元素删除，并将删除的元素返回。 示例：@array=("one", "two"); $rm=shift(@array); #这时 @array=("two"); 而$rm="one"; 指令：push 语法：push(@array, $newelement/@newarray) 说明：在数组@array的最后加新的元素到数组@array中。 示例：@array=("one",

指令：shift 语法：shift(@array) 说明：将数组@array的第一个元素删除，并将删除的元素返回。 示例：@array=("one", "two"); $rm=shift(@array); #这时 @array=("two"); 而$rm="one"; 指令：push 语法：push(@array, $newelement/@newarray) 说明：在数组@array的最后加新的元素到数组@array中。 示例：@array=("one", "two"); push(@array, "three"); #这时 @array=("one", "two", "three") 指令：unshift 语法：unshift(@array, $newelement/@newarray) 说明：在数组@array的 第一个元素前附加新的元素到数组@array中。 示例：@array=("one", "two"); unshift(@array, "three"); #这时 @array=("three", "one", "two") 指令：join 语法：join($string, @array) 说明：在一数组@array的元素之间加上一指定的字符$string, 并将结果返回。 示例：@array=("one", "two", "three"); $total=join("：", @array); 这时$total="one：two：three";

#!/usr/bin/perl # Simple List operations # Address an element in the list @string. Instruments

#!/usr/bin/perl # Simple List operations # Address an element in the list @string. Instruments = ("violin", "viola", "cello", "bas s"); @brass = ("trumpet", "horn", "trombone", " euphonium", "tuba"); $biggest. Instrument = $string. Instruments[2]; print("The biggest instrument: ", $biggest. Instrument, "n"); # Join elements at positions 0, 1, 2 and 4 into a white-space delimited string print("orchestral brass: ", join(" ", @brass[0, 1, 2, 4]), "n"); ################ @unsorted_num = ('3', '5', '2', '1', '4'); @sorted_num = sort( @unsorted_num ); # Sort the list print("Numbers (Sorted, 1 -5): ", @sorted_num, "n"); Array Example #Add a few more numbers @numbers_10 = @sorted_num; push(@numbers_10, ('6', '7', '8', '9', '10')); print("Numbers (1 -10): ", @numbers_10, "n"); # Remove the last pop(@numbers_10); print("Numbers (1 -9): ", @numbers_10, "n"); # Remove the first shift(@numbers_10); print("Numbers (2 -9): ", @numbers_10, "n"); # Combine two ops print("Count elements (2 -9): ", scalar( @numbers_10 ), "n");

2. Perl – if 语句 #!/usr/bin/perl $a=10; $b=15; if ($a > $b) { print

2. Perl – if 语句 #!/usr/bin/perl $a=10; $b=15; if ($a > $b) { print "a=$a is bigger!"; } else { print "b=$b is bigger!"; } ###### • if 和 else 可以不成对出 现，即，可以只有if没有else if ($a == 5) • elsif可以有许多个 { print '$a is 5'; } elsif ($a == 10) { print '$a is 10'; } elsif ($a == 15) { print '$a is 15'; } else { print '$a is not (5 or 10 or 15)'; }

2. Perl – for 语句 #!/usr/bin/perl @a=(1, 12, 33, 25, 98, 34, 55, 76,

2. Perl – for 语句 #!/usr/bin/perl @a=(1, 12, 33, 25, 98, 34, 55, 76, 18, 10); $n=scalar(@a); for ($i=0; $i<$n; $i++) { print "No. $i = $a[$i]n"; } ###### foreach (@a) { if ($_ % 2 == 0) { print "$_ is even. n"; } else { print "$_ is odd. n"; } } • foreach语句中， 用$_代表抓到的每一个 当前变量。

2. Perl – Pattern Matching • A pattern is a sequence of characters to

2. Perl – Pattern Matching • A pattern is a sequence of characters to be searched for in a character string – /pattern/ • Match operators – =~: tests whether a pattern is matched – !~: tests whether patterns is not matched • Match & Substitute – Match: m/pattern/ or /pattern/ – Substitute: s/pattern 1/pattern 2/

2. Perl – Regular Expression 模式的匹配： 可以用（）捕获特定的模式 并依次存入 $1 $2 $3 中 $output="robert 27

2. Perl – Regular Expression 模式的匹配： 可以用（）捕获特定的模式 并依次存入 $1 $2 $3 中 $output="robert 27 mn 2013"; if ($output =~ m/([a-z]+)s+(d{1, 3})s+[mf]s+2013$/) { print "name: $1nage: $2"; }

2. Perl – File I/O #读入文件 #续写文件 “>>” open(FH, "test. pdb"); @get=<FH>; close FH;

2. Perl – File I/O #读入文件 #续写文件 “>>” open(FH, "test. pdb"); @get=<FH>; close FH; open(FH, ">>test 2. pdb"); print FH $get[1]; close FH; print $get[0]; #覆盖写文件 “>” #写入文件 open(FH, ">test 2. pdb"); print FH $get[1]; close FH; open(FH, ">test 2. pdb"); print FH $get[0]; close FH;

2. Perl – File I/O #屏幕输入 print "What's your name? n"; $name = <STDIN>;

2. Perl – File I/O #屏幕输入 print "What's your name? n"; $name = <STDIN>; #$name由屏幕输入赋值 chomp($name); #去掉$name末尾的n, 如果有 print "Hello $name!";

2. Perl – Web Connection #!/usr/bin/perl use LWP: : Simple; $url='http: //www. uniprot. org/uniprot/Q

2. Perl – Web Connection #!/usr/bin/perl use LWP: : Simple; $url='http: //www. uniprot. org/uniprot/Q 6 GV 17. fasta'; $content = get $url; die "Couldn't get $url" unless defined $content; print $content; ###### open (FH, ">seq. fasta"); @ids=("Q 6 GV 17", "Q 9 BXR 5", "B 3 Y 669", "C 0 LSK 8"); foreach (@ids) { $url="http: //www. uniprot. org/uniprot/$_. fasta"; $content = get $url; print FH "$content"; } close FH;

2. Perl –Example #!/usr/bin/perl use LWP: : Simple; print "Please enter the Uniprot ID:

2. Perl –Example #!/usr/bin/perl use LWP: : Simple; print "Please enter the Uniprot ID: n"; $id = <STDIN>; chomp $id; $url="http: //www. uniprot. org/uniprot/$id. fasta"; $content = get $url; die "Couldn't get $url" unless defined $content; @get 1 = split(/n/, $content); $count_aa=0; shift @get 1; while ($sequence =~ m/$aa/ig) $sequence = join("", @get 1); { $count_aa++; } print "Which amino acid? n"; $aa = <STDIN>; chomp $aa; $len = length($sequence); $aa_percent=$count_aa/$len; print "$aa in $id: $aa_percent";

3. HTML文档的结构： <HTML> <HEAD> <!--头部信息--> <title>My Site</title> <meta http-equiv="Content-Type" content="text/html; charset=gb 2312"/> </HEAD> <BODY>

3. HTML文档的结构： <HTML> <HEAD> <!--头部信息--> <title>My Site</title> <meta http-equiv="Content-Type" content="text/html; charset=gb 2312"/> </HEAD> <BODY> <!--文档主体，正文部分--> </BODY> </HTML>

• 表格标签： <table border="1" width="300" height="300"> <th>姓名</th> <th>性别</th> <tr> <td align=“center”><b>张三</b></td> <td>女</td> </tr>

• 表格标签： <table border="1" width="300" height="300"> <th>姓名</th> <th>性别</th> <tr> <td align=“center”><b>张三</b></td> <td>女</td> </tr> <td align="center" colspan="2">李四</td> </tr> </table> <table border="1" width="300" height="300"> <th>姓名</th> <th>性别</th> <tr> <td align=“center” rowspan=“ 2”><b>张三</b></td> <td>女</td> </tr> <td>男</td> </tr> </table>

3. HTML 常用的标签： • 表单标签： <html> <body> <FORM action=". . /cgi-bin/test. cgi" method="post" enc.

3. HTML 常用的标签： • 表单标签： <html> <body> <FORM action=". . /cgi-bin/test. cgi" method="post" enc. Type="multipart/form-data"> <input name="name" size="40"/> <input type="submit" name="submit" value="submit"/> </FORM> </body> </html> 源文件 test. html 文件 网页

3. HTML 常用的标签： • 表单标签： #!/usr/bin/perl use CGI; $cgi = new CGI; $name =

3. HTML 常用的标签： • 表单标签： #!/usr/bin/perl use CGI; $cgi = new CGI; $name = $cgi->param("name"); print $cgi->header( -type=> "text/html"); print "<p>Hallo $name!</p>"; 源文件 test. cgi 文件

3. HTML 常用的标签： • 表单标签： name: <input name="name" size=“ 40"/> <input type="radio" name="sex" value="male"

3. HTML 常用的标签： • 表单标签： name: <input name="name" size=“ 40"/> <input type="radio" name="sex" value="male" /> Male <br/> <input type="radio" name="sex" value="female" /> Female <input type="checkbox" name="fruit" value="apple">apple<br/> <input type="checkbox" name="fruit" value="mango">mango<br/> <textarea name="comment" rows="3" cols="20"> xxx </textarea> <input type="submit" name="submit" value="submit"/>

http: //www. w 3 school. com. cn/tags/index. asp

http: //www. w 3 school. com. cn/tags/index. asp

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