[Study Notes] Bioinformatics of Shandong University - Perl Language Basics + Advanced

8.3 Getting Started with Perl Language Basics

• See the video for details: Introduction to Perl Language Basics-01 P137

● Perl : Free download from the official website of Practical Extraction and Report Language (may not be opened if the network is not good), and supports multiple operating systems

• Literal translation language : Interpreted Language
• Sequence processing : especially suitable for string (sequence) processing
• File processing : convenient and concise file writing and writing
• Pattern matching : full support for regular expressions

8.3.1 The first Perl

• Create a text file named test.pl
• The first line writes Perl execution environment (installation path)
  linux writes: #!/usr/bin/perl
  Windows writes:#!C:/Strawberry/perl/bin/perl.exe
• The second line writes a simple statement, such as:print "He1lo world!";
• Save test.pl and open the cmd command window.
• Change to the directory where test.pl is located.cd Desktop
• Execute perl test.plthe command to run your first program.
  

8.3.2 Basic rules of Perl

• Each statement must be followed by " ;".
• Add " " in front of the comment# , it is only valid for a single line .
• The definition of variables is extremely simple and casual:
  ◆ There is no need to declare variables in advance, and they can be defined as they are used;
  ◆ There is no need to define variable types , and the program will automatically judge after assignment ;
  ◆ Variable names are case-sensitive , start with a letter , and cannot have special characters ;
  ◆ Variable names Add " $" in front, use " " =to assign value.$scalar = expression

● The use of various quotation marks :

• Single quotes'' completely literal translation of everything inside quotes.
  
• Double quotes can identify ""variables and antonyms in quotes .
  
• Backticks execute ``the content inside the quotes as a command .
  

● The use of various operators :

• Comparison Operators Comparison Operators: Comparison operators
  for strings are different from comparison operators for numbers !
  ◆ Numbers are smaller than letters !
  ◆ Uppercase letters are smaller than lowercase letters!
  ◆ From small to large : numbers [0-9], uppercase letters [AZ], lowercase letters [az]
  

• Logical Operators Logical Operators:
  You can write directly: or, and, not
  or use symbols instead: ||, &&, !
  Special logical operators: xor XOR
  △ a xor b = (a' and b) or (a and b')(a' = not a)
  If the two values ​​of a and b are not the same , the XOR result is 1. If the two values ​​of a and b are the same , the XOR result is 0.

• String Operators String Operators:
  .string splicing and concatenation
  x , repeated copying of strings, assignment of
  .= strings after splicing and concatenation

  $string1 = "potato";
  $string2 = "head";
  $string3 = $string1 . $string2;	#patatohead
  $string4 = $string1 x 2;		#patato
  $string1 .= $string2; 			#string1 = patatohead
  

8.3.3 String Common Functions

• Perl has many pre - defined functions: 函数名 ( 参数 1, 参数 2,... 参数 n)
  Note: the commas
  between the parameters are essential , and the parentheses surrounding the parameters are optional
  

• lengthFunction:
  Syntax: length($string);
  Description: Find the byte value (length) of the string $string.

  $string="Per15";
  $size=length($string); #这时 $size=5
  
  #计算一条氨基酸序列的长度
  $seq="GHMGSSVLEELVQLVKDKNIDISIKYDPRKDSEVEANRVITDDIELLKKILAYFLPEDAILKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAE";
  $len=length($seq);
  print "The protein contains $len amino acids.";
  

• substrFunction:
  Syntax: substr($string, offset, 1ength);
  Description: Intercept the substring of the string $string .
  ★ Note: The first digit is 0, not 1.
  offsetRepresents the position of the starting character , and if offset is a negative value , the specified character will start from the right side of the string .
  lengthRepresents the length of the referenced string. If length is omitted , it represents the length from the start value to the last character of the string.
  

  $s1=substr("perl5",2,2);   	#$s="rl" 从第二个字符串后开始截取 2 个字符串
  $s2=substr("perl5",1);   	#$s="erl5" 从第一个字符串后开始截取剩余字符串
  $s3=substr("perl5",-5,3);    #$s="per" 从倒数第五个字符串开始截取 3 个字符串
  
  #提取出蛋白质序列的功能区，功能区位于第 12 个氨基酸到第 23 个氨基酸。
  $seq="GHMGSSVLEELVQLVKDKNIDISIKYDPRKDSEVEANRVITDDIELLKKILAYFLPEDALKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAE";
  $begin=11;
  $end=22;
  $length=$end-$begin+1; 
  $region=substr($seq, $begin, $length);
  print "The functional region is $region.";
  

• indexFunction:
  Syntax: index($string, $substring, position)
  Description: Return the position of the character you want to find$substring in the string ($stringreturns only the first position found) and returns if not found-1 . $substringIt is the character to be searched for ;
  positionit represents the position from which to start searching, if omitted, it will start from the beginning .

  $s1=index("pell5","p");		#$s1=0
  $s2=index("pell5","l",2);	#$s2=2  只返回找到的第一个位置
  $s3=index("pell5", "perl");	#$s3=-1
  
  #查找某功能区在一条蛋白质序列里的位置。
  $seq="GHMGSSVLEELVQLVKDKNIDISIKYDPRKDSEVEANRVITDDELLKKILAYFLPEDAILKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAE";
  $region="KEFLESSPNT";
  $begin=index($seq, $region)+1;  #起始位置，注意获取 index 后加一
  $end=$begin+length($region)-1;  #结束位置，注意减一
  $begin_aa=substr($region,0,1);  #第一个氨基酸
  $end_aa=substr($region,-1,1); #最后一个氨基酸
  print "The functional region is from $begin_aa$begin to $end_aa$end.";
  

8.3.4 Array common functions

• An Array is a set of elements enclosed in parentheses() .
  - Elements can be any value or empty , separated by commas
  - The number of elements can be increased or decreased
  at any time - Arrays are @represented by symbols, for example: - An element@arr("A","T","C","G")
  in an array is equal to a variable , written as:$arr[index_number]

  print $arr[0];  #A
  print $arr[1,3]; #TG
  print @arr; #ATCG
  

• scalarFunction: Number of elements
  Syntax: scalar(@array)
  Description: Returns the number of elements@array in the array .

  @arr=("A","B","C"); #定义一个数组
  $num=scalar(@arr); #这时$num=3
  
  #批量处理一组 Uniprot ID 前，先数数这一组 ID 的个数。
  @ids=("Q6GV17", "Q9BXR5", "B3Y669", "COLSK8");
  $count=scalar(@ids);
  print "$count ids : @ids";
  

• reverseFunction: Reverse Order
  Syntax: reverse(@array)
  Description: Reversely arrange@array the elements in the array from back to front .

• sortFunction: Ascending
  Syntax: sort[{$a<=>$b}](@array)
  Description: Sort @arraythe elements in the array in ascending order of ASCII codes . After adding, sort by numerical size .{$a<=>$b}

  @arr1=(21,1,2,12);
  @arr2=reverse(@arr1); #@arr2=(12,2,1,21); 元素逆序
  @arr3=sort(@arr); #@arr2=(1,12,2,21) 按字符串大小排序
  @arr4=sort{
        
        $a<=>$b}(@arr); #@arr3=(1,2,12,21) 按数字大小排序
  
  #将一组计算结果数值升序/降序排列。
  @value=(10,34,24,16,4,7);
  @value1=sort{
        
        $a<=>$b}(@value);  # 升序
  @value2=reverse(@value1); # 降序
  print "ascending order : @value1\n";  #\n 代表换行
  print "descending order : @value2";
  

• popFunction: Delete the last
  Syntax: pop(@array)
  Description: Delete the last element@array of the array and return the deleted element .

  @arr=("A","B","C");
  $rm=pop(@arr); #@arr=("A", "B"), $rm="C" 
  

• pushFunction: Add at the end
  Syntax: push(@array，$newelement/@newarray)
  Description: Add a new element or a new array@array at the end of the array .

  @arr=("A","B","C") ;
  push(@arr,"D") ;  #@arr=("A", "B","C","D")
  
  #由大到小排序，同时去掉最小值，并在最后添加元素的个数。
  @value=(10,34,24,16,4,7);
  @value1=sort{
        
        $a<=>$b}(@value);
  @value=reverse(@value);
  pop(@value);
  push(@value, scalar(@value)); 
  print "new value : @value";
  

• shiftFunction: Delete the first
  Syntax: shift(@array)
  Description: Similar to pop, delete the first element@array of the array and return the deleted element .

  @arr=("A","B","C");
  $rm=shift(@arr); #@arr=("B", "C"), $rm="A" 
  

• unshiftFunction: Add in front
  Syntax: unshift(@array，$newelement/@newarray)
  Description: Similar to push, add a new element or a new array at the front@array of the array .

  @arr=("A","B");
  unshift(@arr,"X") ;  #@arr=("X", "A","B")
  
  #由大到小排序，同时去掉最大值，并在最前面添加元素的个数。
  @value=(10,34,24,16,4,7);
  @value1=sort{
        
        $a<=>$b}(@value);
  @value=reverse(@value);
  shift(@value);
  unshift(@value, scalar(@value)); 
  print "new value : @value";
  

• joinFunction: Concatenation :
  Syntax: Description: Concatenate the elements in the array into a string join($string, @array)
  with the specified character , and return the string as the result.$string@array

  @arr=("A" , "B" , "C") ;
  $get=join(":", @arr);  #$get="A:B:C"
  

• splitFunction: Split :
  Syntax: split(/pattern/, $string)
  Description: Split the string $stringaccording to pattern( delimiter ), and put the split result into an array .

  $seq="15:32:54";
  @arr=split(/:/, $seq) ; #@arr=("15","32","54")
  
  # 获取 FASTA 格式序列的纯序列部分。
  $fasta=">sp|P33316|DUT_HUMAN
  MTPLCPRPALCYHFLTSLLRSAMQNARGARQRA
  EAAVLSGPGPPLGRAAQHGIPRPLSSAGRLSQG 
  CRGASTVGAAGWKGELPKAGGSPAPGPETP";
  @line=split(/\n/, $fasta); # 按换行符分割成行数 n 个字符串并放入数组 line
  shift(@line); # 去掉数组中的第 1 个字符串，即">"开头的第一行
  $seq=join("", @line); #拼接其他字符串，即纯序列
  print $seq;
  

---

8.4 Perl Language Basics Advanced

8.4.1 if conditional statement

● Grammar one :

• The " condition " of the if conditional statement is placed in parentheses, ()and
  the "condition" in the parentheses is a logical expression.
  If the logical expression is judged as true: execute the statement in ifthe following curly braces If the logical expression is judged as : execute the statement in the following curly braces Note : if and else can not appear in pairs , that is, there can be only if without else, but not only else without if!{}
falseelse{}
  

  $a=10;
  $b=15;
  if ($a > $b) {
        
        
      print "a is bigger!";
  }
  else {
        
        
      print "b is bigger!";
  }
  

●Grammar two :

• If logical expression 1 is judged as true: execute statement1
• If the logical expression 1 is judged as false:
  continue to judge elsifthe following logical expression 2
  If the logical expression 2 is judged to be true: execute statement2
  If the logical expression 2 is judged to be false: execute statement3

  if ($a == 5) {
        
        
      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)';
  }
  

8.4.2 for loop statement

●grammar one：for

1. init will be executed first, and will only be executed once. This step is to declare and initialize the loop control variables. For example:$i=1;
2. Next, the condition will be judged . If true, the loop body is executed. If false, no execution. for example:$i<10;
3. After executing the loop body, the flow of control jumps back to the increment statement and updates the loop control variable. for example:$i++
4. Judge the condition again , and repeat the above process until the condition becomes false, and the loop terminates.

   # 九九乘法表
   for ($i=1; $i<10; $i++) {
         
         
       for($j=1; $j<10; $j++) {
         
         
           $x=$i*$j;
           print "$i x $j = $x\t";
       }
       print "\n";
   }
   

● grammar two：foreach

foreach (@array) {
    
    
    statement1;
    ……
}

1. For @arrayeach element in the array, execute the body of the loop. ( traversing the array )

2. Use the variable to represent the current element$_ captured in the current cycle .

3. After each element in the array is rotated in turn, the loop ends.

   # 奇数偶数？
   @a=(1, 12, 33, 25, 98, 34, 55, 76, 18, 10);
   
   foreach (@a) {
         
         
       if ($_ % 2 == 0)  # % 取余数
       {
         
           print "$_ is even. \n"; }
       else 
       {
         
           print "$_ is odd. \n"; }
   }
   

8.4.3 File reading and writing

• Read in file :
  open(FH, "read.txt");Open the read.txt file in the current path. FH is the identifier of a file read and write event, and the name can be defined by itself.
  @get = <FH>;Store the read file content into an array @get, and divide the elements according to the newline "\n" , that is, one element per line .
  close FH;After reading, close the file flag FH.

  open(FH, "read.txt");
  @get = <FH>;
  close FH;
  

• Write file :
  open(FH, ">write.txt");open/create the write.txt file in the current path, and write content to it. " >" means to write out , and the original content in the file will be overwritten .
  print FH "Hello world!\n";"print FH" means to write out the contents of the double quotes to the file represented by the file identifier FH instead of writing to the screen.
  close FH;After writing, close the file flag FH.

  open(FH, ">write.txt");
  print FH "Hello world!\n";
  close FH;
  

• Continue writing file :
  open(FH, ">>write.txt");open/create the write.txt file in the current path, and write content to it. " >>" stands for continuation , and the original content in the file will not be overwritten .
  print FH "Hello world!\n";Write the same file.
  close FH;After writing, close the file flag FH.

  open(FH, ">>write.txt");
  print FH "Hello world!\n";
  close FH;
  

• Screen input :
  print "What's your name?\n";The screen prints a sentence
  $name = <STDIN>; to STDIN indicating that the value $nameshould be assigned through screen input . The cursor will stay there waiting for the user to input content, and press Enter after input.
  chomp($name); The chomp function is used to remove the carriage return at the end of the input content on the screen .
  print "Hello $name!";Print the obtained screen input value.

  print "What's your name?\n";
  $name = <STDIN>;
  chomp($name);
  print "Hello $name!";
  

8.4.4 Get the download page

• Basic statement :

# 引用 LWP 模块，以使用 get 函数
use LWP::Simple;  
# 将一个 FASTA 序列的网址赋值给变量 $url
$url='http://www.uniprot.org/uniprot/Q6GV17.fasta';  
# get 函数获取$url 网址打开页面的全部内容（获取页面源代码）
$content = get $url; 
# 如果网址无法打开，die 函数将强制结束程序，并屏幕打印告知。
die "Couldn't get $url" unless defined $content;
# 将获取的网页内容打印出来。
print $countent;

8.4.5 Application example: Batch download and save sequence

• Batch download and save sequences

use LWP::Simple;  
open (FH, ">seq.fasta");
@ids= ("Q6GV17" , "Q9BXR5" , "B3Y669" , "COLSK8");
foreach (@ids) {
    
    
    $url= "http://www.uniprot.org/uniprot/$_.fasta";
    $content = get $url;
    die "Couldn't get $url" unless defined $content;
    print FH "$countent";
}
close FH;