Mac Unix & Perl

houbin

• On a Mac, plugged in drives appear as subdirectories in the special 'Volumes' directory.
  
• cd ~ and cd achieve the same thing: go to home directory (/Users/whatever)
  
• ls -l (L): list, the long version. ls -a: list all file(include hidden one).
  
• Space view next page, b view previous page，q to quit. j scroll down a line, k scroll up a line.(man man). h to bring up a help page.
  
• rm: remove file; rm -i *.txt: ask for confirmation before deleting; rmdir: remove a directory(empty), mkdir: generate a directory. mkdir -p Temp1/Temp2
  
• touch: to create a new, empty file. eg: touch heaven.txt.
  
• mv: move files. mv heaven.txt Temp/
  
• wildcard: ? caracterizing a single character, and * means everything that matches.
  
• cp: copy file. the default behavior of copy is to overwrite. cp -R Storage Storage1: copy directory.
  
• less: to view text files, not edit.
  
• ls -l: add a letter d to specify that it is a directory. ls -p use trailing slash.
  
• $ alias ls='ls -p' make ls equals ls -p. Aliases only exist in the current terminal session.
  
• nano profile: create a text editor file named profile. write into it and save(Ctrl + O):
  
  
  # some useful command line short-cuts
  alias ls='ls -p'
  alias rm='rm -i'
  
• 
  
  
  $ source profile
  
  　　to tell Unix to read the contents of a file and treat it as a series of Unix commands
  
  
• to show hidden files on mac:
  
  
  • defaults write com.apple.finder AppleShowAllFiles 1
    
  
  
• turn off hidden files on mac: ("killall finder" to see effect)
  
  
  • defaults write com.apple.finder AppleShowAllFiles 0
    
  
  
• Type: source /Volumes/USB/Unix_and_Perl_course/.profile each time when you open terminal.
  
  
• grep: search for matched lines, -v to invert. -i to ignore case. -c to count.
  
• 
  
  
  $ grep "ATGTGA" intro_IME_data.fasta | less
  $ grep -i ACGTC * | head 　　                #show first 10 lines of matched item
  $ head -n 1 chr1.fasta | sed 's/Chr1/Chromosome 1/'   # head -n 1 means the first line. sed to substitute.
  　　concept of pipe. then press "/" to search some kind of pattern say "ATGTGA", "?" to search backward
  
  
  
  
• wc At_genes.gff; wc -l At_genes.gff: wc count lines, words, bytes, -l count only lines.
  
• 
  
  
  #!/usr/bin/perl
  # scalar.pl by Wade
  use warnings；
  $x = 3;
  print($x,"\n");
  
  　　the first line tell us that we can type: $ scalar.pl instead of $ perl scalar.pl.
  
  
• Any text between single quotes will print exactly as shown: print '$x $s\n'  #=> $x $s\n
  
• if we turen on strict: use strict; it becomes mandatory to say whether the variable is a local or global variable.
  
  
  • 
    
    
    my $pi = 3.14;
    
    　　my: means this is a local variable.
    
    
  
  
• eq (equal to); ne (not equal to); gt (greater than); lt (less than); . (concatenation); cmp (comparison);
  
• print $x == $y ? "yes\n" : "no\n";
  
• method, length(); ord() : convert to number; chr() : convert to letters;
  
• =~ m// equals =~ // : matching; != // : not matching; =~ s/// : substitution(the first met) =~ s///g(global); =~ tr/// : transliteration;
  
• 
  
  
  die "non-DNA character in input\n" if ($input =~ /[efijlopqxz]/i);
  
  　　die ... if syntax : to stop perl if necessary.
  
  
• 
  
  
  $sequence =~ tr/A-Z/a-z/;
  push @animals, "fox";
  my $length = @animals;
  my @gene_names = qw(unc-10 cyc-1 act-1 let-7 dyf-2);
  my $joined_names = join(", ", @gene_names);
  my @digest = split("", $dna);  # split at every possible position at $dna (string);
  
  
  • 　　If you assign a list to a scalar variable, then the scalar variable becomes the length of the list.
    
  
  
• difference between :
  
  
  • $length = @animals;    # variable $length means the size of the array;
    
  • ($length) = @animals; # list ($length) contains one element of array @animals;
    
  
  
• Array:
  

• 
  
  
  
  • pop(@array); shift(@array); push(@array, "element"); unshift(@array, "element"); splice();
    
  • scalar(@array) : function that calculate the length of the array;
    
  • index at 1.2, 1.7, .. rounded to 2.  -1 means count from tail.
    
  
  
  

• @sorted_list = sort{$a <=> $b or uc($a) cmp uc($b)} @list;
  
• foreach $animal (@animals) {print "$animal\n"}
  
• for my $i (0..5) {print "$i\n"}
  
• 0 ""(null string) be considered false.
  
• next redo last => continue, redo, break;
  
• while(<>) equals while($_ = <>). chomp() function removes a \n character from the end of a line if present.
  
• 
  
  
  #!/usr/bin/perl
  # filemunge.pl
  use strict; use warnings;
  open(IN, "<$ARGV[0]") or die "error reading $ARGV[0] for reading";
  open(OUT, ">$ARGV[0].munge") or die "error creating $ARGV[0].munge";
  while(<IN>) {
  chomp;
  my $rev = reverse $_;
  print OUT "$rev\n";
  }
  close IN;
  close OUT:
  
• how to do I/Os: http://www.ualberta.ca/~hquamen/303/filehandles.html ; $! to store error messages. select handle. Perl now allows you to use a regular scalar as a filehandle.
  
• reverse() function both reverse arrays and strings.
  
• 
  
  
  #hash
  %genetic_code = (
  ATG => 'Met';
  AAA => 'Lys';
  CCA => 'Pro';        
  );
  foreach $key (keys %genetic_code) {
  print "$key $genetic_code{key}\n";   
  }
  if (exists $genetic_code{AAA}) {print "AAA codon has a value\n"}
  else 　　                      {print "No values set for AAA codon\n"}
  delete $genetic_code{AAA};
  　　The keys() function returns an array of keys, function values() returns an array of values.
  
  
• sort function: http://perldoc.perl.org/functions/sort.html
  
• varible $&: The string matched by the last successful pattern match.
  
• uc(), lc() function: make string uppercase or lowercase:
  
  
  my $str = "What is Perl Language for";
  lc($str);
  print $str, "\n";
  # displays: What is Perl Language for
  $str = lc($str);
  print $str, "\n";
  # displays: what is perl language for
  
• \s matches whitespaces \S matches non-whitespaces. "=~ m/[^ATGC]/i" (negated character class)
  
• 
  
  
  if($text =~ m/A{1,3}/) {...} # matches between 1 and 3 As
  if($text =~ m/C{42}/) {...} # matches exactly 42 Cs
  if($text =~ m/T{6,}/) {...} # matches at least 6 Ts
  # to match a "." you have to use backslash "\." eg. $sequence =~ m/A\. thaliana/ {...}
  my @fields = split; # \s+ or $_ are assumed, and space-delimited
  
• Regular expressions in list context return values from parenthesized patterns: my ($beg, $end) = $line =~ /(\d+)\.\.(\d+)/;
  
• file handler can only be processed one at a time. "If your inner loop is a filehandle iterator, then you will need to reset it."
  
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