Mac Unix & Perl
[*]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 =~ //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") or die "error reading $ARGV for reading";
open(OUT, ">$ARGV.munge") or die "error creating $ARGV.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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