Download Three main topics for this Intro lecture

Bioinformatics
生物信息学理论和实践
唐继军
[email protected]
13928761660
More Conditions
But
• Use ==, <, <=, >, >=, !=, ||, && for numeric
numbers
• Use eq, lt, le, gt, ge, ne, or, and for string
comparisons
More Arithmatics
• +, -, *, **, /, %
• +=, -=, *=, **=, /=, %=
• ++, --
$x = 28;
$x = $x/2;
print $x/=2, "\n";
print $x--, "\n";
print $x, "\n";
print --$x, "\n";
print $x, "\n";
print $x % 3, "\n";
print $x**2, "\n";
#!/usr/bin/perl -w
print "Please type the filename of the DNA sequence data: ";
$dna_filename = <STDIN>;
chomp $dna_filename;
open(DNAFILE, $dna_filename);
$name = <DNAFILE>;
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join('', @DNA);
$DNA =~ s/\s//g;
$count_of_CG = 0;
$position = 0;
while ( $position < length $DNA) {
$base = substr($DNA, $position, 1);
if ( $base eq 'C' or $base eq 'G') {
++$count_of_CG;
}
$position++;
}
print "CG content is ", $count_of_CG/(length $DNA)*100, "%\n";
#!/usr/bin/perl –w
print "Please type the filename of the DNA sequence data: ";
$dna_filename = <STDIN>;
chomp $dna_filename;
open(DNAFILE, $dna_filename);
$name = <DNAFILE>;
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join('', @DNA);
$DNA =~ s/\s//g;
$count_of_CG = 0;
for ( $position = 0 ; $position < length $DNA ; ++$position ) {
$base = substr($DNA, $position, 1);
if ( $base eq 'C' or $base eq 'G') {
++$count_of_CG;
}
}
print "CG content is ", $count_of_CG/(length $DNA)*100, "%\n";
#!/usr/bin/perl –w
print "Please type the filename of the DNA sequence data: ";
$dna_filename = <STDIN>;
chomp $dna_filename;
open(DNAFILE, $dna_filename);
$name = <DNAFILE>;
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join('', @DNA);
$DNA =~ s/\s//g;
$count_of_CG = 0;
while($DNA =~ /c/ig) {$count_of_CG++;}
while($DNA =~ /g/ig) {$count_of_CG++;}
print "CG content is ", $count_of_CG/(length $DNA)*100, "%\n";
$DNA = "ACCTAAACCCGGGAGAATTCCCACCAATTCTACGTAAC";
$s = "";
for ($i = 0, $j = 5; $i < $j; $i+=2, $j++) {
$s .= substr($DNA, $i, $j);
}
print $s, "\n";
$DNA = "ACCTAAACCCGGGAGAATTCCCACCAATTCTACGTAAC";
$s = "";
for ($i = 0, $j = 5; $i < $j; $i+=2, $j++) {
$s .= substr $DNA, $i, $j;
}
print ($s, "\n");
Call functions/subroutines
• Name p1, p2, p3;
• Name(p1, p2, p3);
• print $DNA1, $DNA2, "\n";
• print ($DNA1, $DNA2, "\n");
Exercise 1
•
•
•
•
Ask for a protein file in fasta format
Ask for an amino acid
Count the frequency of that amino acid
TKFHSNAHFYDCWRMLQYQLDMRCMRAISTF
SPHCGMEHMPDQTHNQGEMCKPRMWQVS
MNQSCNHTPPFRKTYVEWDYMAKALIAPYTL
GWLASTCFIW
Exercise 2
•
•
•
•
•
Ask for an RNA file in fasta format
Convert it to RNA
Ask for a codon
Count the frequency of that codon
TCGTACTTAGAAATGAGGGTCCGCTTTTGCCC
ACGCACCTGATCGCTCCTCGTTTGCTTTTAAG
AACCGGACGAACCACAGAGCATAAGGAGAA
CCTCTAGCTGCTTTACAAAGTACTGGTTCCCT
TTCCAGCGGGATGCTTTATCTAAACGCAATGA
Subroutine
• Some code needs to be reused
• A good way to organize code
• Called “function” in some languages
• Name
• Return
• Parameters (@_)
#!/usr/bin/perl –w
print "Please type the filename: ";
$dna_filename = <STDIN>;
chomp $dna_filename;
open(DNAFILE, $dna_filename);
$name = <DNAFILE>;
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join('', @DNA);
$DNA =~ s/\s//g;
$count_of_G = countG($DNA);
print $count_of_G;
sub countG {
my($dna) = @_;
my($count) = 0;
$count = ( $dna =~ tr/Gg//);
return $count;
}
#!/usr/bin/perl –w
print "Please type the filename: ";
$dna_filename = <STDIN>;
chomp $dna_filename;
open(DNAFILE, $dna_filename);
$name = <DNAFILE>;
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join('', @DNA);
$DNA =~ s/\s//g;
$count_of_G = count($DNA, 'Gg');
print $count_of_G;
sub count {
my($dna, $pattern) = @_;
my($count) = 0;
$count = ( eval("$dna =~ tr/$pattern//") );
return $count;
}
Codon
sub codon2aa {
my($codon) = @_;
if
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
elsif
(
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(
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$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
$codon
=~
=~
=~
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=~
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=~
=~
=~
=~
=~
=~
=~
=~
=~
=~
=~
/TCA/i
/TCC/i
/TCG/i
/TCT/i
/TTC/i
/TTT/i
/TTA/i
/TTG/i
/TAC/i
/TAT/i
/TAA/i
/TAG/i
/TGC/i
/TGT/i
/TGA/i
/TGG/i
/CTA/i
/CTC/i
/CTG/i
/CTT/i
/CCA/i
/CCC/i
/CCG/i
/CCT/i
/CAC/i
)
)
)
)
)
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{
{
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return
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return
'S'
'S'
'S'
'S'
'F'
'F'
'L'
'L'
'Y'
'Y'
'_'
'_'
'C'
'C'
'_'
'W'
'L'
'L'
'L'
'L'
'P'
'P'
'P'
'P'
'H'
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
Serine
Serine
Serine
Serine
Phenylalanine
Phenylalanine
Leucine
Leucine
Tyrosine
Tyrosine
Stop
Stop
Cysteine
Cysteine
Stop
Tryptophan
Leucine
Leucine
Leucine
Leucine
Proline
Proline
Proline
Proline
Histidine
sub codon2aa {
my($codon) = @_;
if ( $codon =~ /GC./i)
{ return 'A' }
# Alanine
elsif ( $codon =~ /TG[TC]/i)
{ return 'C' }
# Cysteine
elsif ( $codon =~ /GA[TC]/i)
{ return 'D' }
# Aspartic Acid
elsif ( $codon =~ /GA[AG]/i)
{ return 'E' }
# Glutamic Acid
elsif ( $codon =~ /TT[TC]/i)
{ return 'F' }
# Phenylalanine
elsif ( $codon =~ /GG./i)
{ return 'G' }
# Glycine
elsif ( $codon =~ /CA[TC]/i)
{ return 'H' }
# Histidine
elsif ( $codon =~ /AT[TCA]/i)
{ return 'I' }
# Isoleucine
elsif ( $codon =~ /AA[AG]/i)
{ return 'K' }
# Lysine
elsif ( $codon =~ /TT[AG]|CT./i) { return 'L' }
# Leucine
elsif ( $codon =~ /ATG/i)
{ return 'M' }
# Methionine
elsif ( $codon =~ /AA[TC]/i)
{ return 'N' }
# Asparagine
elsif ( $codon =~ /CC./i)
{ return 'P' }
# Proline
elsif ( $codon =~ /CA[AG]/i)
{ return 'Q' }
# Glutamine
elsif ( $codon =~ /CG.|AG[AG]/i) { return 'R' }
# Arginine
elsif ( $codon =~ /TC.|AG[TC]/i) { return 'S' }
# Serine
elsif ( $codon =~ /AC./i)
{ return 'T' }
# Threonine
elsif ( $codon =~ /GT./i)
{ return 'V' }
# Valine
elsif ( $codon =~ /TGG/i)
{ return 'W' }
# Tryptophan
elsif ( $codon =~ /TA[TC]/i)
{ return 'Y' }
# Tyrosine
elsif ( $codon =~ /TA[AG]|TGA/i) { return '_' }
# Stop
else {print STDERR "Bad codon \"$codon\"!!\n"; exit; }
}
Exercise
• Make the subroutine of converting codon
to aa
• Read in a dna fasta file, print out an Amino
Acid sequence
#!/usr/bin/perl -w
$dna = 'CGACGTCTTCGTACGGGACTAGCTCGTGTCGGTCGC';
$protein = '';
for(my $i=0; $i < (length($dna) - 2) ; $i += 3) {
$codon = substr($dna,$i,3);
$protein .= codon2aa($codon);
}
print "I translated the DNA\n\n$dna\n\n
protein\n\n$protein\n\n";
sub codon2aa {
#...
}
into the
Reading Frame
5'
3'
atgcccaagctgaatagcgtagaggggttttcatcatttgaggacgatgtataa
1 atg ccc aag ctg aat agc gta gag ggg ttt tca tca ttt gag gac gat gta taa
M
P
K
L
N
S
V
E
G
F
S
S
F
E
D
D
V
*
2 tgc cca agc tga ata gcg tag agg ggt ttt cat cat ttg agg acg atg tat
C
P
S
*
I
A
*
R
G
F
H
H
L
R
T
M
Y
3
gcc caa gct gaa tag cgt aga ggg gtt ttc atc att tga gga cga tgt ata
A
Q
A
E
*
R
R
G
V
F
I
I
*
G
R
C
I
three in the forward reading, three in the reverse complement
reading
Exercise 3
• Make the subroutine of converting codon
to aa
• Read in a dna fasta file, print out an Amino
Acid sequence
• There are 6 reading frame, can you try to
print all 6 version?
#!/usr/bin/perl –w
print "Please type the filename: ";
$dna_filename = <STDIN>; chomp $dna_filename;
open(DNAFILE, $dna_filename);
$name = <DNAFILE>;@DNA = <DNAFILE>;close DNAFILE;
$DNA = join( '', @DNA);$DNA =~ s/\s//g;
print "First
print "Second
print "Third
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
$DNA = reverse
print "Fourth
print "Fifth
print "Sixth
$DNA;
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
sub dna2peptide {
my ($dna) = @_;
my $protein = "";
for(my $i=0; $i < (length($dna) - 2) ; $i += 3) {
$codon = substr($dna,$i,3);
$protein .= codon2aa($codon);
}
return $protein;
}
sub codon2aa {
#...
}
Modules
• A Perl Module is a self-contained pieceof
[Perl] code that can be used by a Perl
program later
• Like a library
• End with extension .pm
• Needs a 1 at the end
#Bio.pm
sub codon2aa {
#....
#....
}
sub dna2peptide {
#....
#....
}
1
#!/usr/bin/perl -w
use Bio;
print "Please type the filename: ";
$dna_filename = <STDIN>; chomp $dna_filename;
open(DNAFILE, $dna_filename);
$name = <DNAFILE>;@DNA = <DNAFILE>;close DNAFILE;
$DNA = join( '', @DNA);$DNA =~ s/\s//g;
print "First
print "Second
print "Third
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
$DNA = reverse $DNA;
$DNA =~ tr/ACGTacgt/TGCAtgca/;
print "Fourth
print "Fifth
print "Sixth
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
#Bio.pm
sub codon2aa {
#....
#....
}
sub dna2peptide {
#....
#....
}
sub fasta_read {
print "Please type the filename: ";
my $dna_filename = <STDIN>; chomp $dna_filename;
unless (open(DNAFILE, $dna_filename)) {
print "Cannot open file ", $dna_filename, "\n";
}
$name = <DNAFILE>;@DNA = <DNAFILE>;close DNAFILE;
$DNA = join( '', @DNA);$DNA =~ s/\s//g;
return $DNA;
}
1
#!/usr/bin/perl -w
use Bio;
$DNA = fasta_read();
print "First
print "Second
print "Third
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
$DNA = reverse $DNA;
$DNA =~ tr/ACGTacgt/TGCAtgca/;
print "Fourth
print "Fifth
print "Sixth
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
Scope
• my provides lexical scoping; a variable
declared with my is visible only within the
block in which it is declared.
• Blocks of code are hunks within curly
braces {}; files are blocks.
• Use use vars qw([list of var names]) or our
([var_names]) to create package globals.
#!/usr/bin/perl -w
use Bio;
use strict;
use warnings;
$DNA = fasta_read();
print "First
print "Second
print "Third
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
$DNA = reverse $DNA;
$DNA =~ tr/ACGTacgt/TGCAtgca/;
print "Fourth
print "Fifth
print "Sixth
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
Variable "$DNA" is not imported at frame2.pl line 6.
Variable "$DNA" is not imported at frame2.pl line 8.
Variable "$DNA" is not imported at frame2.pl line 9.
Variable "$DNA" is not imported at frame2.pl line 10.
Variable "$DNA" is not imported at frame2.pl line 12.
Variable "$DNA" is not imported at frame2.pl line 12.
Variable "$DNA" is not imported at frame2.pl line 13.
Variable "$DNA" is not imported at frame2.pl line 14.
Variable "$DNA" is not imported at frame2.pl line 15.
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Global symbol "$DNA" requires explicit package name at frame2.pl
Execution of frame2.pl aborted due to compilation errors.
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#!/usr/bin/perl -w
use Bio;
use strict;
use warnings;
my $DNA = fasta_read();
print "First
print "Second
print "Third
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";
$DNA = reverse $DNA;
$DNA =~ tr/ACGTacgt/TGCAtgca/;
print "Fourth
print "Fifth
print "Sixth
", dna2peptide($DNA), "\n";
", dna2peptide(substr($DNA, 1)), "\n";
", dna2peptide(substr($DNA, 2)), "\n";