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Bioinformatics 生物信息学理论和实践 唐继军 jtang@cse.sc 13928761660

Bioinformatics 生物信息学理论和实践 唐继军 jtang@cse.sc.edu 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;

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Bioinformatics 生物信息学理论和实践 唐继军 jtang@cse.sc 13928761660

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  1. Bioinformatics生物信息学理论和实践唐继军jtang@cse.sc.edu13928761660Bioinformatics生物信息学理论和实践唐继军jtang@cse.sc.edu13928761660

  2. More Conditions

  3. But • Use ==, <, <=, >, >=, !=, ||, && for numeric numbers • Use eq, lt, le, gt, ge, ne, or, and for string comparisons

  4. More Arithmatics • +, -, *, **, /, % • +=, -=, *=, **=, /=, %= • ++, --

  5. $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";

  6. #!/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";

  7. #!/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";

  8. #!/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";

  9. $DNA = "ACCTAAACCCGGGAGAATTCCCACCAATTCTACGTAAC"; $s = ""; for ($i = 0, $j = 5; $i < $j; $i+=2, $j++) { $s .= substr($DNA, $i, $j); } print $s, "\n";

  10. $DNA = "ACCTAAACCCGGGAGAATTCCCACCAATTCTACGTAAC"; $s = ""; for ($i = 0, $j = 5; $i < $j; $i+=2, $j++) { $s .= substr $DNA, $i, $j; } print ($s, "\n");

  11. Call functions/subroutines • Name p1, p2, p3; • Name(p1, p2, p3); • print $DNA1, $DNA2, "\n"; • print ($DNA1, $DNA2, "\n");

  12. Exercise 1 • Ask for a protein file in fasta format • Ask for an amino acid • Count the frequency of that amino acid • TKFHSNAHFYDCWRMLQYQLDMRCMRAISTFSPHCGMEHMPDQTHNQGEMCKPRMWQVSMNQSCNHTPPFRKTYVEWDYMAKALIAPYTLGWLASTCFIW

  13. Exercise 2 • Ask for an RNA file in fasta format • Convert it to RNA • Ask for a codon • Count the frequency of that codon • TCGTACTTAGAAATGAGGGTCCGCTTTTGCCCACGCACCTGATCGCTCCTCGTTTGCTTTTAAGAACCGGACGAACCACAGAGCATAAGGAGAACCTCTAGCTGCTTTACAAAGTACTGGTTCCCTTTCCAGCGGGATGCTTTATCTAAACGCAATGAGAGAGGTATTCCTCAGGCCACATCGCTTCCTAGTTCCGCTGGGATCCATCGTTGGCGGCCGAAGCCGCCATTCCATAGTGAGTTCTTCGTCTGTGTCATTCTGTGCCAGATCGTCTGGCAAATAGCCGATCCAGTTTATCTCTCGAAACTATAGTCGTACAGATCGAAATCTTAAGTCAAATCACGCGACTAGACTCAGCTCTATTTTAGTGGTCATGGGTTTTGGTCCCCCCGAGCGGTGCAACCGATTAGGACCATGTAGAACATTAGTTATAAGTCTTCTTTTAAACACAATCTTCCTGCTCAGTGGTACATGGTTATCGTTATTGCTAGCCAGCCTGATAAGTAACACCACCACTGCGACCCTAATGCGCCCTTTCCACGAACACAGGGCTGTCCGATCCTATATTACGACTCCGGGAAGGGGTTCGCAAGTCGCACCCTAAACGATGTTGAAGGCTCAGGATGTACACGCACTAGTACAATACATACGTGTTCCGGCTCTTATCCTGCATCGGAAGCTCAATCATGCATCGCACCAGCGTGTTCGTGTCATCTAGGAGGGGCGCGTAGGATAAATAATTCAATTAAGATATCGTTATGCTAGTATACGCCTACCCGTCACCGGCCAACAGTGTGCAGATGGCGCCACGAGTTACTGGCCCTGATTTCTCCGCTTCTAATACCGCACACTGGGCAATACGAGCTCAAGCCAGTCTCGCAGTAACGCTCATCAGCTAACGAAAGAGTTAGAGGCTCGCTAAATCGCACTGTCGGGGTCCCTTGGGTATTTTACACTAGCGTCAGGTAGGCTAGCATGTGTCTTTCCTTCCAGGGGTATG

  14. Subroutine • Some code needs to be reused • A good way to organize code • Called “function” in some languages • Name • Return • Parameters (@_)

  15. #!/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; }

  16. #!/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; }

  17. Codon

  18. sub codon2aa { my($codon) = @_; if ( $codon =~ /TCA/i ) { return 'S' } # Serine elsif ( $codon =~ /TCC/i ) { return 'S' } # Serine elsif ( $codon =~ /TCG/i ) { return 'S' } # Serine elsif ( $codon =~ /TCT/i ) { return 'S' } # Serine elsif ( $codon =~ /TTC/i ) { return 'F' } # Phenylalanine elsif ( $codon =~ /TTT/i ) { return 'F' } # Phenylalanine elsif ( $codon =~ /TTA/i ) { return 'L' } # Leucine elsif ( $codon =~ /TTG/i ) { return 'L' } # Leucine elsif ( $codon =~ /TAC/i ) { return 'Y' } # Tyrosine elsif ( $codon =~ /TAT/i ) { return 'Y' } # Tyrosine elsif ( $codon =~ /TAA/i ) { return '_' } # Stop elsif ( $codon =~ /TAG/i ) { return '_' } # Stop elsif ( $codon =~ /TGC/i ) { return 'C' } # Cysteine elsif ( $codon =~ /TGT/i ) { return 'C' } # Cysteine elsif ( $codon =~ /TGA/i ) { return '_' } # Stop elsif ( $codon =~ /TGG/i ) { return 'W' } # Tryptophan elsif ( $codon =~ /CTA/i ) { return 'L' } # Leucine elsif ( $codon =~ /CTC/i ) { return 'L' } # Leucine elsif ( $codon =~ /CTG/i ) { return 'L' } # Leucine elsif ( $codon =~ /CTT/i ) { return 'L' } # Leucine elsif ( $codon =~ /CCA/i ) { return 'P' } # Proline elsif ( $codon =~ /CCC/i ) { return 'P' } # Proline elsif ( $codon =~ /CCG/i ) { return 'P' } # Proline elsif ( $codon =~ /CCT/i ) { return 'P' } # Proline elsif ( $codon =~ /CAC/i ) { return 'H' } # Histidine elsif ( $codon =~ /CAT/i ) { return 'H' } # Histidine elsif ( $codon =~ /CAA/i ) { return 'Q' } # Glutamine elsif ( $codon =~ /CAG/i ) { return 'Q' } # Glutamine elsif ( $codon =~ /CGA/i ) { return 'R' } # Arginine elsif ( $codon =~ /CGC/i ) { return 'R' } # Arginine elsif ( $codon =~ /CGG/i ) { return 'R' } # Arginine elsif ( $codon =~ /CGT/i ) { return 'R' } # Arginine elsif ( $codon =~ /ATA/i ) { return 'I' } # Isoleucine elsif ( $codon =~ /ATC/i ) { return 'I' } # Isoleucine elsif ( $codon =~ /ATT/i ) { return 'I' } # Isoleucine elsif ( $codon =~ /ATG/i ) { return 'M' } # Methionine elsif ( $codon =~ /ACA/i ) { return 'T' } # Threonine elsif ( $codon =~ /ACC/i ) { return 'T' } # Threonine elsif ( $codon =~ /ACG/i ) { return 'T' } # Threonine elsif ( $codon =~ /ACT/i ) { return 'T' } # Threonine elsif ( $codon =~ /AAC/i ) { return 'N' } # Asparagine elsif ( $codon =~ /AAT/i ) { return 'N' } # Asparagine elsif ( $codon =~ /AAA/i ) { return 'K' } # Lysine elsif ( $codon =~ /AAG/i ) { return 'K' } # Lysine elsif ( $codon =~ /AGC/i ) { return 'S' } # Serine elsif ( $codon =~ /AGT/i ) { return 'S' } # Serine elsif ( $codon =~ /AGA/i ) { return 'R' } # Arginine elsif ( $codon =~ /AGG/i ) { return 'R' } # Arginine elsif ( $codon =~ /GTA/i ) { return 'V' } # Valine elsif ( $codon =~ /GTC/i ) { return 'V' } # Valine elsif ( $codon =~ /GTG/i ) { return 'V' } # Valine elsif ( $codon =~ /GTT/i ) { return 'V' } # Valine elsif ( $codon =~ /GCA/i ) { return 'A' } # Alanine elsif ( $codon =~ /GCC/i ) { return 'A' } # Alanine elsif ( $codon =~ /GCG/i ) { return 'A' } # Alanine elsif ( $codon =~ /GCT/i ) { return 'A' } # Alanine elsif ( $codon =~ /GAC/i ) { return 'D' } # Aspartic Acid elsif ( $codon =~ /GAT/i ) { return 'D' } # Aspartic Acid elsif ( $codon =~ /GAA/i ) { return 'E' } # Glutamic Acid elsif ( $codon =~ /GAG/i ) { return 'E' } # Glutamic Acid elsif ( $codon =~ /GGA/i ) { return 'G' } # Glycine elsif ( $codon =~ /GGC/i ) { return 'G' } # Glycine elsif ( $codon =~ /GGG/i ) { return 'G' } # Glycine elsif ( $codon =~ /GGT/i ) { return 'G' } # Glycine else { print STDERR "Bad codon \"$codon\"!!\n"; exit; } # }

  19. 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; } }

  20. Exercise • Make the subroutine of converting codon to aa • Read in a dna fasta file, print out an Amino Acid sequence

  21. #!/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$dna\n\n into the protein\n\n$protein\n\n"; sub codon2aa { #... }

  22. 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

  23. 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?

  24. #!/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 ", dna2peptide($DNA), "\n"; print "Second ", dna2peptide(substr($DNA, 1)), "\n"; print "Third ", dna2peptide(substr($DNA, 2)), "\n"; $DNA = reverse $DNA; print "Fourth ", dna2peptide($DNA), "\n"; print "Fifth ", dna2peptide(substr($DNA, 1)), "\n"; print "Sixth ", dna2peptide(substr($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 { #... }

  25. 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

  26. #Bio.pm sub codon2aa { #.... #.... } sub dna2peptide { #.... #.... } 1

  27. #!/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 ", dna2peptide($DNA), "\n"; print "Second ", dna2peptide(substr($DNA, 1)), "\n"; print "Third ", dna2peptide(substr($DNA, 2)), "\n"; $DNA = reverse $DNA; $DNA =~ tr/ACGTacgt/TGCAtgca/; print "Fourth ", dna2peptide($DNA), "\n"; print "Fifth ", dna2peptide(substr($DNA, 1)), "\n"; print "Sixth ", dna2peptide(substr($DNA, 2)), "\n";

  28. #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

  29. #!/usr/bin/perl -w use Bio; $DNA = fasta_read(); print "First ", dna2peptide($DNA), "\n"; print "Second ", dna2peptide(substr($DNA, 1)), "\n"; print "Third ", dna2peptide(substr($DNA, 2)), "\n"; $DNA = reverse $DNA; $DNA =~ tr/ACGTacgt/TGCAtgca/; print "Fourth ", dna2peptide($DNA), "\n"; print "Fifth ", dna2peptide(substr($DNA, 1)), "\n"; print "Sixth ", dna2peptide(substr($DNA, 2)), "\n";

  30. 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.

  31. #!/usr/bin/perl -w use Bio; use strict; use warnings; $DNA = fasta_read(); print "First ", dna2peptide($DNA), "\n"; print "Second ", dna2peptide(substr($DNA, 1)), "\n"; print "Third ", dna2peptide(substr($DNA, 2)), "\n"; $DNA = reverse $DNA; $DNA =~ tr/ACGTacgt/TGCAtgca/; print "Fourth ", dna2peptide($DNA), "\n"; print "Fifth ", dna2peptide(substr($DNA, 1)), "\n"; print "Sixth ", dna2peptide(substr($DNA, 2)), "\n";

  32. 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 line 6. Global symbol "$DNA" requires explicit package name at frame2.pl line 8. Global symbol "$DNA" requires explicit package name at frame2.pl line 9. Global symbol "$DNA" requires explicit package name at frame2.pl line 10. Global symbol "$DNA" requires explicit package name at frame2.pl line 12. Global symbol "$DNA" requires explicit package name at frame2.pl line 12. Global symbol "$DNA" requires explicit package name at frame2.pl line 13. Global symbol "$DNA" requires explicit package name at frame2.pl line 14. Global symbol "$DNA" requires explicit package name at frame2.pl line 15. Execution of frame2.pl aborted due to compilation errors.

  33. #!/usr/bin/perl -w use Bio; use strict; use warnings; my $DNA = fasta_read(); print "First ", dna2peptide($DNA), "\n"; print "Second ", dna2peptide(substr($DNA, 1)), "\n"; print "Third ", dna2peptide(substr($DNA, 2)), "\n"; $DNA = reverse $DNA; $DNA =~ tr/ACGTacgt/TGCAtgca/; print "Fourth ", dna2peptide($DNA), "\n"; print "Fifth ", dna2peptide(substr($DNA, 1)), "\n"; print "Sixth ", dna2peptide(substr($DNA, 2)), "\n";

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