Writing Bioinformatics Software Biological Databases - Lecture Notes | CMSC 423, Study notes of Computer Science

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CMSC423: Bioinformatic Algorithms,

Databases and Tools

Lecture 4

Writing bioinformatics software Biological databases

Writing bioinformatics software

Bio::Perl

• http://www.bioperl.org use Bio::Perl; my $seq = read_sequence(“mytest.fa”, “fasta”); my $gbseq = read_sequence(“mytest.gb”, “genbank”); write_sequence(“>test.fasta”, 'fasta', $gbseq); ' vs “?

Bio::Perl

• Homework question # use Bio:Perl; while ($seq = read_sequence(“test.fa”, 'fasta')) { if ($seq ->length() > 500) { print $seq->primary_id(), “\n”; } } Note: you still need to write your own version...

BioJava

• http://www.biojava.org import org.biojava.bio.*; String filename = args[0]; BufferedInputStream is = new BufferedInputStream(new FileInputStream(filename)); //get the appropriate Alphabet Alphabet alpha = AlphabetManager.alphabetForName(args[1]); //get a SequenceDB of all sequences in the file SequenceDB db = SeqIOTools.readFasta(is, alpha);

BioJava

• Question 5 BufferedReader br = new BufferedReader(new FileReader(args[0])); String format = args[1]; String alphabet = args[2]; SequenceIterator iter = (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, br); while (iter.hasNext()){ Sequence seq = iter.nextSequence(); if (seq.length() > 500) {System.out.println(seq.getName());} }

BioPython

• http://www.biopython.org from Bio import SeqIO handle = open(“file.fasta”) seq_record = SeqIO.parse(handle, “fasta”) SeqIO.write(my_records, handle2, "fasta")

BioPython

• Question 5 from Bio import SeqIO handle = open("test.fasta") for seq_record in SeqIO.parse(handle, "fasta") : if len(seq_record) > 500 : print seq_record.id handle.close()

BioRuby

• http://www.bioruby.org require 'bio' input_seq = ARGF.read # reads all files inarguments my_naseq = Bio::Sequence::NA.new(input_seq)

BioRuby

• Question 5 #!/usr/bin/env ruby require 'bio' ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF) ff.each_entry do |f| if f.length > 500 puts f.entry_id end end

SeqAn

• http://www.seqan.de #include <seqan/sequence.h> #include <seqan/file.h> using namespace seqan; using namespace std; String seq; String name; fstream f; f.open(“test.fasta”); readMeta(f, name, Fasta()); readMeta(f, seq, Fasta());

SeqAn

• Question 5 String seq; String name; fstream f; f.open(“test.fasta”); while (! f.eof()){ readMeta(f, name, Fasta()); readMeta(f, seq, Fasta()); if (length(seq)){ cout << name << endl; } }

R/BioConductor

• http://www.bioconductor.org
• Mainly for statistical applications, e.g. microarray analysis library("affy") library("geneplotter") library("gplots") data <- ReadAffy() eset <- rma(data) e <- exprs(eset) heatmap.2(e, margin=c(15,15), trace="none", col=redgreen(25), cexRow=0.5)

R/BioConductor

• Book has lots of examples
• Worth learning more about it – easy to do various cool things
• example... if time