Perl Programming for Biologists
Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusableand maintainable scripts that spare the rote repetition of code.
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Variables and Data Types
Arrays and Hashes
Perl Programming for Biologists D Curtis Jamison
Input and Output
Perl Modules and Packages
Appendix A Partial Perl Reference
Appendix B Bioinformatics File Formats
accessors argument ARGV array assign ATGTGGTG ATOM ATOM ATOM binary files bioinformatics Bioperl bless Blue-Plate Special CAPZA2 CFTR CGI.pm Chapter character child process cjamison staff code block codon command line constructor contains CPAN CPAN shell create Curtis Jamison ISBN data structure database default EMBL entries evaluate example execute exit Fasta filehandle foreach format function GenBank gene names grep hash haydn Hello hello.pl HETATM input install interpolation iterate language length look loop maps\n matches method mRNA multidrug resistance namespace nucleotides object-oriented object-oriented programming operator output package parameters parentheses pattern Perl module Perl Programming Perl script perldoc position primer pair print gene Programming for Biologists reference regular expression reverse complement Sbase scalar scalar value Seq object shift simply Skey slot SmySeq sort specific Sself Sseq start codons stored string subroutine switch TFEC undef Unix usr/bin/perl variable name write