Tutorial

libsequence tutorialKevin ThorntonApril 13, 2006Contents1 Introduction 41.1 What this document isn’t . . . . . . . . . . . . . . . . . . . . 41.2 you need to already know . . . . . . . . . . . . . . . . . 41.3 Compiler requirements . . . . . . . . . . . . . . . . . . . . . . 51.4 Compiling and linking . . . . . . . . . . . . . . . . . . . . . . 51.5 Physical Structure of the Library . . . . . . . . . . . . . . . . 61.6 namespace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61.7 Exception Handling . . . . . . . . . . . . . . . . . . . . . . . . 61.8 Further documentation . . . . . . . . . . . . . . . . . . . . . . 72 Reading sequences 82.1 Inheritance hierarchy . . . . . . . . . . . . . . . . . . . . . . . 82.2 Typecast to std::string . . . . . . . . . . . . . . . . . . . . 82.3 Example: reverse and complement a file of FASTA sequences . 82.4 get a list of sequence names from a file of FASTAsequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92.5 Other useful sequence features . . . . . . . . . . . . . . . . . . 102.5.1 Typecast to std::string . . . . . . . . . . . . . . . . 102.6 Is it a valid sequence? . . . . . . . . . . . . . . . . . . . . . . 112.7 Translating sequences . . . . . . . . . . . . . . . . . . . . . . . 122.8 Generating Codon Tables. . . . . . . . . . . . . . . . . . . . . 133 Handling Alignments 153.1 Example: reading an alignment of FASTA sequences . . . . . 153.2 convert a clustalw output file to ...