Beginning Perl for Bioinformatics

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O

 object-oriented programming , 2nd

 octal (base 8) numbers

    See : byte offsets offsets

 online manuals, Perl

    See : web sites online resources , 2nd

 open function , 2nd

 open reading frames (ORFs)

 open system call , 2nd  , 3rd

 newlines in filenames and

 opening files

 GenBank

 testing for file existence before attempting

 operating systems

 Bioperl, problems with

 command line, running programs from

 desktop workstations for GenBank

 filenames, characters not allowed in

 opening files on

 operators , 2nd

 arithmetic , 2nd

assignment

 equality vs.

 autoincrement

 binding , 2nd  , 3rd  , 4th

 bitwise , 2nd

 cmp (alphabetical comparison)

 command input

 concatenation , 2nd

 context and

 file test

 input , 2nd  , 3rd

logical

 range operator, using with

 next

 precedence of

 qx// (quoted execution)

 s/// (substitution) , 2nd

 string

 optical computing

or operator

 | (bitwise OR) , 2nd

logical or

 control flow, using for

    See : precedence order of evaluation

organization

 of DNA

 of proteins

output

BLAST files

 presenting data

 directing to STDOUT, STDERR and files

 directing with STDOUT

 functions for

 program results, designing for

 stride program, parsing

© 2002, O'Reilly & Associates, Inc.