


User Contributed Perl Documentation                     Simple(3)



NNNNAAAAMMMMEEEE
     CompBio::Simple.pm  - Simple OO interface to some basic
     methods useful in bioinformatics.

SSSSYYYYNNNNOOOOPPPPSSSSIIIISSSS
     use CompBio::Simple;

     my $cbs = CompBio::Simple->new;

DDDDEEEESSSSCCCCRRRRIIIIPPPPTTTTIIIIOOOONNNN
     Originally developed at the BioMolecular Engineering
     Research Center (http://bmerc-www.bu.edu), this module is
     intended to take a number of small commonly used methods,
     and make them into a single package.

     The early versions of this module assumed installation on
     our local system.  Although I have tried to correct this in
     the current version, you may find this package requires a
     litle twidling to get working. I'll try to leave comments
     where I think it is most likely, but hopefully use of a
     relational database and local setting changes in the base
     module CompBio.pm will have taken care of it. If not
     _please_ email me at seanq@darwin.bu.edu with the details.

     Thanks!

MMMMeeeetttthhhhooooddddssss
     A couple of important general notes. All methods will
     describe the key required arguments and will also indicate
     which arg is the optional %params hash. %params can be
     passed as a hash or reference. Also, most arguments that
     handle sequences or ids accept input as scalar, arrays (by
     reference) or hashes (by reference).  If I miss documenting
     it, try it just in case. Unless a parameter option is
     available to signify otherwise, I assume 'doing the right
     thing' is to return the same type of data construct as
     recieved.

     nnnneeeewwww

     Construct an object for invoking methods in CompBio::Simple.

     hhhheeeellllpppp

     Quits current application and uses perldoc to display the
     POD.

     ttttbbbbllll____ttttoooo____ffffaaaa

     Converts a sequence record in table (tab delimited, usually
     .tbl file extension) format to fasta format.




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User Contributed Perl Documentation                     Simple(3)



             C<$fa_seq = $cbs->tbl_to_fa($tblseq,%params);>

     $seqdat can be either scalar, array by reference, 2d array
     by reference, or a hash by reference; return data type is
     same as submitted. Scalar may be either sequence records
     (one record per line), or a filename. Array's should contain
     an entire sequence record (loci\tsequence) in each indexed
     position. 2D arrays should be ids in the first column,
     sequences in the second, such that $array[2][1] would be the
     aa sequence for the third record. Hash's should have the
     loci as the key, and only the sequence as the value.

EEEEXXXXPPPPOOOORRRRTTTT
     None by default.

HHHHIIIISSSSTTTTOOOORRRRYYYY
     0.01    Original version; created by h2xs 1.20 with options

               -AXC -n CompBio::Simple


     0.42    Got initial set of methods linking to CompBio in.
             Developed the _munge stuff.

     0.43    Brought tests up to same point as in CompBio. Added
             six_frame. Moved the data handeling for
             dna_to_protein to own _munge type internal method.
             Added RETURN_TYPE parameter to _munge input so user
             can pick. Created the CompBio::Simple::ArrayFile
             module to TIE a sequence file to an array. Added
             six_frame using same _munge as dna_to_protein.

TTTTOOOO DDDDOOOO
     _munge_seq_imput needs to also detect when it just has a
     list of loci and hand request to DB to attempy to fulfil,
     and/or accept a DB param.

     check_type invoked from here should make a few type checks
     with random samples from the dataset when possible.

CCCCOOOOPPPPYYYYRRRRIIIIGGGGHHHHTTTT
     Copyright Sean Quinlan, Trustees of Boston University
     2000-2001.

     All rights reserved. This program is free software; you can
     redistribute it and/or modify it under the same terms as
     Perl itself.

AAAAUUUUTTTTHHHHOOOORRRR
     Sean Quinlan, seanq@darwin.bu.edu





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User Contributed Perl Documentation                     Simple(3)



     Please email me with any changes you make or suggestions for
     changes/additions.  Latest version is available under
     ftp://mcclintock.bu.edu/BMERC/perl/.

     Thank you!

SSSSEEEEEEEE AAAALLLLSSSSOOOO
     _p_e_r_l(1), _C_o_m_p_B_i_o(3).















































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