


User Contributed Perl Documentation    CompBio::Simple::Simple(3)



NNNNAAAAMMMMEEEE
     CompBio::Simple.pm  - Simple OO interface to some basic
     methods useful in bioinformatics.

SSSSYYYYNNNNOOOOPPPPSSSSIIIISSSS
     use CompBio::Simple;

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

DDDDEEEESSSSCCCCRRRRIIIIPPPPTTTTIIIIOOOONNNN
     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!

MMMMeeeetttthhhhooooddddssss
     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.

     nnnneeeewwww

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

     hhhheeeellllpppp

     Quits current application and uses perldoc to display the
     POD.

     ttttbbbbllll____ttttoooo____ffffaaaa

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




2001-08-16          Last change: perl v5.6.0                    1






User Contributed Perl Documentation    CompBio::Simple::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.

EEEEXXXXPPPPOOOORRRRTTTT
     None by default.

HHHHIIIISSSSTTTTOOOORRRRYYYY
     0.01    Original version; created by h2xs 1.20 with options

               -AXC -n CompBio::Simple


     0.74    Copy over functions from original BMERC::bio, making
             small improvements to code, mostly by removing
             lingering locale assumptions and (hopefully)
             improving interface, and converting to OOP.

TTTTOOOO DDDDOOOO
     _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.

CCCCOOOOPPPPYYYYRRRRIIIIGGGGHHHHTTTT
     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.

AAAAUUUUTTTTHHHHOOOORRRR
     Sean Quinlan, seanq@darwin.bu.edu

     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!





2001-08-16          Last change: perl v5.6.0                    2






User Contributed Perl Documentation    CompBio::Simple::Simple(3)



SSSSEEEEEEEE AAAALLLLSSSSOOOO
     _p_e_r_l(1), _C_o_m_p_B_i_o(3).





















































2001-08-16          Last change: perl v5.6.0                    3



