CompBio - Core library for some basic methods useful in computational biology/bioinformatics.
use CompBio;
my $cbc = new->CompBio;
$AR_faseqs = $cbc->tbl_to_fa(\@tblseqs);
or
use CompBio qw(tbl_to_fa);
$AR_faseqs = tbl_to_fa(\@tblseqs);
The CompBio module set is being developed as a new implementation of the code base originally developed at the BioMolecular Engineering Research Center (http://bmerc-www.bu.edu). CompBio.pm is intended to take a number of small, commonly used methods for supporting bioinformatics research, and make them into a single package. Many of the utils included with this distribution are just command line interfaces to the methods contained herein.
The CompBio module set is _not_ intended to replace the bioperl project (http://www.bioperl.org/). Although I do welcome suggestions for improving or adding to the methods available in these modules, particularly I would love any help with things on the TO DO list, these modules are not intended to provide the depth that the bioperl suite can provide.
CompBio has a limited API. It expects it's input to be in specific formats, as described in each methods description, and it's output is in a format that makes the most sense to me for that method. It does no error checking by and large, so incorrect input could cause bizzare behavior and/or a noisy death. If you want a flexible interface with lots of error checking and deep levels of verbosity, use the Simple (the CompBio::Simple manpage) module - that's its job.
Latest version is available through SourceForge http://compbio.sourceforge.net/, or on the CPAN http://www.cpan.org/authors/id/S/SE/SEANQ/.
Thanks!
Other modules available (or that will be available) in the CompBio set are:
The DB (the CompBio::DB manpage) module will only be imediately useful if you import the databases as
used by us here at the BMERC(ftp://mcclintock.bu.edu/BMERC/mysql/) or develop
your own on the same basic design scheme. Otherwise I hope you find it useful
as a source of design ideas for rolling your own. Please note however that I
intend to expand the methods in CompBio/Simple.pm to allow seemless access to
data through the DB module. Although at no time will including the DB module be
required for Simple to work, I think that if you have the space for it, you will
find having the data locally and adding this module (or adapting it to work with
databases already installed) will have an imense and imediate benifiacial
impact. It did for us at least! :)
The Profile module was designed to work with our PIMA-II sofware and the PIMA modules. The PIMA suite is available for license from Boston University for a nominal fee, and free for academic use. For examples and more info see http://bmerc-www.bu.edu/PIMA/. Unless you have or are interested in that package, this module will have no functional value.
You may note that the majority of the methods here are for converting sequences from one format to another. Mainly this is for converting other formats to table format, which is used by most of these programs. This is not meant to be a comprhensive collection of format guessing and transformation methods. If you are looking for a converter for a format CompBio doesn't handle, I suggest you look into bioperls SeqIO package or the READSEQ program (java), found at http://iubio.bio.indiana.edu/soft/molbio/readseq/
Construct an object for invoking methods in CompBio.
Quits current application and uses perldoc to display the POD.
Checks a given sequence or set of sequences for it's type. Currently groks
fasta(.fa), table(.tbl), raw genome(.raw), intelligenics[?](.ig) and coding
dna sequence(.cdna) types. Each index of the referenced array should
be an entire sequence record. * It is however not recomended that you load
up an entire raw genome into memory to do this test - see perlfunc read *
$type = check_type(\@seqs,%parameters);
Possible return types are CDNA, TBL, FA, IG, RAW and UNKNOWN.
Be warned, this is intended only as a quick check and only uses as many records as necisarry in the reference provided, stating with the first. check_type assumes the rest of the records look the same and does not do any kind of deep QA on the set. If you are not sure, invoke check_type with a few random samples from your set, or use the CompBio::Simple manpage, which does that by default.
Converts a sequence record in table (tab delimited, usually .tbl file extension) format to fasta format.
$aref_faseqs = $cbc-tbl_to_fa(\@seqdat,%params);>
Each index in the @seqdat array must contain entire record (loci\tsequence) for single sequence. Return is an array reference, still one sequence per index.
Extra data fields in the table format will be added to the annotation line (>) in the fasta output.
Converts a sequence in table (tab delimited) format to .ig format. Accepts sequences in a referenced array, one record per index.
$aref_igseqs = $cbc->tbl_to_ig(\@tbl_seqs,%params);
Extra data fields in the table format will be placed on a single comment line (;) in the ig output.
Accepts fasta format sequences in a referenced array, one complete sequence
record per index. This method returns the sequence(s) in table(.tbl) format
contained in a referenced array.
$aref_faseqs = $cbc-fa_to_tbl(\@fa_seq);>
Extra data fields in the fasta format will be placed as extra tab delimited values after the sequence record.
Options:
CLEAN: Reduces signifier to the first strech of non white space characters found at least 4 characters long with no of the characters (| \ ? / ! *)
Accepts ig format sequences in a referenced array, one complete sequence
record per index. This method returns the sequence(s) in table(.tbl) format
contained in a referenced array.
$aref_igseqs = $cbc-ig_to_tbl(\@fa_seq);>
Extra comment lines in the ig format will be placed as extra tab delimited values after the sequence record.
Converts a dna sequence, containing no whitespace, submited as a scalar reference, to the amino acid residues as coded by the standard 'universal' genetic code. Return is a reference to a scalar. dna sequence may contain standard special characters (i.e. R,S,B,N, ect.).
$aa = dna_to_aa(\$dna_seq,%params);
Options:
C: Set to a true value to indicate dna should be converted to it's complement before translation.
ALTCODE: A reference to a hash containing alternate coding keys where the value is the new aa to code for. Stop codons are represented by ``.''. Multiple allowable values for the final dna in the codon may be provided in the format AT[TCA].
SEQFIX: Set to true to alter first position, making V or L an M, and removing stop in last position.
Converts dna to it's complementary strand. DNA sequence is submitted as scalar by reference. There is no return as sequence is modified. To maintain original sequence, send a reference to a copy (or see documentation for CompBio::Simple::complement).
complement(\$dna);
Converts a submitted dna sequence into all 6 frame translations to aa. Value
submitted may be a reference to a scalar containing the dna or a filename.
Either way dna must be in RAW(.raw) format (Not whitespace within sequence,
only one newline allowed at end of record). Output id's have start and stop
positions encoded; if first value is larger, translated from anti-sense.
$result = six_frame($raw_file,$id,$seq_len,$out_file);
Options:
ALTCODE: A reference to a hash containing alternate coding keys where the value is the new aa to code for. Stop codons are represented by ``.''. Multiple allowable values for the final dna in the codon may be provided in the format AT[TCA].
ID: Prefix for translated segment identifiers, default is SixFrame.
SEQLEN: Minimum length of aa sequence to return, default is 10.
OUTPUT: A filename to pipe results to. This is recomended for large dna sequences such as large contigs or whole chromosomes, otherwise results are stored in memory until process complete. If the value of OUTFILE is STDOUT results will be sent directly to standard out.
A simple interface to the Washington University distribution of blast. Only recently tested with full 2.0MP-WashU release. I do however stick to using the compatability features so it it should work with both the licensed and free releases of WUblast.
wu_blast requires two arguments, a sequence database filename or a reference to
an array containing the sequence(s) to search, and the query sequence filename or
a reference to an array containing the sequence to query with. Sequence files need
to be in fasta format and sequences contained in arrays need to be in table format.
For more versatility, use CompBio::Simple::blast. One thing wu_blast will do is
prepare the db for searching if it isn't set up in advance; this does require
you have write permision in the location of the base sequence file, and sufficient
room in your quota (if used).
Options:
METHOD: Alternate method to use for sequence comparison. Default is blastp.
PARAMS: Optional parameters to hand to the blast method. See the your local documentation for the method chosen to see what options are available.
SERVER: Machine to use as the blast server. Defaults to the global $CPUSERVER. rsh is currently used to launch the proccess.
BLASTPREP: Alternate method to use to prepare a sequence database for being searched using the chosen blast method. Default is setdb.
$blast_out = blast($fa_file,$queryfile,(PARAMS => "-B=0 -matrix=BLOSUM62"));
Creates a hash table with amino acid lookups by codon. Includes all cases where even an alternate na code (such as M for A or C) would return an unambiguous aa. Also consistent with the complement method in this package, ie, lower cases in some contexts, for ease of use with six_frame.
C<%aa_hash = aa_hash;>
None by default.
-AXC -n CompBio
Project has been added to SourceForge and the modules list on CPAN.
Worked out some more bugs, mostly cropping up from interactions with utils such as tbl_to_fa, which interface through Simple. Mainly found places where lazy programming broke using the files tied to an array, so had to use less of $_. Things are shaking out nicely, and I think all the core bits are now in place. Once the utils are done, I'll do a major code cleanup and comment run and step up to 0.5 and push release. Finishing adding converters and fixing any reported bugs (new converters shouldn't add any new bugs, except inside the new methods) will benchmark going to 0.6.
I like the basic design so far - except where large sequence sets are to be munged. There this becomes a seriouse memory hog. Some faster & more efficient way needs to be provided when dealing with files & large data sets.
complement and dna_to_aa need to be loop enabled, also alowing &$RET_CODE(\@ret,$str); to be used. Why am I using _munge_array?!?
**Got it - needs work!** Get the full release of WashU Blast and make sure the blast stuff works with it as well.
OK, rethink blast method(s) completely. Old and kludged and needs to die.
Add a method for handeling ncbi blast. CompBio::Simple should only have a blast method that will DTRT and use the appropriate core methods. Need to revisit only loading modules as needed, as this method should use the XML output preferentially.
Stop using lowercase abiguity codes after complementing! (i.e. out of %AA)
If make install isn't putting right perl line in executibles, run perl config myself?
Add DNA* and GCG format handelers
Add handler for the genbank report type format: 1 attgc gtgct 11 gtgtg gacaa Which, though annoying, seems a certain candidate for recieving in cut and paste operations, particularly through the web.
Better way to handle CPUSERVER. There must be some way to allow the user to define (presumably during ./config?) how to submit jobs for more intensive computational tools such as Blast and PIMA. Things like rsh, submitting to a batch queue, etc should all be definable at install somehow.
write configure script to populate these globals as part of install process.
modify tests to look for inclusion of Profile.pm or such and skip testing where apropriate if the PIMA suite is not installed.
Find out if there is a way using OOP to allow a user to only need to include
this module and create new objects for the submodules, or even better just
DTRT. Can this be done just through inheritence? Should it be triggered by
requested export (like use CompBio qw(Simple DB)? Or through an AUTOLOAD
type interface, returning the correct object ($cbs = CompBio->Simple(``new'')
or some such)? I think that would be far more desirable than _having_ to
use a bunch of modules all in the CompBio namespace.
_error (all packages) needs to correctly report line where error occured. Can this be done through caller or do I need to pass manually?
hmmm, how about a simple tm calculator for primers? I seem to be able to find lots of them that work through web interface, or more complex primer selection software, but none that plug and play to a perl program, and I'm needing one. Not a primer selecter, just a _solid_ (more than just GC content), straight foward Tm calculator.
Developed at the BioMolecular Engineering Research Center at Boston University under the NHLBI's Programs for Genomic Applications grant.
Copyright Sean Quinlan, Trustees of Boston University 2000-2002.
All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
Sean Quinlan, seanq@darwin.bu.edu
Please email me with any changes you make or suggestions for changes/additions. Latest version is available through SourceForge http://sourceforge.net/projects/compbio/, or on the CPAN http://www.cpan.org/authors/id/S/SE/SEANQ/. Thank you!
I would like to thank the staff at the BMERC for being my guinee pigs for the past few years, Jim Freeman who got me into this and left me with flint and tinder rather than the ember in a clay pot he started with, and my boss and (tor)mentor Dr. Temple F. Smith! I would never have gotten this far or learned this much without them.
perl(1), CompBio::Simple(1).