CDB (Constant DataBase) indexing and retrieval tools for FASTA files

This is a brief introduction to a couple of platform independent file-based
hashing tools (cdbfasta and cdbyank) that can be used for creating indices for
quick retrieval of any particular sequences from large  multi-FASTA files. The
last version has the option to compress data records in order to save space.
The index files are now architecture independent, the same index file can be
created and used on many  different Unix platform (be it 32bit/64bit,
big-endian or little-endian architectures) and even Windows.

1.Install instructions
2.Typical usage
3.Retrieving sequence ranges or only the defline
4.Data compression option
5.Development notes


1.Install instructions
===============================
Clone this repository and run 'make' in the cdbfasta directory. 
Make sure you have the zlib library and development files installed on your linux system.

Note: if no compression support is needed, change the BASEFLAGS variable in the Makefile
to have -DENABLE_COMPRESSION=0 instead of -DENABLE_COMPRESSION=0 
  
Running 'make' should produce the binaries 'cdbfasta' (the indexer program) 
and 'cdbyank' (the query program) in the current directory.

2.Typical usage
===============

Use cdbfasta to create the index file for a multi-FASTA file and cdbyank to
pull records based on that index file. An usage message is displayed if the
commands cdbyank or cdbyank are run without any  parameters.

In order to create an index file, only the name of the fasta file must be
provided:

cdbfasta <fasta_file>

The fasta file can be specified with the whole path (if it's not in the current
directory), e.g.

cdbfasta /usr/local/db/GUDB.human

By default cdbfasta creates an index file with the same name as the database
file but with the  .cidx suffix added to the original name. So in the example
above, a file GUDB.human.cidx will be created in  /usr/local/db/. The default
usage considers the key for a FASTA record to be the first space-delimited
token following the ">" starting character from the definition line.  For
example, if a FASTA record had a defline like this:

>AA141526

Then we can use the string 'AA141526' with cdbyank to retrieve the full FASTA
record associated to that sequence name:

cdbyank -a 'AA141526' /usr/local/db/GUDB.human.cidx

Sometimes all the space delimited tokens in the defline need to be declared as
keys in the index file, pointing to the same fasta record. This can be
accomplished by cdbfasta by using the "-m" switch. 

For long and complex fastA file accessions like this:
EGAD|61|GP|186739|gb|AAA63210.1||M60828 there is an option to create the
index file in such a way that there is no need to provide the full string to
cdbyank in order to retrieve such a sequence, but only the first
"<db>|<accession>" pair (i.e. a substring ending at the second '|' character)
should be enough. (EGAD|61 in the example above). In  order to enable this
feature, there are two alternative options for cdbfasta:


 -c : the index file is built only by storing the "shortcut key" (the first
     "db|accession" pair found in the defline of each fasta record). In this
     case, cdbyank will only be able to accept these "shortcut"  accessions for
     record retrieval.

 -C : the index file is built by storing both the "shortcut key" and the full
     keys (which are considered to end at the first space character in the
     defline). In this case, two strings are stored as keys for each  fastA
     record so any of them can be used as an accession for retrieval of the
     same record with cdbyank.

In order to retrieve records from the database file, cdbyank should be provided
with the name of the index file created previously with cdbfasta, e.g.:

cdbyank -a 'human|Z98492' /usr/local/db/GUDB.human.cidx

A list of accessions is expected at stdin if -a option is not provided, e.g.:

cat seq_list | cdbyank /usr/local/db/GUDB.human.cidx

This way the output will be a series a fasta records at stdout. By redirecting
this output to a file a multifasta file is obtained. cdbyank locates the
database file by stripping the '.cidx' suffix off the index filename.  But this
is not enforced, because by using the -d option, cdbyank can make use of a
user-provided database to be used by the given index file. In the example
above, if the index file  "GUDB.human.cidx" is moved into another directory, a
cdbyank command (in that other directory) can be issued like that:

cdbyank -a 'human|Z98492' -d /usr/local/db/GUDB.human GUDB.human.cidx

The position of the index file in the list of arguments of cdbyank is not
enforced. For the -a usage, the error status returned by cdbyank to the shell
will be 1 if the given key was not found and 0 for success. 

The total number of fasta records indexed and the list of the keys stored in a
specific cdb index file can be retrieved with cdbyank's -n and -l switches,
respectively. This information is obtained from the index  file directly (the
database file is not needed for that). There is also a -s option that displays
a summary of the indexing information stored in the index at index time. These
are the initial name of the fastA file, its  size, how the index was created
(e.g. was -m (multiple keys) option given ? was -c or -C (shortcut keys) option
given?), the number of keys stored in the file as well as the number of fasta
records indexed -  the latter being the same with what -n option returns.

As an extra feature, cdbfasta and cdbyank can also be used for some special
cases where databases may have different records but with the same key
(non-unique keys). Although the performance will  degrade a little, cdbfasta is
able to index this kind of files, but by default cdbyank only outputs the first
record found. If you want all the possible records sharing the same key
(accession) to be retrieved and  displayed, the -x option should be given to
cdbyank.

3.Retrieving sequence ranges or only the defline
================================================

There are two cdbyank options added for convenience: -F option returns the
definition line of each requested FASTA record (the first line for each
record).  The -R option of cdbyank is intended for FASTA files containing
actual genetic sequences (nucleotide or protein) and expects each of the
retrieval commands to have the following format (space delimited)

<key> <right_coordinate> <left_coordinate>

For example if we only want to retrieve the sequence range 24...178 (letter
numbering starts at 1) from sequence with the name 'human|Z98492', then the
cdbyank command would look like this:

cdbyank -a 'human|Z98492 24 178' -R GUDB.human.cidx

Multiple sequence ranges can be extracted this way by providing a file having
each line following the format above (key followed by the two coordinates).
Then, as before, such file can be piped into  cdbyank with -R option to pull
specific sequence ranges for each of the sequences specified in the input file.


cat seqlistranges | cdbyank -R GUDB.human.cidx

Note that this range option works by actually parsing and looping through the
retrieved record characters internally - so the performance is poor when some
terminal range is pulled from a very large record.

4.Data compression option
=========================
(This only applies if the programs were built with compression support enabled)

The indexing program cdbfasta has the  -z <compressed_db> option which creates
a compressed file from the input file and at the same time creates an index
file for this compressed file. The original input file  can then be discarded
(if it is only needed for random access through cdbyank). The entire input file
can be recovered from the resulting <compressed_db> by using the -z option of
cdbyank. Because each record is compressed separately, compression is poor if
the records are small. Compression is only advised when:

 * data records are large enough for the compression algorithm to adapt (at
   least 1KB, the more the better)

 * only random access is needed to the data records (so the original file can
   be discarded) 

The compression can be quite slow for large files and there is also some
performance penalty for cdbyank as it has to decompress the retrieved records
on the fly.

The input data for cdbfasta compression can be collected from stdin if '-' is
used instead of a file name:

cat my_data_files* | cdbfasta - -z mydata.cdbz

This option is useful especially when the total size of input data files is
extremely large (over the file-system limits or over the 4GB internal limit of
cdbfasta) while the compressed output can be small enough to  fall under such
limits.

With compressed databases cdbyank can be used normally without extra options as
it will auto-detect the compression (from the index file info) and activate
on-the-fly decompression of the retrieved records.  

The -F and -R options are not yet accepted when working with compressed
records.

5.Development notes
===================

These tools were developed in C++, based on the publicly available cdb
("constant database") code written by D.J. Bernstein
(http://cr.yp.to/djb.html). "Constant databases" are those that we don't need
to add to or remove records from. The original C source was (rather crudely)
wrapped into C++ classes and adjusted to automatically index fasta records and
to create an external index instead of storing the original data records like
the original cdb library code does.  Also the "endianness" is now checked at
runtime and the bytes are swapped accordingly such that the file offsets and
record sizes are always  read/written in the same way in the index file. 

The compression option uses zlib's "deflate" method. The program uses deflate()
with Z_FULL_FLUSH after each record, such that random record decompression is
possible after the first dummy record is  decompressed.

The index file contains an info chunk (actually stored at the end of the file)
which maintains a summary data and flags about the indexing process (the -s
option of cdbyank retrieves this information). Since the  compression option
was added, cdbyank is always trying to read this information first (before
opening the data file) in order to determine if the data records are compressed
or not.

--
Geo Pertea 
gpertea@tigr.org
06/09/2003

Current author contact:
gpertea@jhu.edu

This software is Open Source Software, distributed under an Artistic License:
https://opensource.org/licenses/artistic-license-2.0
