Zerg(3pm)

NAME
Zerg - a lexical scanner for BLAST reports.

SYNOPSIS
use Zerg;

DESCRIPTION
This manpage describes the Zerg library and its interface for use with Perl.

The Zerg library contains a C/flex lexical scanner for BLAST reports and a set of supporting functions. It is centered on a "get_token" function that scans the input for specified lexical elements and, when one is found, returns its code and value to the user.

It is intended to be fast: for that we used flex, which provides simple regular expression matching and input buffering in the generated C scanner. And it is intended to be simple in the sense of providing just a lexical scanner, with no features whose support could slow down its main function.

  FUNCTIONS
zerg_get_token() is the core function of this module. Each time it is called, it scans the input BLAST report for the next "interesting" lexical element and returns its code and value. Codes are listed in the section "EXPORTED CONSTANTS (TOKEN CODES)". Code zero (not listed) means end of file.

  ($code, $value) = Zerg::zerg_get_token();

zerg_open_file($filename) opens $filename in read-only mode and set it as the input to the scanner. If this function is not called, the standard input is used.

  Zerg::zerg_open_file($filename);

zerg_close_file() closes the file opened with zerg_open_file().

zerg_get_token_offset() returns the byte offset (relative to the beginning of file) of the last token read. (See section BUGS).

zerg_ignore($code) instructs zerg_get_token not to return when it finds a token with code $code.

zerg_ignore_all() does zerg_ignore on all token codes.

zerg_unignore($code) instructs zerg_get_token to return when it finds a token with code $code.

zerg_unignore_all() does zerg_unignore on all token codes.

  Example:
  Zerg::zerg_ignore_all();
  Zerg::zerg_unignore(QUERY_NAME);
  Zerg::zerg_unignore(SUBJECT_NAME);

  EXPORTED CONSTANTS (TOKEN CODES)
    ALIGNMENT_LENGTH
    BLAST_VERSION
    CONVERGED
    DATABASE
    DESCRIPTION_ANNOTATION
    DESCRIPTION_EVALUE
    DESCRIPTION_HITNAME
    DESCRIPTION_SCORE
    END_OF_REPORT
    EVALUE
    GAPS
    HSP_METHOD
    IDENTITIES
    NOHITS
    PERCENT_IDENTITIES
    PERCENT_POSITIVES
    POSITIVES
    QUERY_ALI
    QUERY_ANNOTATION
    QUERY_END
    QUERY_FRAME
    QUERY_LENGTH
    QUERY_NAME
    QUERY_ORIENTATION
    QUERY_START
    REFERENCE
    ROUND_NUMBER
    ROUND_SEQ_FOUND
    ROUND_SEQ_NEW
    SCORE
    SCORE_BITS
    SEARCHING
    SUBJECT_ALI
    SUBJECT_ANNOTATION
    SUBJECT_END
    SUBJECT_FRAME
    SUBJECT_LENGTH
    SUBJECT_NAME
    SUBJECT_ORIENTATION
    SUBJECT_START
    TAIL_OF_REPORT
    UNMATCHED

  NOTES ON THE SCANNER
Some BLAST parsers rely on some simple regular expression matches to conclude about token types and values. For example: an input line matching /^Query=\s(\S+)/ should make such a "loose" parser to infer that a token was found, it is a query name and its value is $1. Although improbable, it is perfectly possible for an anotation field to match /^Query=\s(\S+)/. Worse than this is the fact that those parsers are often unable to detect corrupt or truncated BLAST reports, possibly producing inaccurate information.

The scanner provided by this library is much more stringent: for a token to match it must be in its place in the context of a BLAST report. For example: in a single BLAST report, a QUERY_NAME cannot follow another QUERY_NAME. The scanner can be thought as, and in fact it is, a big regular expression that matches an entire BLAST report.

A special token code (UNMATCHED) is provided for cases in which the input text does not match any other lexical rule of the scanner. When an umnacthed character is found, either the report is corrupt or the scanner has a bug.

If you are interested in only a few token codes, try to zerg_ignore() as much codes you can. This will avoid unnecessary function calls that eat a lot of CPU.

EXAMPLES
This program prints the code and the value of each token it finds.

  #!/usr/bin/perl -w
  use strict;
  use Zerg;

  my ($code, $value);
  while((($code, $value)= Zerg::zerg_get_token()) && $code)
  {
      print "$code\t$value\n";
  }

The program below is a "syntax checker". The presence of UNMATCHEDs is a strong indicator of problems in the BLAST report. (See section NOTES ON THE SCANNER)

  #!/usr/bin/perl -w
  use strict;
  use Zerg;

  my ($code, $value);

  Zerg::zerg_ignore_all();
  Zerg::zerg_unignore(UNMATCHED);

  while((($code, $value)= Zerg::zerg_get_token()) && $code)
  {
      print "UNMATCHED CHAR:\t$value\n";
  }

BUGS
The tokens DESCRIPTION_ANNOTATION, DESCRIPTION_SCORE and DESCRIPTION_EVALUE are scanned all at once and released one by one on user request. So, if the user wants to get any of these fields, they must be unignored BEFORE scanning DESCRIPTION_ANNOTATION.

zerg_get_token_offset() may return incorrect values for these tokens and those that are modified by the parser, namely: QUERY_LENGTH, SUBJECT_LENGTH, EVALUE, GAPS.

TODO
Add more tokens to the scanner as the need for that appears.

AUTHOR
Apuã Paquola, IQ-USP Bioinformatics Lab, apua@iq.usp.br

Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany

SEE ALSO
perl(1), flex(1), http://www.bioperl.org, http://www.ncbi.nlm.nih.gov/BLAST