Revision history for Bio-ASN1-Entrezgene

1.73      2018-09-24 21:31:26-05:00 America/Chicago
  * Fix regex warnings for Perl 5.28.
  * New module 'Bio::SeqIO::entrezgene' imported from the BioPerl
    distribution.  This means Bio-ASN1-Entrezgene now "Enhances"
    BioPerl's Bio::SeqIO instead of being a hard dependency of

1.72      2016-09-02 06:49:48-05:00 America/Chicago
  * Full release (no changes from 1.71 beyond version)

1.71      2016-09-01 22:57:25-05:00 America/Chicago (TRIAL RELEASE)
  * Minor bump for impending BioPerl 1.7 release.
  * #2 : 'Unescaped left brace in regex is deprecated' with newer versions of perl
    fixed [fjossandon]

1.70      2013-09-14 14:39:54 America/Chicago
  * Bio::ASN1::EntrezGene is now able to parse EntrezGene-set in which case
    next_seq() will return the next set of sequences with each sequence as
    an element in the array ref instead of an array ref with a single element.

version 1.10: Important update if you see segmentation fault when running the
              parser - so far I only saw it happen on Perl 5.8 (Perl 5.10 is 
              fine) due to an exceedingly long (and invalid) URL in one 
              Arabidopsis entry. It's due to Perl regex engine core dumps when
              matching the long string exhausted the stack. I changed the 
              particular regex in and to solve the 
              issue. The overall parsing runs 2-3% faster after the change.

version 1.09: Added parser/indexer for NCBI's ASN.1-formatted
                sequence files (like Genbank records).
              Updated test, example scripts and documentation
              Minor fix on
              Added code to deal with CCDS xref and Hugo symbol (under
                gene properties! unlike before) in
              Updated parser & indexer file handle code to work with perl version 
                5.005_03 (previous code since 1.07 only works with 5.6 or higher).
              Commented out count_records call in testindex.t to allow successful
                test on 5.005_03-compatible bioperl versions.

version 1.08: Split test script into two for better testing
              Minor change in documentation and test scripts
              NO change in parser/indexer code!

version 1.07: Added indexing capability through a new module
              Added testing script for make test
              Added example script for indexing, reorganized examples scripts
              Fixed a bug in next_seq
              Reset line number after input_file() or fh() calls
              Added rawdata(), fh() functions and -file, -fh, fh to new()
              Updated documentation to reflect all changes

version 1.06: integrated code from into
              changed packaging to Perl standard
              changed next_seq() default option to 2, so now the call
                $parser->next_seq() is equivalent to the call
                $parser->next_seq(2) in version 1.05
              updated documentation to reflect all changes

version 1.05: added support to parse the NCBI 4/5/2005 download, which
              inexplicably added a useless space before ',' on all lines, broke
              some lines into two yet condensed others (brackets) to one line.
              This unfortunately slows down my parser because I have to use
              lookahead regexes to fix the parser for this weird new format.
              I also fixed a minor mistake in error reporting function

version 1.04: added attempt at opening large file (2 GB) on Perl that does
              not support it; added 'file' option to new(); added file
              name in error reporting message; updated documentation

version 1.03: added validating capability such that anything that does not
              conform to the current NCBI Entrez Gene ASN.1 format would
              raise error and stops program. Position of the offending
              data item would be reported.

version 1.02: added input_file function that accepts filename input, and
              next_seq function that returns the next record

version 1.01: unescaped double quote escapes in double quoted strings

version 1.0: released