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
BioPerl.
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 EntrezGene.pm and Sequence.pm 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 parse_entrez_gene_example.pl
Added code to deal with CCDS xref and Hugo symbol (under
gene properties! unlike before) in parse_entrez_gene_example.pl
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 Util.pm into EntrezGene.pm.
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