Christopher Fields
and 1 contributors

Modules

Changes for version 1.70

  • 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