Entrez Gene Parser in Perl / News: Recent posts

EntrezGene parser V1.09 - critical for Perl 5.005_03 users

Added feature over V1.08 includes:

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
Fixed incompatibility with Perl 5.005_03 in codes introduced in V1.07 after Indexer was implemented.

Posted by Dr. Mingyi Liu 2005-04-29

Notes about 1.07 release, please upgrade!

Added a fast indexer (This indexer indexes human file in 21 seconds on one Xeon 2.4 GHz CPU).
Added test scripts
Minor bug fixes
Added new convenient methods (rawdata() and fh())
Now file handles are accepted too (by new() and fh(). new() also now accept '-file', '-fh', 'fh' in addition to 'file')
Updated documentation

Posted by Dr. Mingyi Liu 2005-04-14

V1.05 (critical update!) still contains all 4 parsers

Version 1.05 is released in response to the new NCBI Entrez Gene download file. NCBI introduced some changes to the file format that broke earlier versions of my parsers.

This version 1.05 works for both the new NCBI format and the previous NCBI format, so it is recommended that you download this version. Note that, however, this version is about 30% slower than version 1.04 due to the changes.

IMPORTANT NOTE: I only fixed my regex-based parser on this new NCBI Entrez Gene file, which means that from this version on, the other parsers in the package will cease to work on the latest NCBI Entrez Gene downloads. Version 1.05 will also be the last version of my packages that contain ALL FOUR parsers I created.... read more

Posted by Dr. Mingyi Liu 2005-04-05