Changes between Version 6 and Version 7 of BioPerlRoundTripSecondPass

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Timestamp:
2008/02/13 17:09:13 (11 years ago)
Author:
heikki
Comment:

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  • BioPerlRoundTripSecondPass

    v6 v7  
    5151 * ~~MAJOR: line BASE not present in recent genbank format, but it is still generated by !BioPerl~~ 
    5252   * This should be safe line to drop, because GenPept has never had it and all (most?) parsers can deal with both. 
    53    * fixed SVN revision 14503. 
     53   * fixed: SVN revision 14503. 
    5454 * minor: features are not returned in order 
    5555 
    5656== swiss-prot == 
    5757 
    58  * minor: No full stop at the end of the DT lines 
    59  * MAJOR: GN line returning only value from key/value pairs (e.g. 
     58 * ~~MAJOR: No full stop at the end of the DT lines~~ 
     59   * This is actually important to have. The parser will not grab the sequence version without the stop character. 
     60   * Changed the parser to work regardless of the end stop character 
     61   * write_seq now writes out the stops 
     62   * fixed: SVN revision 14504. 
     63 * ~~MAJOR: PE (evidence) line returned between CC and DR lines when it should be between DR and KW lines~~ 
     64   * fixed: SVN revision 14505. 
     65 * ~~MAJOR: RX line:DOI key/value pair lost~~ 
     66   * The parser rexerps depend on the order of references. It will be easier to maintain without this restriction. 
     67   * The parser does not take into account that any of the refs can be missing 
     68   * Rewrote RX line parsing and writing 
     69   * fixed: SVN revision 14505. 
     70 * MAJOR: GN line returning only values from key/value pairs (e.g. 
    6071{{{ 
    6172GN   Name=DOF3.7; Synonyms=BBFA, DAG1;...    
     
    6374GN   DOF3.7 OR BBFA OR DAG1 ... 
    6475}}} 
     76 * MAJOR: Extra spaces and a stop added to FT HELIX and STRAND lines: 
     77{{{ 
     78FT   STRAND      910    913 
     79-> 
     80FT   STRAND      910    913       . 
     81}}} 
    6582 * minor: OC line word wrapping differences 
    6683 * minor: extra spaces at the end of the first RT line when there are more than one of them 
    67  * MAJOR: RX line:DOI key/value pair lost 
    68  * MAJOR: PE (evidence) line returned between CC and DR lines when it should be between DR and KW lines 
    6984 * minor: extra space after first FT line 
    7085 * minor: FTid sometimes not written on its own line 
    7186 * minor: extra space written to the end of the sequence line 
     87   *'''Note:''' All these extra spaces at the end of the line  come from _write_line_swissprot_regex(). Check if this can be fixed! 
    7288