BioPythonTip for GenBank

<<TableOfContents>>

== 파싱한 후 취할 수 있는 객체들 ==

=== RecordParser를 썼을때 ===
{{{
parser = GenBank.RecordParser()
iterator = GenBank.Iterator()
while 1:
    cur_record = iterator.next()
    if cur_record is None:
        break
    cur_record.어쩌구저쩌구
}}}
위 파서는 핵산DB, 단백질 DB모두에게 적용된다.

 * locus - The name specified after the LOCUS keyword in the GenBank record. This may be the accession number, or a clone id or something else.
 * size - The size of the record.
 * residue_type - The type of residues making up the sequence in this record. Normally something like RNA, DNA or PROTEIN, but may be as esoteric as 'ss-RNA circular'.
 * data_file_division - The division this record is stored under in GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT -> bacteria...)
 * date - The date of submission of the record, in a form like '28-JUL-1998'
 * accession - list of all accession numbers for the sequence.
 * nid - Nucleotide identifier number.
 * pid - Proteint identifier number
 * version - The accession number + version (ie. AB01234.2)
 * db_source - Information about the database the record came from
 * gi - The NCBI gi identifier for the record.
 * keywords - A list of keywords related to the record.
 * segment - If the record is one of a series, this is info about which segment this record is (something like '1 of 6').
 * source - The source of material where the sequence came from.
 * organism - The genus and species of the organism (ie. 'Homo sapiens')
 * taxonomy - A listing of the taxonomic classification of the organism, starting general and getting more specific.
 * references - A list of Reference objects.
  * number - The number of the reference in the listing of references.
  * bases - The bases in the sequence the reference refers to.
  * authors - String with all of the authors.
  * title - The title of the reference.
  * journal - Information about the journal where the reference appeared.
  * medline_id - The medline id for the reference.
  * pubmed_id - The pubmed_id for the reference.
  * remark - Free-form remarks about the reference.
 * comment - Text with any kind of comment about the record.
 * features - A listing of Features making up the feature table.
  * key - The key name of the featue (ie. source)
  * location - The string specifying the location of the feature.
  * qualfiers - A listing Qualifier objects in the feature.
   * key - The key name of the qualifier (ie. /organim=)
   * value - The value of the qualifier ("Dictyostelium discoideum").
 * base_counts - A string with the counts of bases for the sequence.
 * origin - A string specifying info about the origin of the sequence.
 * sequence - A string with the sequence itself.


=== FeatureParser 를 썼을때 ===
{{{
parser = GenBank.FeatureParser()
iterator = GenBank.Iterator()
while 1:
    cur_record = iterator.next()
    if cur_record is None:
        break
    cur_record.어쩌구저쩌구
}}}
가장 자세히 파싱할 수 있는 파서이며, 위 cur_record 객체는 SeqFeature를 따르는 객체로, BioCorba로 연동도 될 수 있다.

 * features
  * location - the location of the feature on the sequence
   * position - The position of the boundary.
   * extension - An optional argument which must be zero since we don't have an extension. The argument is provided so that the same number of arguments can be passed to all position types.
  * type - the specified type of the feature (ie. CDS, exon, repeat...)
  * ref - A reference to another sequence. This could be an accession number for some different sequence.
  * ref_db - A different database for the reference accession number.
  * qualifier - A dictionary of qualifiers on the feature. These are analagous to the qualifiers from a GenBank feature table. The keys of the dictionary are qualifier names, the values are the qualifier values.
  * sub_features - Additional SeqFeatures which fall under this 'parent' feature. For instance, if we having something like: 
   {{{CDS    join(1..10,30..40,50..60)}}} The the top level feature would be a CDS from 1 to 60, and the sub features would be of 'CDS_span' type and would be from 1 to 10, 30 to 40 and 50 to 60, respectively.

 * references
  * location - A list of Location objects specifying regions of the sequence that the references correspond to. If no locations are specified, the entire sequence is assumed.
  * authors - A big old string, or a list split by author, of authors for the reference.
  * title - The title of the reference.
  * journal - Journal the reference was published in.
  * medline_id - A medline reference for the article.
  * pubmed_id - A pubmed reference for the article.
  * comment - A place to stick any comments about the reference.

 * name : Version
 * annotations
 * discription : Definition