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Hold GenBank information in a format similar to the original record.
The Record class is meant to make data easy to get to when you are
just interested in looking at GenBank data.
Attributes:
o 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.
o size - The size of the record.
o 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'.
o data_file_division - The division this record is stored under in
GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT -> bacteria...)
o date - The date of submission of the record, in a form like '28-JUL-1998'
o accession - list of all accession numbers for the sequence.
o nid - Nucleotide identifier number.
o pid - Proteint identifier number
o version - The accession number + version (ie. AB01234.2)
o db_source - Information about the database the record came from
o gi - The NCBI gi identifier for the record.
o keywords - A list of keywords related to the record.
o segment - If the record is one of a series, this is info about which
segment this record is (something like '1 of 6').
o source - The source of material where the sequence came from.
o organism - The genus and species of the organism (ie. 'Homo sapiens')
o taxonomy - A listing of the taxonomic classification of the organism,
starting general and getting more specific.
o references - A list of Reference objects.
o comment - Text with any kind of comment about the record.
o features - A listing of Features making up the feature table.
o base_counts - A string with the counts of bases for the sequence.
o origin - A string specifying info about the origin of the sequence.
o sequence - A string with the sequence itself.
o contig - A string of location information for a CONTIG in a RefSeq file
o project - The genome sequencing project numbers
(will be replaced by the dblink cross-references in 2009).
o dblinks - The genome sequencing project number(s) and other links.
(will replace the project information in 2009).
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Provide a GenBank formatted output option for a Record. The objective of this is to provide an easy way to read in a GenBank record, modify it somehow, and then output it in 'GenBank format.' We are striving to make this work so that a parsed Record that is output using this function will look exactly like the original record. Much of the output is based on format description info at: ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt |
Output for the NID line. Use of NID is obsolete in GenBank files. |
Output for PID line. Presumedly, PID usage is also obsolete. |
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| Generated by Epydoc 3.0.1 on Sun May 3 17:14:19 2009 | http://epydoc.sourceforge.net |