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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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