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Bio.SeqIO support for the "genbank" and "embl" file formats.
You are expected to use this module via the Bio.SeqIO functions. Note that internally this module calls Bio.GenBank to do the actual parsing of GenBank, EMBL and IMGT files.
See also:
International Nucleotide Sequence Database Collaboration http://www.insdc.org/
GenBank http://www.ncbi.nlm.nih.gov/Genbank/
EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl/
DDBJ (DNA Data Bank of Japan) http://www.ddbj.nig.ac.jp/
IMGT (use a variant of EMBL format with longer feature indents) http://imgt.cines.fr/download/LIGM-DB/userman_doc.html http://imgt.cines.fr/download/LIGM-DB/ftable_doc.html http://www.ebi.ac.uk/imgt/hla/docs/manual.html
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_InsdcWriter Base class for GenBank and EMBL writers (PRIVATE). |
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GenBankWriter | |||
EmblWriter | |||
ImgtWriter |
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__package__ =
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Breaks up a Genbank file into SeqRecord objects. Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features. Note that for genomes or chromosomes, there is typically only one record. |
Breaks up an EMBL file into SeqRecord objects. Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features. Note that for genomes or chromosomes, there is typically only one record. |
Breaks up an IMGT file into SeqRecord objects. Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features. Note that for genomes or chromosomes, there is typically only one record. |
Breaks up a Genbank file into SeqRecord objects for each CDS feature. Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given). |
Breaks up a EMBL file into SeqRecord objects for each CDS feature. Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given). |
Build a GenBank/EMBL position string (PRIVATE). Use offset=1 to add one to convert a start position from python counting. |
Build a GenBank/EMBL location string from a SeqFeature (PRIVATE). There is a choice of how to show joins on the reverse complement strand, GenBank used "complement(join(1,10),(20,100))" while EMBL used to use "join(complement(20,100),complement(1,10))" instead (but appears to have now adopted the GenBank convention). Notice that the order of the entries is reversed! This function therefore uses the first form. In this situation we expect the parent feature and the two children to all be marked as strand == -1, and in the order 0:10 then 19:100. Also need to consider dual-strand examples like these from the Arabidopsis thaliana chloroplast NC_000932: join(complement(69611..69724),139856..140650) gene ArthCp047, GeneID:844801 or its CDS (protein NP_051038.1 GI:7525057) which is further complicated by a splice: join(complement(69611..69724),139856..140087,140625..140650) For mixed this mixed strand feature, the parent SeqFeature should have no strand (either 0 or None) while the child features should have either strand +1 or -1 as appropriate, and be listed in the order given here. |
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