ivy.genbank module

ivy.genbank.ac2gi(ac)

ivy.genbank.batch(iterable, size)

Take an iterable and return it in chunks (sub-iterables)

Parameters:

• iterable – Any iterable
• size (int) – Size of chunks

Yields:

Chunks of size size

ivy.genbank.blast(query, e=10, n=100, entrez_query=u'')

ivy.genbank.blast_closest(fasta, e=10)

ivy.genbank.create_fastas(data, genes)

ivy.genbank.extract_gbac(s)

Extract genbank accession

Parameters:s (str) – text string of genbank file Returns:Accession number(s) Return type:list

ivy.genbank.extract_gene(seq, gene)

RR: Not sure what format seq should be in -CZ

ivy.genbank.fetch_DNA_seqs(terms, maxn=10000, batchsize=1000)

terms: sequence of search terms, quoted appropriately, with Entrez

specifiers, e.g. [‘“Mus musculus”[organism]’]

maxn: maximum number of sequences to return returns list of SeqRecord objects

ivy.genbank.fetch_aclist(aclist, batchsize=1000)

ivy.genbank.fetch_gilist(gilist, batchsize=1000)

ivy.genbank.fetchseq(gi)

ivy.genbank.fetchtax(taxid)

ivy.genbank.gi2tax(gi)

ivy.genbank.gi2webenv(gilist)

ivy.genbank.merge_fastas(fnames, name=u'merged')

ivy.genbank.organism_id(s)

ivy.genbank.search_taxonomy(q)

ivy.genbank.seqrec_taxid(seqrec)

extract the NCBI taxon id from a sequence record

ivy.genbank.start_codons(seq)

ivy.genbank.trimpos(rec)

return the positions of the first and last ungapped base