sugar.index.fastaindex module¶

FASTA indexer

class sugar.index.fastaindex.FastaBinarySearchFile[source]¶

Custom BinarySeachFile used to store the index

class sugar.index.fastaindex.FastaIndex(dbname=None, create=False, path='{dbpath}', mode=None)[source]¶

Index FASTA files and query (sub-) sequences

Parameters:

dbname (str) – Name of index file, default: last used index file
create (str) – Create a new index file
path (str) – Common path for FASTA file names, default '{dbpath}', i.e. filenames are relative to path of index file, only needed for new index file
mode (str) – 'binary' uses a binary search file, 'db' uses a database via Python’s dbm module, only needed for new index file

get_basket(seqids)[source]¶

Return BioBasket with all corresponding sequences

See iter() for documentation of seqids argument.

get_fasta(seqids)[source]¶

Return FASTA string with all sequences

See iter() for documentation of seqid argument.

get_fastaheader(seqids)[source]¶

Return FASTA header from all sequences

See iter() for documentation of seqid argument.

get_seq(seqid)[source]¶

Return a BioSeq given its id

See iter() for documentation of seqid argument.

iter(seqids)[source]¶

Yield BioSeq sequences from given sequence ids

Parameters:: seqids – List of sequence ids, might also be a single seqid, a 3-len tuple with start and stop indices (seqid, start, stop) (start or stop can be None), or a list with 3-len tuples

iter_fasta(seqids)[source]¶

Yield FASTA strings from given sequence ids

See iter() for documentation of seqids argument.

iter_fastaheader(seqids)[source]¶

Yield FASTA headers from given sequence ids

See iter() for documentation of seqids argument.