ó Y_Sc@@s$dZddlmZddlTddlmZmZmZmZm Z m Z m Z m Z m Z mZmZmZddd d d d d ddddddddddgZeee eeee e e e eef ad„Zd„Zeeee ee ee eef ad„Zdd„ZdS(s\ Sequence file reading and writing. Biological sequence data is stored and transmitted using a wide variety of different file formats. This package provides convenient methods to read and write several of these file fomats. CoreBio is often capable of guessing the correct file type, either from the file extension or the structure of the file: >>> import corebio.seq_io >>> afile = open("test_corebio/data/cap.fa") >>> seqs = corebio.seq_io.read(afile) Alternatively, each sequence file type has a separate module named FILETYPE_io (e.g. fasta_io, clustal_io). >>> import corebio.seq_io.fasta_io >>> afile = open("test_corebio/data/cap.fa") >>> seqs = corebio.seq_io.fasta_io.read( afile ) Sequence data can also be written back to files: >>> fout = open("out.fa", "w") >>> corebio.seq_io.fasta_io.write( fout, seqs ) Supported File Formats ---------------------- Module Name Extension read write features --------------------------------------------------------------------------- array_io array, flatfile yes yes none clustal_io clustalw aln yes yes fasta_io fasta, Pearson fa yes yes none genbank_io genbank gb yes intelligenetics_io intelligenetics ig yes yes msf_io msf msf yes nbrf_io nbrf, pir pir yes nexus_io nexus nexus yes phylip_io phylip phy yes plain_io plain, raw yes yes none table_io table tbl yes yes none Each IO module defines one or more of the following functions and variables: read(afile, alphabet=None) Read a file of sequence data and return a SeqList, a collection of Seq's (Alphabetic strings) and features. read_seq(afile, alphabet=None) Read a single sequence from a file. iter_seq(afile, alphabet =None) Iterate over the sequences in a file. index(afile, alphabet = None) Instead of loading all of the sequences into memory, scan the file and return an index map that will load sequences on demand. Typically not implemented for formats with interleaved sequences. write(afile, seqlist) Write a collection of sequences to the specifed file. write_seq(afile, seq) Write one sequence to the file. Only implemented for non-interleaved, headerless formats, such as fasta and plain. example A string containing a short example of the file format names A list of synonyms for the file format. E.g. for fasta_io, ( 'fasta', 'pearson', 'fa'). The first entry is the preferred format name. extensions A list of file name extensions used for this file format. e.g. fasta_io.extensions is ('fa', 'fasta', 'fast', 'seq', 'fsa', 'fst', 'nt', 'aa','fna','mpfa'). The preferred or standard extension is first in the list. Attributes : - formats -- Available seq_io format parsers - format_names -- A map between format names and format parsers. - format_extensions -- A map between filename extensions and parsers. i(tabsolute_importi(t*i( t clustal_iotfasta_iotmsf_iotnbrf_iotnexus_iotplain_iot phylip_iot stockholm_iotintelligenetics_iottable_iotarray_iot genbank_ioRRRRRRRtnull_ioR R R R R treadtformatst format_namestformat_extensionscC@sKi}x>tD]6}x-|jD]"}||ks5t‚|||tD]6}x-|jD]"}||ks5t‚||||s4  R * $