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# Copyright 2008-2010 by Peter Cock.  All rights reserved. 

# This code is part of the Biopython distribution and governed by its 

# license.  Please see the LICENSE file that should have been included 

# as part of this package. 

 

"""Multiple sequence alignment input/output as alignment objects. 

 

The Bio.AlignIO interface is deliberately very similar to Bio.SeqIO, and in 

fact the two are connected internally.  Both modules use the same set of file 

format names (lower case strings).  From the user's perspective, you can read 

in a PHYLIP file containing one or more alignments using Bio.AlignIO, or you 

can read in the sequences within these alignmenta using Bio.SeqIO. 

 

Bio.AlignIO is also documented at U{http://biopython.org/wiki/AlignIO} and by 

a whole chapter in our tutorial: 

- U{http://biopython.org/DIST/docs/tutorial/Tutorial.html} 

- U{http://biopython.org/DIST/docs/tutorial/Tutorial.pdf} 

 

Input 

===== 

For the typical special case when your file or handle contains one and only 

one alignment, use the function Bio.AlignIO.read().  This takes an input file 

handle (or in recent versions of Biopython a filename as a string), format 

string and optional number of sequences per alignment.  It will return a single 

MultipleSeqAlignment object (or raise an exception if there isn't just one 

alignment): 

 

    >>> from Bio import AlignIO 

    >>> align = AlignIO.read("Phylip/interlaced.phy", "phylip") 

    >>> print(align) 

    SingleLetterAlphabet() alignment with 3 rows and 384 columns 

    -----MKVILLFVLAVFTVFVSS---------------RGIPPE...I-- CYS1_DICDI 

    MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTL...VAA ALEU_HORVU 

    ------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSL...PLV CATH_HUMAN 

 

For the general case, when the handle could contain any number of alignments, 

use the function Bio.AlignIO.parse(...) which takes the same arguments, but 

returns an iterator giving MultipleSeqAlignment objects (typically used in a 

for loop). If you want random access to the alignments by number, turn this 

into a list: 

 

    >>> from Bio import AlignIO 

    >>> alignments = list(AlignIO.parse("Emboss/needle.txt", "emboss")) 

    >>> print(alignments[2]) 

    SingleLetterAlphabet() alignment with 2 rows and 120 columns 

    -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKER...--- ref_rec 

    LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHP...HKE gi|94967506|receiver 

 

Most alignment file formats can be concatenated so as to hold as many 

different multiple sequence alignments as possible.  One common example 

is the output of the tool seqboot in the PHLYIP suite.  Sometimes there 

can be a file header and footer, as seen in the EMBOSS alignment output. 

 

Output 

====== 

Use the function Bio.AlignIO.write(...), which takes a complete set of 

Alignment objects (either as a list, or an iterator), an output file handle 

(or filename in recent versions of Biopython) and of course the file format:: 

 

    from Bio import AlignIO 

    alignments = ... 

    count = SeqIO.write(alignments, "example.faa", "fasta") 

 

If using a handle make sure to close it to flush the data to the disk:: 

 

    from Bio import AlignIO 

    alignments = ... 

    with open("example.faa", "w") as handle: 

        count = SeqIO.write(alignments, handle, "fasta") 

 

In general, you are expected to call this function once (with all your 

alignments) and then close the file handle.  However, for file formats 

like PHYLIP where multiple alignments are stored sequentially (with no file 

header and footer), then multiple calls to the write function should work as 

expected when using handles. 

 

If you are using a filename, the repeated calls to the write functions will 

overwrite the existing file each time. 

 

Conversion 

========== 

The Bio.AlignIO.convert(...) function allows an easy interface for simple 

alignnment file format conversions. Additionally, it may use file format 

specific optimisations so this should be the fastest way too. 

 

In general however, you can combine the Bio.AlignIO.parse(...) function with 

the Bio.AlignIO.write(...) function for sequence file conversion. Using 

generator expressions provides a memory efficient way to perform filtering or 

other extra operations as part of the process. 

 

File Formats 

============ 

When specifying the file format, use lowercase strings.  The same format 

names are also used in Bio.SeqIO and include the following: 

 

- clustal   - Output from Clustal W or X, see also the module Bio.Clustalw 

               which can be used to run the command line tool from Biopython. 

- emboss    - EMBOSS tools' "pairs" and "simple" alignment formats. 

- fasta     - The generic sequence file format where each record starts with 

               an identifer line starting with a ">" character, followed by 

               lines of sequence. 

- fasta-m10 - For the pairswise alignments output by Bill Pearson's FASTA 

               tools when used with the -m 10 command line option for machine 

               readable output. 

- ig        - The IntelliGenetics file format, apparently the same as the 

               MASE alignment format. 

- nexus     - Output from NEXUS, see also the module Bio.Nexus which can also 

               read any phylogenetic trees in these files. 

- phylip    - Interlaced PHYLIP, as used by the PHLIP tools. 

- phylip-sequential - Sequential PHYLIP. 

- phylip-relaxed - PHYLIP like format allowing longer names. 

- stockholm - A richly annotated alignment file format used by PFAM. 

 

Note that while Bio.AlignIO can read all the above file formats, it cannot 

write to all of them. 

 

You can also use any file format supported by Bio.SeqIO, such as "fasta" or 

"ig" (which are listed above), PROVIDED the sequences in your file are all the 

same length. 

""" 

 

 

from __future__ import print_function 

from Bio._py3k import basestring 

 

__docformat__ = "epytext en"  # not just plaintext 

 

#TODO 

# - define policy on reading aligned sequences with gaps in 

#   (e.g. - and . characters) including how the alphabet interacts 

# 

# - Can we build the to_alignment(...) functionality 

#   into the generic Alignment class instead? 

# 

# - How best to handle unique/non unique record.id when writing. 

#   For most file formats reading such files is fine; The stockholm 

#   parser would fail. 

# 

# - MSF multiple alignment format, aka GCG, aka PileUp format (*.msf) 

#   http://www.bioperl.org/wiki/MSF_multiple_alignment_format 

 

from Bio.Align import MultipleSeqAlignment 

from Bio.Align.Generic import Alignment 

from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet 

from Bio.File import as_handle 

 

from . import StockholmIO 

from . import ClustalIO 

from . import NexusIO 

from . import PhylipIO 

from . import EmbossIO 

from . import FastaIO 

 

#Convention for format names is "mainname-subtype" in lower case. 

#Please use the same names as BioPerl and EMBOSS where possible. 

 

_FormatToIterator = {  # "fasta" is done via Bio.SeqIO 

                     "clustal": ClustalIO.ClustalIterator, 

                     "emboss": EmbossIO.EmbossIterator, 

                     "fasta-m10": FastaIO.FastaM10Iterator, 

                     "nexus": NexusIO.NexusIterator, 

                     "phylip": PhylipIO.PhylipIterator, 

                     "phylip-sequential": PhylipIO.SequentialPhylipIterator, 

                     "phylip-relaxed": PhylipIO.RelaxedPhylipIterator, 

                     "stockholm": StockholmIO.StockholmIterator, 

                     } 

 

_FormatToWriter = {  # "fasta" is done via Bio.SeqIO 

                     # "emboss" : EmbossIO.EmbossWriter, (unfinished) 

                   "nexus": NexusIO.NexusWriter, 

                   "phylip": PhylipIO.PhylipWriter, 

                   "phylip-sequential": PhylipIO.SequentialPhylipWriter, 

                   "phylip-relaxed": PhylipIO.RelaxedPhylipWriter, 

                   "stockholm": StockholmIO.StockholmWriter, 

                   "clustal": ClustalIO.ClustalWriter, 

                   } 

 

 

def write(alignments, handle, format): 

    """Write complete set of alignments to a file. 

 

    Arguments: 

     - alignments - A list (or iterator) of Alignment objects (ideally the 

                   new MultipleSeqAlignment objects), or (if using Biopython 

                   1.54 or later) a single alignment object. 

     - handle    - File handle object to write to, or filename as string 

                   (note older versions of Biopython only took a handle). 

     - format    - lower case string describing the file format to write. 

 

    You should close the handle after calling this function. 

 

    Returns the number of alignments written (as an integer). 

    """ 

    from Bio import SeqIO 

 

    #Try and give helpful error messages: 

    if not isinstance(format, basestring): 

        raise TypeError("Need a string for the file format (lower case)") 

    if not format: 

        raise ValueError("Format required (lower case string)") 

    if format != format.lower(): 

        raise ValueError("Format string '%s' should be lower case" % format) 

 

    if isinstance(alignments, Alignment): 

        #This raised an exception in older versions of Biopython 

        alignments = [alignments] 

 

    with as_handle(handle, 'w') as fp: 

        #Map the file format to a writer class 

        if format in _FormatToWriter: 

            writer_class = _FormatToWriter[format] 

            count = writer_class(fp).write_file(alignments) 

        elif format in SeqIO._FormatToWriter: 

            #Exploit the existing SeqIO parser to do the dirty work! 

            #TODO - Can we make one call to SeqIO.write() and count the alignments? 

            count = 0 

            for alignment in alignments: 

                if not isinstance(alignment, Alignment): 

                    raise TypeError( 

                        "Expect a list or iterator of Alignment objects.") 

                SeqIO.write(alignment, fp, format) 

                count += 1 

        elif format in _FormatToIterator or format in SeqIO._FormatToIterator: 

            raise ValueError("Reading format '%s' is supported, but not writing" 

                             % format) 

        else: 

            raise ValueError("Unknown format '%s'" % format) 

 

    assert isinstance(count, int), "Internal error - the underlying %s " \ 

           "writer should have returned the alignment count, not %s" \ 

           % (format, repr(count)) 

 

    return count 

 

 

#This is a generator function! 

def _SeqIO_to_alignment_iterator(handle, format, alphabet=None, seq_count=None): 

    """Uses Bio.SeqIO to create an MultipleSeqAlignment iterator (PRIVATE). 

 

    Arguments: 

     - handle    - handle to the file. 

     - format    - string describing the file format. 

     - alphabet  - optional Alphabet object, useful when the sequence type 

                   cannot be automatically inferred from the file itself 

                   (e.g. fasta, phylip, clustal) 

     - seq_count - Optional integer, number of sequences expected in each 

                   alignment.  Recommended for fasta format files. 

 

    If count is omitted (default) then all the sequences in the file are 

    combined into a single MultipleSeqAlignment. 

    """ 

    from Bio import SeqIO 

    assert format in SeqIO._FormatToIterator 

 

    if seq_count: 

        #Use the count to split the records into batches. 

        seq_record_iterator = SeqIO.parse(handle, format, alphabet) 

 

        records = [] 

        for record in seq_record_iterator: 

            records.append(record) 

            if len(records) == seq_count: 

                yield MultipleSeqAlignment(records, alphabet) 

                records = [] 

        if len(records) > 0: 

            raise ValueError("Check seq_count argument, not enough sequences?") 

    else: 

        #Must assume that there is a single alignment using all 

        #the SeqRecord objects: 

        records = list(SeqIO.parse(handle, format, alphabet)) 

        if records: 

            yield MultipleSeqAlignment(records, alphabet) 

    raise StopIteration 

 

 

def _force_alphabet(alignment_iterator, alphabet): 

    """Iterate over alignments, over-riding the alphabet (PRIVATE).""" 

    #Assume the alphabet argument has been pre-validated 

    given_base_class = _get_base_alphabet(alphabet).__class__ 

    for align in alignment_iterator: 

        if not isinstance(_get_base_alphabet(align._alphabet), 

                          given_base_class): 

            raise ValueError("Specified alphabet %s clashes with " 

                             "that determined from the file, %s" 

                             % (repr(alphabet), repr(align._alphabet))) 

        for record in align: 

            if not isinstance(_get_base_alphabet(record.seq.alphabet), 

                              given_base_class): 

                raise ValueError("Specified alphabet %s clashes with " 

                                 "that determined from the file, %s" 

                           % (repr(alphabet), repr(record.seq.alphabet))) 

            record.seq.alphabet = alphabet 

        align._alphabet = alphabet 

        yield align 

 

 

def parse(handle, format, seq_count=None, alphabet=None): 

    """Iterate over an alignment file as MultipleSeqAlignment objects. 

 

    Arguments: 

     - handle    - handle to the file, or the filename as a string 

                   (note older versions of Biopython only took a handle). 

     - format    - string describing the file format. 

     - alphabet  - optional Alphabet object, useful when the sequence type 

                   cannot be automatically inferred from the file itself 

                   (e.g. fasta, phylip, clustal) 

     - seq_count - Optional integer, number of sequences expected in each 

                   alignment.  Recommended for fasta format files. 

 

    If you have the file name in a string 'filename', use: 

 

    >>> from Bio import AlignIO 

    >>> filename = "Emboss/needle.txt" 

    >>> format = "emboss" 

    >>> for alignment in AlignIO.parse(filename, format): 

    ...     print("Alignment of length %i" % alignment.get_alignment_length()) 

    Alignment of length 124 

    Alignment of length 119 

    Alignment of length 120 

    Alignment of length 118 

    Alignment of length 125 

 

    If you have a string 'data' containing the file contents, use: 

 

    from Bio import AlignIO 

    from StringIO import StringIO 

    my_iterator = AlignIO.parse(StringIO(data), format) 

 

    Use the Bio.AlignIO.read() function when you expect a single record only. 

    """ 

    from Bio import SeqIO 

 

    #Try and give helpful error messages: 

    if not isinstance(format, basestring): 

        raise TypeError("Need a string for the file format (lower case)") 

    if not format: 

        raise ValueError("Format required (lower case string)") 

    if format != format.lower(): 

        raise ValueError("Format string '%s' should be lower case" % format) 

    if alphabet is not None and not (isinstance(alphabet, Alphabet) or 

                                     isinstance(alphabet, AlphabetEncoder)): 

        raise ValueError("Invalid alphabet, %s" % repr(alphabet)) 

    if seq_count is not None and not isinstance(seq_count, int): 

        raise TypeError("Need integer for seq_count (sequences per alignment)") 

 

    with as_handle(handle, 'rU') as fp: 

        #Map the file format to a sequence iterator: 

        if format in _FormatToIterator: 

            iterator_generator = _FormatToIterator[format] 

            if alphabet is None: 

                i = iterator_generator(fp, seq_count) 

            else: 

                try: 

                    #Initially assume the optional alphabet argument is supported 

                    i = iterator_generator(fp, seq_count, alphabet=alphabet) 

                except TypeError: 

                    #It isn't supported. 

                    i = _force_alphabet(iterator_generator(fp, seq_count), 

                                        alphabet) 

 

        elif format in SeqIO._FormatToIterator: 

            #Exploit the existing SeqIO parser to the dirty work! 

            i = _SeqIO_to_alignment_iterator(fp, format, 

                                                alphabet=alphabet, 

                                                seq_count=seq_count) 

        else: 

            raise ValueError("Unknown format '%s'" % format) 

 

        #This imposes some overhead... wait until we drop Python 2.4 to fix it 

        for a in i: 

            yield a 

 

 

def read(handle, format, seq_count=None, alphabet=None): 

    """Turns an alignment file into a single MultipleSeqAlignment object. 

 

    Arguments: 

     - handle    - handle to the file, or the filename as a string 

                   (note older versions of Biopython only took a handle). 

     - format    - string describing the file format. 

     - alphabet  - optional Alphabet object, useful when the sequence type 

                   cannot be automatically inferred from the file itself 

                   (e.g. fasta, phylip, clustal) 

     - seq_count - Optional integer, number of sequences expected in each 

                   alignment.  Recommended for fasta format files. 

 

    If the handle contains no alignments, or more than one alignment, 

    an exception is raised.  For example, using a PFAM/Stockholm file 

    containing one alignment: 

 

    >>> from Bio import AlignIO 

    >>> filename = "Clustalw/protein.aln" 

    >>> format = "clustal" 

    >>> alignment = AlignIO.read(filename, format) 

    >>> print("Alignment of length %i" % alignment.get_alignment_length()) 

    Alignment of length 411 

 

    If however you want the first alignment from a file containing 

    multiple alignments this function would raise an exception. 

 

    >>> from Bio import AlignIO 

    >>> filename = "Emboss/needle.txt" 

    >>> format = "emboss" 

    >>> alignment = AlignIO.read(filename, format) 

    Traceback (most recent call last): 

        ... 

    ValueError: More than one record found in handle 

 

    Instead use: 

 

    >>> from Bio import AlignIO 

    >>> filename = "Emboss/needle.txt" 

    >>> format = "emboss" 

    >>> alignment = next(AlignIO.parse(filename, format)) 

    >>> print("First alignment has length %i" % alignment.get_alignment_length()) 

    First alignment has length 124 

 

    You must use the Bio.AlignIO.parse() function if you want to read multiple 

    records from the handle. 

    """ 

    iterator = parse(handle, format, seq_count, alphabet) 

    try: 

        first = next(iterator) 

    except StopIteration: 

        first = None 

    if first is None: 

        raise ValueError("No records found in handle") 

    try: 

        second = next(iterator) 

    except StopIteration: 

        second = None 

    if second is not None: 

        raise ValueError("More than one record found in handle") 

    if seq_count: 

        assert len(first) == seq_count 

    return first 

 

 

def convert(in_file, in_format, out_file, out_format, alphabet=None): 

    """Convert between two alignment files, returns number of alignments. 

 

     - in_file - an input handle or filename 

     - in_format - input file format, lower case string 

     - output - an output handle or filename 

     - out_file - output file format, lower case string 

     - alphabet - optional alphabet to assume 

 

    NOTE - If you provide an output filename, it will be opened which will 

    overwrite any existing file without warning. This may happen if even the 

    conversion is aborted (e.g. an invalid out_format name is given). 

    """ 

    #TODO - Add optimised versions of important conversions 

    #For now just off load the work to SeqIO parse/write 

    with as_handle(in_file, 'rU') as in_handle: 

        #Don't open the output file until we've checked the input is OK: 

        alignments = parse(in_handle, in_format, None, alphabet) 

 

        #This will check the arguments and issue error messages, 

        #after we have opened the file which is a shame. 

        with as_handle(out_file, 'w') as out_handle: 

            count = write(alignments, out_handle, out_format) 

 

    return count 

 

 

if __name__ == "__main__": 

    from Bio._utils import run_doctest 

    run_doctest()