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test_AlignIO.py

# Copyright 2008 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.

import os
from StringIO import StringIO
from Bio import SeqIO
from Bio import AlignIO
from Bio.Align.Generic import Alignment
from Bio.Align import AlignInfo

test_write_read_alignment_formats = sorted(AlignIO._FormatToWriter)
test_write_read_align_with_seq_count = test_write_read_alignment_formats \
                                     + ["fasta", "tab"]

# test_files is a list of tuples containing:
# - string:  file format
# - integer: number of sequences per alignment
# - integer: number of alignments
# - string:  relative filename
#
# Most of the input files are also used by test_SeqIO.py,
# and by other additional tests as noted below.
test_files = [ \
#Following examples are also used in test_Clustalw.py
    ("clustal", 2, 1, 'Clustalw/cw02.aln'),
    ("clustal", 7, 1, 'Clustalw/opuntia.aln'),
    ("clustal", 5, 1, 'Clustalw/hedgehog.aln'),
    ("clustal", 2, 1, 'Clustalw/odd_consensus.aln'),
    ("clustal",20, 1, 'Clustalw/protein.aln'), #Used in the tutorial
    ("clustal",20, 1, 'Clustalw/promals3d.aln'), #Nonstandard header
#Following examples are also used in test_GFF.py
    ("fasta", 3, 1, 'GFF/multi.fna'), #Trivial nucleotide alignment
#Following example is also used in test_Nexus.py
    ("nexus", 9, 1, 'Nexus/test_Nexus_input.nex'),
    ("stockholm", 2, 1, 'Stockholm/simple.sth'),
    ("stockholm", 5, 1, 'Stockholm/funny.sth'),
    ("phylip", 6, 1, 'Phylip/reference_dna.phy'),
    ("phylip", 6, 1, 'Phylip/reference_dna2.phy'),
    ("phylip",10, 1, 'Phylip/hennigian.phy'),
    ("phylip",10, 1, 'Phylip/horses.phy'),
    ("phylip",10, 1, 'Phylip/random.phy'),
    ("phylip", 3, 1, 'Phylip/interlaced.phy'),
    ("phylip", 4, 1, 'Phylip/interlaced2.phy'),
    ("emboss", 4, 1, 'Emboss/alignret.txt'),
    ("emboss", 2, 5, 'Emboss/needle.txt'),
    ("emboss", 2, 1, 'Emboss/needle_asis.txt'),
    ("emboss", 2, 1, 'Emboss/water.txt'),
    ("emboss", 2, 1, 'Emboss/water2.txt'),
    ("emboss", 2, 1, 'Emboss/matcher_simple.txt'),
    ("emboss", 2, 5, 'Emboss/matcher_pair.txt'),
    ("fasta-m10", 2, 4, 'Fasta/output001.m10'),
    ("fasta-m10", 2, 6, 'Fasta/output002.m10'),
    ("fasta-m10", 2, 3, 'Fasta/output003.m10'),
    ("fasta-m10", 2, 1, 'Fasta/output004.m10'),
    ("fasta-m10", 2, 1, 'Fasta/output005.m10'),
    ("fasta-m10", 2, 1, 'Fasta/output006.m10'),
    ("ig", 16, 1, 'IntelliGenetics/VIF_mase-pro.txt'),
    ("pir", 2, 1,  'NBRF/clustalw.pir'),
    ]

def str_summary(text, max_len=40):
    if len(text) <= max_len:
        return text
    else:
        return text[:max_len-4] + "..." + text[-3:]

def alignment_summary(alignment, index="  ", vertical_threshold=5):
    """Returns a concise summary of an Alignment object as a string."""
    answer = []
    alignment_len = alignment.get_alignment_length()
    rec_count = len(alignment)
    if rec_count < vertical_threshold:
        #Show each sequence row horizontally
        for record in alignment:
            answer.append("%s%s %s" \
            % (index,str_summary(record.seq.tostring()),record.id))
    else:
        #Show each sequence row vertically
        for i in range(min(5,alignment_len)):
            answer.append(index + str_summary(alignment.get_column(i)) \
                                + " alignment column %i" % i)
        if alignment_len > 5:
            i = alignment_len - 1
            answer.append(index + str_summary("|" * rec_count) \
                                + " ...")
            answer.append(index + str_summary(alignment.get_column(i)) \
                                + " alignment column %i" % i)
    return "\n".join(answer)


def check_simple_write_read(alignments, indent=" "):
    #print indent+"Checking we can write and then read back these alignments"
    for format in test_write_read_align_with_seq_count:
        records_per_alignment = len(alignments[0])
        for a in alignments:
            if records_per_alignment != len(a):
                records_per_alignment = None
        #Can we expect this format to work?
        if not records_per_alignment \
        and format not in test_write_read_alignment_formats:
            continue
        
        print indent+"Checking can write/read as '%s' format" % format
        
        #Going to write to a handle...
        handle = StringIO()
        
        try:
            c = AlignIO.write(alignments, handle=handle, format=format)
            assert c == len(alignments)
        except ValueError, e:
            #This is often expected to happen, for example when we try and
            #write sequences of different lengths to an alignment file.
            print indent+"Failed: %s" % str(e)
            #Carry on to the next format:
            continue

        #First, try with the seq_count
        if records_per_alignment:
            handle.flush()
            handle.seek(0)
            try:
                alignments2 = list(AlignIO.parse(handle=handle, format=format, \
                                                 seq_count=records_per_alignment))
            except ValueError, e:
                #This is BAD.  We can't read our own output.
                #I want to see the output when called from the test harness,
                #run_tests.py (which can be funny about new lines on Windows)
                handle.seek(0)
                raise ValueError("%s\n\n%s\n\n%s" \
                                  % (str(e), repr(handle.read()), repr(alignments2)))
            simple_alignment_comparison(alignments, alignments2, format)

        if format in test_write_read_alignment_formats:
            #Don't need the seq_count
            handle.flush()
            handle.seek(0)
            try:
                alignments2 = list(AlignIO.parse(handle=handle, format=format))
            except ValueError, e:
                #This is BAD.  We can't read our own output.
                #I want to see the output when called from the test harness,
                #run_tests.py (which can be funny about new lines on Windows)
                handle.seek(0)
                raise ValueError("%s\n\n%s\n\n%s" \
                                  % (str(e), repr(handle.read()), repr(alignments2)))
            simple_alignment_comparison(alignments, alignments2, format)

        if len(alignments)>1:
            #Try writing just one Alignment (not a list)
            handle = StringIO()
            SeqIO.write(alignments[0], handle, format)
            assert handle.getvalue() == alignments[0].format(format)

def simple_alignment_comparison(alignments, alignments2, format):
    assert len(alignments) == len(alignments2)
    for a1, a2 in zip(alignments, alignments2):
        assert a1.get_alignment_length() == a2.get_alignment_length()
        assert len(a1) == len(a2)
        for r1, r2 in zip(a1,a2):
            #Check the bare minimum (ID and sequence) as
            #many formats can't store more than that.

            #Check the sequence
            assert r1.seq.tostring() == r2.seq.tostring()
            
            #Beware of different quirks and limitations in the
            #valid character sets and the identifier lengths!
            if format=="phylip":
                assert r1.id.replace("[","").replace("]","")[:10] == r2.id, \
                       "'%s' vs '%s'" % (r1.id, r2.id)
            elif format=="clustal":
                assert r1.id.replace(" ","_")[:30] == r2.id, \
                       "'%s' vs '%s'" % (r1.id, r2.id)
            elif format=="stockholm":
                assert r1.id.replace(" ","_") == r2.id, \
                       "'%s' vs '%s'" % (r1.id, r2.id)
            elif format=="fasta":
                assert r1.id.split()[0] == r2.id
            else:
                assert r1.id == r2.id, \
                       "'%s' vs '%s'" % (r1.id, r2.id)
    return True

#Check parsers can cope with an empty file
for t_format in AlignIO._FormatToIterator:
     handle = StringIO()
     alignments = list(AlignIO.parse(handle, t_format))
     assert len(alignments) == 0

#Check writers can cope with no alignments
for t_format in list(AlignIO._FormatToWriter)+list(SeqIO._FormatToWriter):
     handle = StringIO()
     assert 0 == AlignIO.write([], handle, t_format), \
            "Writing no alignments to %s format should work!" \
            % t_format

#Check writers reject non-alignments
list_of_records = list(AlignIO.read(open("Clustalw/opuntia.aln"),"clustal"))
for t_format in list(AlignIO._FormatToWriter)+list(SeqIO._FormatToWriter):
    handle = StringIO()
    try:
        AlignIO.write([list_of_records], handle, t_format)
        print False, "Writing non-alignment to %s format should fail!" \
            % t_format
    except (TypeError, AttributeError, ValueError):
        pass
    del handle
del list_of_records, t_format

#Main tests...
for (t_format, t_per, t_count, t_filename) in test_files:
    print "Testing reading %s format file %s with %i alignments" \
          % (t_format, t_filename, t_count)
    assert os.path.isfile(t_filename), t_filename

    #Try as an iterator using handle
    alignments  = list(AlignIO.parse(handle=open(t_filename,"r"), format=t_format))
    assert len(alignments)  == t_count, \
         "Found %i alignments but expected %i" % (len(alignments), t_count)
    for alignment in alignments:
        assert len(alignment) == t_per, \
            "Expected %i records per alignment, got %i" \
            % (t_per, len(alignment))

    #Try using the iterator with a for loop and a filename not handle
    alignments2 = []
    for record in AlignIO.parse(t_filename, format=t_format):
        alignments2.append(record)
    assert len(alignments2) == t_count

    #Try using the iterator with the next() method
    alignments3 = []
    seq_iterator = AlignIO.parse(handle=open(t_filename,"r"), format=t_format)
    while True:
        try:
            record = seq_iterator.next()
        except StopIteration:
            break
        assert record is not None, "Should raise StopIteration not return None"
        alignments3.append(record)

    #Try a mixture of next() and list (a torture test!)
    seq_iterator = AlignIO.parse(handle=open(t_filename,"r"), format=t_format)
    try:
        record = seq_iterator.next()
    except StopIteration:
        record = None
    if record is not None:
        alignments4 = [record]
        alignments4.extend(list(seq_iterator))
    else:
        alignments4 = []
    assert len(alignments4) == t_count

    #Try a mixture of next() and for loop (a torture test!)
    seq_iterator = AlignIO.parse(handle=open(t_filename,"r"), format=t_format)
    try:
        record = seq_iterator.next()
    except StopIteration:
        record = None
    if record is not None:
        alignments5 = [record]
        for record in seq_iterator:
            alignments5.append(record)
    else:
        alignments5 = []
    assert len(alignments5) == t_count

    # Check Bio.AlignIO.read(...)
    if t_count == 1:
        alignment = AlignIO.read(handle=open(t_filename), format=t_format)
        assert isinstance(alignment, Alignment)
    else:
        try:
            alignment = AlignIO.read(open(t_filename), t_format)
            assert False, "Bio.AlignIO.read(...) should have failed"
        except ValueError:
            #Expected to fail
            pass

    #Print the alignment
    for i,alignment in enumerate(alignments):
        if i < 3 or i+1 == t_count:
            print " Alignment %i, with %i sequences of length %i" \
                  % (i,
                     len(alignment),
                     alignment.get_alignment_length())
            print alignment_summary(alignment)
        elif i==3:
            print " ..."

    #Check AlignInfo.SummaryInfo likes the alignment
    summary = AlignInfo.SummaryInfo(alignment)
    dumb_consensus = summary.dumb_consensus()
    #gap_consensus = summary.gap_consensus()
    if t_format != "nexus":
        #Hack for bug 2535
        pssm = summary.pos_specific_score_matrix()
        rep_dict = summary.replacement_dictionary()
        try:
            info_content = summary.information_content()
        except ValueError, e:
            if str(e) != "Error in alphabet: not Nucleotide or Protein, supply expected frequencies":
                raise e
            pass

    if t_count==1 and t_format not in ["nexus","emboss","fasta-m10"]:
        #print " Trying to read a triple concatenation of the input file"
        data = open(t_filename,"r").read()
        handle = StringIO()
        handle.write(data + "\n\n" + data + "\n\n" + data)
        handle.seek(0)
        assert 3 == len(list(AlignIO.parse(handle=handle, format=t_format, seq_count=t_per)))

    #Some alignment file formats have magic characters which mean
    #use the letter in this position in the first sequence.
    #They should all have been converted by the parser, but if
    #not reversing the record order might expose an error.  Maybe.
    alignments.reverse()
    check_simple_write_read(alignments)

print "Finished tested reading files"

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