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EmbossIO.py
# 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.
"""
Bio.AlignIO support for the "emboss" alignment output from EMBOSS tools.

You are expected to use this module via the Bio.AlignIO functions (or the
Bio.SeqIO functions if you want to work directly with the gapped sequences).

This module contains a parser for the EMBOSS pairs/simple file format, for
example from the alignret, water and needle tools.
"""

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Interfaces import AlignmentIterator, SequentialAlignmentWriter

00021 class EmbossWriter(SequentialAlignmentWriter):
    """Emboss alignment writer (WORK IN PROGRESS).

    Writes a simplfied version of the EMBOSS pairs/simple file format.
    A lot of the information their tools record in their headers is not
    available and is ommitted.
    """

    def write_header(self):
        handle = self.handle
        handle.write("########################################\n")
        handle.write("# Program: Biopython\n")
        try:
            handle.write("# Report_file: %s\n" % handle.name)
        except AttributeError:
            pass
        handle.write("########################################\n")

    def write_footer(self):
        handle = self.handle
        handle.write("#---------------------------------------\n")
        handle.write("#---------------------------------------\n")
        
00044     def write_alignment(self, alignment):
        """Use this to write (another) single alignment to an open file."""
        handle = self.handle
        handle.write("#=======================================\n")
        handle.write("#\n")
        handle.write("# Aligned_sequences: %i\n" % len(alignment))
        for i, record in enumerate(alignment):
            handle.write("# %i: %s\n" % (i+1, record.id))
        handle.write("#\n")
        handle.write("# Length: %i\n" % alignment.get_alignment_length())
        handle.write("#\n")
        handle.write("#=======================================\n")
        handle.write("\n")
        #...
        assert False

00060 class EmbossIterator(AlignmentIterator):
    """Emboss alignment iterator.

    For reading the (pairwise) alignments from EMBOSS tools in what they
    call the "pairs" and "simple" formats.
    """
    
    def next(self):

        handle = self.handle

        try:
            #Header we saved from when we were parsing
            #the previous alignment.
            line = self._header
            del self._header
        except AttributeError:      
            line = handle.readline()
        if not line:
            raise StopIteration

        while line.rstrip() != "#=======================================":
            line = handle.readline()
            if not line:
                raise StopIteration

        length_of_seqs = None
        number_of_seqs = None
        ids = []
        seqs = []


        while line[0] == "#":
            #Read in the rest of this alignment header,
            #try and discover the number of records expected
            #and their length
            parts = line[1:].split(":",1)
            key = parts[0].lower().strip()
            if key == "aligned_sequences":
                number_of_seqs = int(parts[1].strip())
                assert len(ids) == 0
                # Should now expect the record identifiers...
                for i in range(number_of_seqs):
                    line = handle.readline()
                    parts = line[1:].strip().split(":",1)
                    assert i+1 == int(parts[0].strip())
                    ids.append(parts[1].strip())
                assert len(ids) == number_of_seqs
            if key == "length":
                length_of_seqs = int(parts[1].strip())

            #And read in another line...
            line = handle.readline()

        if number_of_seqs is None:
            raise ValueError("Number of sequences missing!")
        if length_of_seqs is None:
            raise ValueError("Length of sequences missing!")

        if self.records_per_alignment is not None \
        and self.records_per_alignment != number_of_seqs:
            raise ValueError("Found %i records in this alignment, told to expect %i" \
                             % (number_of_seqs, self.records_per_alignment))

        seqs = ["" for id in ids]
        seq_starts = []
        index = 0

        #Parse the seqs
        while line:
            if len(line) > 21:
                id_start = line[:21].strip().split(None, 1)
                seq_end = line[21:].strip().split(None, 1)
                if len(id_start) == 2 and len(seq_end) == 2:
                    #identifier, seq start position, seq, seq end position
                    #(an aligned seq is broken up into multiple lines)
                    id, start = id_start
                    seq, end = seq_end
                    if start==end:
                        #Special case, either a single letter is present,
                        #or no letters at all.
                        if seq.replace("-","") == "":
                            start = int(start)
                            end = int(end)
                        else:
                            start = int(start) - 1
                            end = int(end)
                    else:
                        assert seq.replace("-","") != ""
                        start = int(start)-1 #python counting
                        end = int(end)

                    #The identifier is truncated...
                    assert 0 <= index and index < number_of_seqs, \
                           "Expected index %i in range [0,%i)" \
                           % (index, number_of_seqs)
                    assert id==ids[index] or id == ids[index][:len(id)]

                    if len(seq_starts) == index:
                        #Record the start
                        seq_starts.append(start)

                    #Check the start...
                    if start == end:
                        assert seq.replace("-","") == "", line
                    else:
                        assert start - seq_starts[index] == len(seqs[index].replace("-","")), \
                        "Found %i chars so far for sequence %i (%s, %s), line says start %i:\n%s" \
                            % (len(seqs[index].replace("-","")), index, id, repr(seqs[index]),
                               start, line)
                    
                    seqs[index] += seq

                    #Check the end ...
                    assert end == seq_starts[index] + len(seqs[index].replace("-","")), \
                        "Found %i chars so far for sequence %i (%s, %s, start=%i), file says end %i:\n%s" \
                            % (len(seqs[index].replace("-","")), index, id, repr(seqs[index]),
                               seq_starts[index], end, line)

                    index += 1
                    if index >= number_of_seqs:
                        index = 0
                else:
                    #just a start value, this is just alignment annotation (?)
                    #print "Skipping: " + line.rstrip()
                    pass
            elif line.strip() == "":
                #Just a spacer?
                pass
            else:
                print line
                assert False

            line = handle.readline()
            if line.rstrip() == "#---------------------------------------" \
            or line.rstrip() == "#=======================================":
                #End of alignment
                self._header = line
                break

        assert index == 0

        if self.records_per_alignment is not None \
        and self.records_per_alignment != len(ids):
            raise ValueError("Found %i records in this alignment, told to expect %i" \
                             % (len(ids), self.records_per_alignment))

        records = []
        for id, seq in zip(ids, seqs):
            if len(seq) != length_of_seqs:
                #EMBOSS 2.9.0 is known to use spaces instead of minus signs
                #for leading gaps, and thus fails to parse.  This old version
                #is still used as of Dec 2008 behind the EBI SOAP webservice:
                #http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl
                raise ValueError("Error parsing alignment - sequences of "
                                 "different length? You could be using an "
                                 "old version of EMBOSS.")
            records.append(SeqRecord(Seq(seq, self.alphabet), \
                                     id=id, description=id))
        return MultipleSeqAlignment(records, self.alphabet)


if __name__ == "__main__":
    print "Running a quick self-test"

    #http://emboss.sourceforge.net/docs/themes/alnformats/align.simple
    simple_example = \
"""########################################
# Program:  alignret
# Rundate:  Wed Jan 16 17:16:13 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 4
# 1: IXI_234
# 2: IXI_235
# 3: IXI_236
# 4: IXI_237
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity:      95/131 (72.5%)
# Similarity:   127/131 (96.9%)
# Gaps:          25/131 (19.1%)
# Score: 100.0
#
#
#=======================================

IXI_234            1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT     50
IXI_235            1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT     41
IXI_236            1 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQAT     48
IXI_237            1 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQAT     45
                     |||||:|||||||||:::::::  |||||:||||:::::|||||:|||||

IXI_234           51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG    100
IXI_235           42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG     81
IXI_236           49 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--G     96
IXI_237           46 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--G     93
                     ||:||||||||||||||||||||:::::::::::|||||||||||||  |

IXI_234          101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    131
IXI_235           82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    112
IXI_236           97 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE    127
IXI_237           94 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE    124
                     |||:||||:|||||:|||||||::|||||||


#---------------------------------------
#---------------------------------------

"""
    
    #http://emboss.sourceforge.net/docs/themes/alnformats/align.pair
    pair_example = \
"""########################################
# Program:  water
# Rundate:  Wed Jan 16 17:23:19 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity:     112/131 (85.5%)
# Similarity:   112/131 (85.5%)
# Gaps:          19/131 (14.5%)
# Score: 591.5
#
#
#=======================================

IXI_234            1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT     50
                     |||||||||||||||         ||||||||||||||||||||||||||
IXI_235            1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT     41

IXI_234           51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG    100
                     ||||||||||||||||||||||||          ||||||||||||||||
IXI_235           42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG     81

IXI_234          101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    131
                     |||||||||||||||||||||||||||||||
IXI_235           82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    112


#---------------------------------------
#---------------------------------------       


"""

    pair_example2 = \
"""########################################
# Program: needle
# Rundate: Sun 27 Apr 2007 17:20:35
# Commandline: needle
#    [-asequence] Spo0F.faa
#    [-bsequence] paired_r.faa
#    -sformat2 pearson
# Align_format: srspair
# Report_file: ref_rec .needle
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94968718|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 124
# Identity:      32/124 (25.8%)
# Similarity:    64/124 (51.6%)
# Gaps:          17/124 (13.7%)
# Score: 112.0
# 
#
#=======================================

ref_rec            1 KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDL     46
                      :|:.||    :.|.|::|.:  :.|.....:|.:|.||:.:..:..|.:
gi|94968718|r      1 -VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAVKLAGELHPRV     47

ref_rec           47 VLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALT     96
                     |::|..:|||.|::..|:::....:|.|:::|.:.|...::.:.|.||..
gi|94968718|r     48 VVMDCAMPGMSGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANG     97

ref_rec           97 HFAK-PFDIDEIRDAV--------    111
                     :..| ..|:|.|: ||        
gi|94968718|r     98 YILKSAIDLDLIQ-AVRRVANGET    120


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94968761|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 119
# Identity:      34/119 (28.6%)
# Similarity:    58/119 (48.7%)
# Gaps:           9/119 ( 7.6%)
# Score: 154.0
# 
#
#=======================================

ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLD     50
                      ||||||:......|:..|...|::.....|.::||:|...:..||:|.|
gi|94968761|r      1 -ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSD     49

ref_rec           51 MKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK    100
                     :.:||.||:.:|:.:|.......|::|:....::|..::..||||....|
gi|94968761|r     50 VVMPGRDGLTLLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEK     99

ref_rec          101 PFDIDEIRDAV--------    111
                     |...|::...|        
gi|94968761|r    100 PLSTDKLLLTVENALKLKR    118


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94967506|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 120
# Identity:      29/120 (24.2%)
# Similarity:    53/120 (44.2%)
# Gaps:           9/120 ( 7.5%)
# Score: 121.0
# 
#
#=======================================

ref_rec            1 -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLL     49
                      .|::|||..|..:.:..||.:.|:..........|.:.:.....||.::
gi|94967506|r      1 LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIV     50

ref_rec           50 DMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA     99
                     |:.:....|:|:|:|.:|....:..:|:|....|:|...|...||:.:..
gi|94967506|r     51 DVYLGSTTGVEVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQ    100

ref_rec          100 KPFDIDEIRDAV--------    111
                     ||.|||.:.:..        
gi|94967506|r    101 KPIDIDALLNIAERALEHKE    120


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94970045|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 118
# Identity:      30/118 (25.4%)
# Similarity:    64/118 (54.2%)
# Gaps:           9/118 ( 7.6%)
# Score: 126.0
# 
#
#=======================================

ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVL     48
                      :|:|:|:..:|....:.....||:...|.:|.:||.:.:|  ||.|:::
gi|94970045|r      1 -VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLI     49

ref_rec           49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF     98
                     .|:.:||:.|..:.:.:..|....:|:.|:.|.: :.:..:.|:.:.:.|
gi|94970045|r     50 TDLVMPGISGRVLAQELVKIHPETKVMYMSGYDD-ETVMVNGEIDSSSAF     98

ref_rec           99 -AKPFDID----EIRDAV    111
                      .|||.:|    :||:.:
gi|94970045|r     99 LRKPFRMDALSAKIREVL    116


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94970041|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 125
# Identity:      35/125 (28.0%)
# Similarity:    70/125 (56.0%)
# Gaps:          18/125 (14.4%)
# Score: 156.5
# 
#
#=======================================

ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVL     48
                     .:|:|:|:.|:|.|:..:.:::||...:|.:|.:||:||  :.::.|::|
gi|94970041|r      1 TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLL     50

ref_rec           49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF     98
                     .|:.:.||.|.|:.:|:::...:::||.|:.|.:..:::.    |.||..
gi|94970041|r     51 SDVVLVGMSGRELSERLRIQMPSLKVIYMSGYTDDAIVRH----GVLTES     96

ref_rec           99 A----KPFDIDEIRDAV--------    111
                     |    |||..|.:...|        
gi|94970041|r     97 AEFLQKPFTSDSLLRKVRAVLQKRQ    121


#---------------------------------------
#---------------------------------------

"""

    pair_example3 = """########################################
# Program: needle
# Rundate: Mon 14 Jul 2008 11:45:42
# Commandline: needle
#    [-asequence] asis:TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC
#    [-bsequence] asis:TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTT
#    -filter
# Align_format: srspair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: asis
# 2: asis
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     210/667 (31.5%)
# Similarity:   210/667 (31.5%)
# Gaps:         408/667 (61.2%)
# Score: 561.0
# 
#
#=======================================

asis               1 TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAAT     50
                                                                       
asis               0 --------------------------------------------------      0

asis              51 AGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGA    100
                                                                       
asis               0 --------------------------------------------------      0

asis             101 CTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTG    150
                                                                       
asis               0 --------------------------------------------------      0

asis             151 GGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGA    200
                                 .||||||                               
asis               1 ------------TTATTAA-------------------------------      7

asis             201 TACTTATTGT------GTAGTAGCTCATTTTCATTATGTTCTTCGAATGG    244
                      .|||||.||      |||..|..||  ||||.||||.||.|    ||.|
asis               8 -TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTTTT----ATTG     50

asis             245 GAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAG    288
                              ||.|.|||||.|||.||||.||||      | |||||||||
asis              51 ---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAG     90

asis             289 GTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTA    331
                     ||.|.|||||||     ||||||||.|  ||.|      |||.|.|||||
asis              91 GTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTA    134

asis             332 TTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTC    377
                     |||                 ||||||    .||||...||||..|||||.
asis             135 TTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTT    167

asis             378 GT-TGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA--------    418
                     .| |||||||||||             ||  ||.||.||.||        
asis             168 ATCTGAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTC    202

asis             419 -------------GGATCTACCTTTTATCTTTCTAAT--CTTTT----GT    449
                                  ||..||.||.|.|||..||||.||  |||||    | 
asis             203 ATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG-    251

asis             450 TTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTT    498
                        ||| |.|||     |||||||||.||| .||||||...|||||||||
asis             252 ---AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTCACAGTCTTTT    292

asis             499 TTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTT    548
                     ||||||||..| ||||||||                              
asis             293 TTTTTATTAAG-AAAGGTTT------------------------------    311

asis             549 TCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGT    598
                                                                       
asis             311 --------------------------------------------------    311

asis             599 GAAAGGGGGTTAATAGC    615
                                      
asis             311 -----------------    311


#---------------------------------------
#---------------------------------------"""

    from StringIO import StringIO

    alignments = list(EmbossIterator(StringIO(pair_example)))
    assert len(alignments) == 1
    assert len(alignments[0]) == 2
    assert [r.id for r in alignments[0]] \
           == ["IXI_234", "IXI_235"]
    
    alignments = list(EmbossIterator(StringIO(simple_example)))
    assert len(alignments) == 1    
    assert len(alignments[0]) == 4
    assert [r.id for r in alignments[0]] \
           == ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]

    alignments = list(EmbossIterator(StringIO(pair_example + simple_example)))
    assert len(alignments) == 2    
    assert len(alignments[0]) == 2
    assert len(alignments[1]) == 4
    assert [r.id for r in alignments[0]] \
           == ["IXI_234", "IXI_235"]
    assert [r.id for r in alignments[1]] \
           == ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]

    alignments = list(EmbossIterator(StringIO(pair_example2)))
    assert len(alignments) == 5
    assert len(alignments[0]) == 2
    assert [r.id for r in alignments[0]] \
           == ["ref_rec", "gi|94968718|receiver"]
    assert [r.id for r in alignments[4]] \
           == ["ref_rec", "gi|94970041|receiver"]


    alignments = list(EmbossIterator(StringIO(pair_example3)))
    assert len(alignments) == 1
    assert len(alignments[0]) == 2
    assert [r.id for r in alignments[0]] \
           == ["asis","asis"]

    print "Done"

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