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test_Emboss.py

# Copyright 2009 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.
"""Runs a few EMBOSS tools to check our wrappers and parsers."""

import os
import sys
import unittest
import subprocess

from Bio.Emboss.Applications import WaterCommandline, NeedleCommandline
from Bio.Emboss.Applications import SeqretCommandline, SeqmatchallCommandline
from Bio import SeqIO
from Bio import AlignIO
from Bio import MissingExternalDependencyError
from Bio.Alphabet import generic_protein, generic_dna, generic_nucleotide
from Bio.Seq import Seq, translate
from Bio.SeqRecord import SeqRecord
#from Bio.Data.IUPACData import ambiguous_dna_letters

#################################################################

exes_wanted = ["water", "needle", "seqret", "transeq", "seqmatchall"]
exes = dict() #Dictionary mapping from names to exe locations
if sys.platform=="win32":
    #The default installation path is C:\mEMBOSS which contains the exes.
    #EMBOSS also sets an environment variable which we will check for.
    try:
        path = os.environ["EMBOSS_ROOT"]
    except KeyError:
        #print >> sys.stderr, "Missing EMBOSS_ROOT environment variable!"
        raise MissingExternalDependencyError(\
            "Install EMBOSS if you want to use Bio.Emboss.")
    if os.path.isdir(path):
        for name in exes_wanted:
            if os.path.isfile(os.path.join(path, name+".exe")):
                exes[name] = os.path.join(path, name+".exe")
    del path, name
else:
    import commands
    for name in exes_wanted:
        #This will "just work" if installed on the path as normal on Unix
        if "not found" not in commands.getoutput("%s -help" % name):
            exes[name] = name
    del name

if len(exes) < len(exes_wanted):
    raise MissingExternalDependencyError(\
        "Install EMBOSS if you want to use Bio.Emboss.")

#################################################################

#Top level function as this makes it easier to use for debugging:
def emboss_convert(filename, old_format, new_format):
    """Run seqret, returns handle."""
    #Setup, this assumes for all the format names used
    #Biopython and EMBOSS names are consistent!
    cline = SeqretCommandline(exes["seqret"],
                              sequence = filename,
                              sformat = old_format,
                              osformat = new_format,
                              auto = True, #no prompting
                              stdout = True)
    #Run the tool,
    child = subprocess.Popen(str(cline),
                             stdin=subprocess.PIPE,
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE,
                             shell=(sys.platform!="win32"))
    child.stdin.close()
    return child.stdout

#Top level function as this makes it easier to use for debugging:
def emboss_piped_SeqIO_convert(records, old_format, new_format):
    """Run seqret, returns records (as a generator)."""
    #Setup, this assumes for all the format names used
    #Biopython and EMBOSS names are consistent!
    cline = SeqretCommandline(exes["seqret"],
                              sformat = old_format,
                              osformat = new_format,
                              auto = True, #no prompting
                              filter = True)
    #Run the tool,
    child = subprocess.Popen(str(cline),
                             stdin=subprocess.PIPE,
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE,
                             shell=(sys.platform!="win32"))
    SeqIO.write(records, child.stdin, old_format)
    child.stdin.close()
    return SeqIO.parse(child.stdout, new_format)

#Top level function as this makes it easier to use for debugging:
def emboss_piped_AlignIO_convert(alignments, old_format, new_format):
    """Run seqret, returns alignments (as a generator)."""
    #Setup, this assumes for all the format names used
    #Biopython and EMBOSS names are consistent!
    cline = SeqretCommandline(exes["seqret"],
                              sformat = old_format,
                              osformat = new_format,
                              auto = True, #no prompting
                              filter = True)
    #Run the tool,
    child = subprocess.Popen(str(cline),
                             stdin=subprocess.PIPE,
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE,
                             shell=(sys.platform!="win32"))
    AlignIO.write(alignments, child.stdin, old_format)
    child.stdin.close()
    return AlignIO.parse(child.stdout, new_format)


#Top level function as this makes it easier to use for debugging:
def compare_records(old_list, new_list):
    """Check two lists of SeqRecords agree, raises a ValueError if mismatch."""
    if len(old_list) != len(new_list):
        raise ValueError("%i vs %i records" % (len(old_list), len(new_list)))
    for old, new in zip(old_list, new_list):
        #Note the name matching is a bit fuzzy, e.g. truncation and
        #no spaces in PHYLIP files.
        if old.id != new.id and old.name != new.name \
        and (old.id not in new.id) and (new.id not in old.id) \
        and (old.id.replace(" ","_") != new.id.replace(" ","_")):
            raise ValueError("'%s' or '%s' vs '%s' or '%s' records" \
                             % (old.id, old.name, new.id, new.name))
        if len(old.seq) != len(new.seq):
            raise ValueError("%i vs %i" % (len(old.seq), len(new.seq)))
        if str(old.seq).upper() != str(new.seq).upper():
            if str(old.seq).replace("X","N")==str(new.seq) :
                raise ValueError("X -> N (protein forced into nucleotide?)")
            if len(old.seq) < 200:
                raise ValueError("'%s' vs '%s'" % (old.seq, new.seq))
            else:
                raise ValueError("'%s...%s' vs '%s...%s'" \
                                 % (old.seq[:60], old.seq[-10:],
                                    new.seq[:60], new.seq[-10:]))
        if old.features and new.features \
        and len(old.features) != len(new.features):
            raise ValueError("%i vs %i features" \
                             % (len(old.features, len(new.features))))
        #TODO - check annotation
    return True

#Top level function as this makes it easier to use for debugging:
def compare_alignments(old_list, new_list):
    """Check two lists of Alignments agree, raises a ValueError if mismatch."""
    if len(old_list) != len(new_list):
        raise ValueError("%i vs %i alignments" % (len(old_list), len(new_list)))
    for old, new in zip(old_list, new_list):
        if len(old) != len(new):
            raise ValueError("Alignment with %i vs %i records" \
                             % (len(old), len(new)))
        compare_records(old,new)
    return True

00158 class SeqRetSeqIOTests(unittest.TestCase):
    """Check EMBOSS seqret against Bio.SeqIO for converting files."""

    def tearDown(self):
        clean_up()

00164     def check_SeqIO_to_EMBOSS(self, in_filename, in_format, skip_formats=[],
                              alphabet=None):
        """Can Bio.SeqIO write files seqret can read back?"""
        if alphabet:
            records = list(SeqIO.parse(open(in_filename), in_format, alphabet))
        else:
            records = list(SeqIO.parse(open(in_filename), in_format))
        for temp_format in ["genbank","fasta"]:
            if temp_format in skip_formats:
                continue
            new_records = list(emboss_piped_SeqIO_convert(records, temp_format, "fasta"))
            try:
                self.assert_(compare_records(records, new_records))
            except ValueError, err:
                raise ValueError("Disagree on file %s %s in %s format: %s" \
                                 % (in_format, in_filename, temp_format, err))
            
00181     def check_EMBOSS_to_SeqIO(self, filename, old_format,
                              skip_formats=[]):
        """Can Bio.SeqIO read seqret's conversion of the file?"""
        #TODO: Why can't we read EMBOSS's swiss output?
        self.assert_(os.path.isfile(filename))
        old_records = list(SeqIO.parse(open(filename), old_format))
        for new_format in ["genbank","fasta","pir","embl", "ig"]:
            if new_format in skip_formats:
                continue
            handle = emboss_convert(filename, old_format, new_format)
            new_records = list(SeqIO.parse(handle, new_format))
            try:
                self.assert_(compare_records(old_records, new_records))
            except ValueError, err:
                raise ValueError("Disagree on %s file %s in %s format: %s" \
                                 % (old_format, filename, new_format, err))

    def check_SeqIO_with_EMBOSS(self, filename, old_format, skip_formats=[],
                                alphabet=None):
        #Check EMBOSS can read Bio.SeqIO output...
        self.check_SeqIO_to_EMBOSS(filename, old_format, skip_formats,
                                   alphabet)
        #Check Bio.SeqIO can read EMBOSS seqret output...
        self.check_EMBOSS_to_SeqIO(filename, old_format, skip_formats)

00206     def test_genbank(self):
        """SeqIO & EMBOSS reading each other's conversions of a GenBank file."""
        self.check_SeqIO_with_EMBOSS("GenBank/cor6_6.gb", "genbank")

00210     def test_genbank2(self):
        """SeqIO & EMBOSS reading each other's conversions of another GenBank file."""
        self.check_SeqIO_with_EMBOSS("GenBank/NC_000932.gb", "genbank")

00214     def test_embl(self):
        """SeqIO & EMBOSS reading each other's conversions of an EMBL file."""
        self.check_SeqIO_with_EMBOSS("EMBL/U87107.embl", "embl")

00218     def test_ig(self):
        """SeqIO & EMBOSS reading each other's conversions of an ig file."""
        #NOTE - EMBOSS considers "genbank" to be for nucleotides only,
        #and will turn "X" into "N" for GenBank output.
        self.check_SeqIO_to_EMBOSS("IntelliGenetics/VIF_mase-pro.txt", "ig",
                                   alphabet=generic_protein,
                                   skip_formats=["genbank"])
        #TODO - What does a % in an ig sequence mean?
        #e.g. "IntelliGenetics/vpu_nucaligned.txt"
        #and  "IntelliGenetics/TAT_mase_nuc.txt"
        #EMBOSS seems to ignore them.

00230     def test_pir(self):
        """SeqIO & EMBOSS reading each other's conversions of a PIR file."""
        #Skip genbank here, EMBOSS mangles the LOCUS line:
        self.check_SeqIO_with_EMBOSS("NBRF/clustalw.pir", "pir",
                               skip_formats=["genbank"])
        #Skip EMBL here, EMBOSS mangles the ID line
        #Skip GenBank, EMBOSS 6.0.1 on Windows won't output proteins as GenBank
        self.check_SeqIO_with_EMBOSS("NBRF/DMB_prot.pir", "pir",
                               skip_formats=["embl","genbank"])
00239     def test_clustalw(self):
        """SeqIO & EMBOSS reading each other's conversions of a Clustalw file."""
        self.check_SeqIO_with_EMBOSS("Clustalw/hedgehog.aln", "clustal",
                                   skip_formats=["embl","genbank"])
        self.check_SeqIO_with_EMBOSS("Clustalw/opuntia.aln", "clustal",
                                   skip_formats=["embl","genbank"])

00246 class SeqRetAlignIOTests(unittest.TestCase):
    """Check EMBOSS seqret against Bio.SeqIO for converting files."""

    def tearDown(self):
        clean_up()

00252     def check_EMBOSS_to_AlignIO(self, filename, old_format,
                              skip_formats=[]):
        """Can AlignIO read seqret's conversion of the file?"""
        self.assert_(os.path.isfile(filename), filename)
        old_aligns = list(AlignIO.parse(open(filename), old_format))
        formats = ["clustal", "phylip", "ig"]
        if len(old_aligns) == 1:
            formats.extend(["fasta","nexus"])
        for new_format in formats:
            if new_format in skip_formats:
                continue
            handle = emboss_convert(filename, old_format, new_format)
            try:
                new_aligns = list(AlignIO.parse(handle, new_format))
            except:
                raise ValueError("Can't parse %s file %s in %s format." \
                                 % (old_format, filename, new_format))
            try:
                self.assert_(compare_alignments(old_aligns, new_aligns))
            except ValueError, err:
                raise ValueError("Disagree on %s file %s in %s format: %s" \
                                 % (old_format, filename, new_format, err))

00275     def check_AlignIO_to_EMBOSS(self, in_filename, in_format, skip_formats=[],
                                alphabet=None):
        """Can Bio.AlignIO write files seqret can read back?"""
        if alphabet:
            old_aligns = list(AlignIO.parse(open(in_filename), in_format,
                                            alphabet))
        else:
            old_aligns = list(AlignIO.parse(open(in_filename), in_format))

        formats = ["clustal", "phylip"]
        if len(old_aligns) == 1:
            formats.extend(["fasta","nexus"])
        for temp_format in formats:
            if temp_format in skip_formats:
                continue
            #PHYLIP is a simple format which explicitly supports
            #multiple alignments (unlike FASTA).
            try:
                new_aligns = list(emboss_piped_AlignIO_convert(old_aligns,
                                                               temp_format,
                                                               "phylip"))
            except ValueError, e:
                #e.g. ValueError: Need a DNA, RNA or Protein alphabet
                #from writing Nexus files...
                continue
            try:
                self.assert_(compare_alignments(old_aligns, new_aligns))
            except ValueError, err:
                raise ValueError("Disagree on file %s %s in %s format: %s" \
                                 % (in_format, in_filename, temp_format, err))

    def check_AlignIO_with_EMBOSS(self, filename, old_format, skip_formats=[],
                                  alphabet=None):
        #Check EMBOSS can read Bio.AlignIO output...
        self.check_AlignIO_to_EMBOSS(filename, old_format, skip_formats,
                                   alphabet)
        #Check Bio.AlignIO can read EMBOSS seqret output...
        self.check_EMBOSS_to_AlignIO(filename, old_format, skip_formats)
        
00314     def test_align_clustalw(self):
        """AlignIO & EMBOSS reading each other's conversions of a ClustalW file."""
        self.check_AlignIO_with_EMBOSS("Clustalw/hedgehog.aln", "clustal")
        self.check_AlignIO_with_EMBOSS("Clustalw/opuntia.aln", "clustal")
        self.check_AlignIO_with_EMBOSS("Clustalw/odd_consensus.aln", "clustal",
                               skip_formats=["nexus"]) #TODO - why not nexus?
        self.check_AlignIO_with_EMBOSS("Clustalw/protein.aln", "clustal")
        self.check_AlignIO_with_EMBOSS("Clustalw/promals3d.aln", "clustal")

00323     def test_clustalw(self):
        """AlignIO & EMBOSS reading each other's conversions of a PHYLIP file."""
        self.check_AlignIO_with_EMBOSS("Phylip/horses.phy", "phylip")
        self.check_AlignIO_with_EMBOSS("Phylip/hennigian.phy", "phylip")
        self.check_AlignIO_with_EMBOSS("Phylip/reference_dna.phy", "phylip")
        self.check_AlignIO_with_EMBOSS("Phylip/reference_dna2.phy", "phylip")
        self.check_AlignIO_with_EMBOSS("Phylip/interlaced.phy", "phylip")
        self.check_AlignIO_with_EMBOSS("Phylip/interlaced2.phy", "phylip")
        self.check_AlignIO_with_EMBOSS("Phylip/random.phy", "phylip")

        
00334 class PairwiseAlignmentTests(unittest.TestCase):
    """Run pairwise alignments with water and needle, and parse them."""

    def tearDown(self):
        clean_up()
        
00340     def pairwise_alignment_check(self, query_seq,
                                 targets, alignments,
                                 local=True):
        """Check pairwise alignment data is sane."""
        #The datasets should be small, so making iterators into lists is OK
        targets = list(targets)
        alignments = list(alignments)
        self.assertEqual(len(targets), len(alignments))
        for target, alignment in zip(targets, alignments):
            self.assertEqual(len(alignment), 2)
            #self.assertEqual(target.id, alignment[1].id) #too strict
            if alignment[1].id not in target.id \
            and alignment[1].id not in target.name:
                raise AssertionError("%s vs %s or %s" \
                                     % (alignment[1].id , target.id, target.name))
            if local:
                #Local alignment
                self.assert_(str(alignment[0].seq).replace("-","") \
                             in query_seq)
                self.assert_(str(alignment[1].seq).replace("-","").upper() \
                             in str(target.seq).upper())
            else:
                #Global alignment
                self.assertEqual(str(query_seq), str(alignment[0].seq).replace("-",""))
                self.assertEqual(str(target.seq).upper(), \
                                 str(alignment[1].seq).replace("-","").upper())
        return True

    def run_water(self, cline):
        #Run the tool,
        child = subprocess.Popen(str(cline),
                                 stdin=subprocess.PIPE,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=(sys.platform!="win32"))
        #Check it worked,
        return_code = child.wait()
        if return_code != 0 : print >> sys.stderr, "\n%s"%cline
        self.assertEqual(return_code, 0)
        errors = child.stderr.read().strip()
        self.assert_(errors.startswith("Smith-Waterman local alignment"),
                     errors)
        if cline.outfile:
            self.assertEqual(child.stdout.read().strip(), "")
            self.assert_(os.path.isfile(cline.outfile))
        else :
            #Don't use this yet... could return stdout handle instead?
            return child.stdout.read()

00389     def test_water_file(self):
        """water with the asis trick, output to a file."""
        #Setup, try a mixture of keyword arguments and later additions:
        cline = WaterCommandline(cmd=exes["water"],
                                 gapopen="10", gapextend="0.5")
        #Try using both human readable names, and the literal ones:
        cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
        cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
        #Try using a property set here:
        cline.outfile = "Emboss/temp with space.water"
        self.assertEqual(str(eval(repr(cline))), str(cline))
        #Run the tool,
        self.run_water(cline)
        #Check we can parse the output...
        align = AlignIO.read(open(cline.outfile),"emboss")
        self.assertEqual(len(align), 2)
        self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
        self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
        #Clean up,
        os.remove(cline.outfile)            
        
00410     def test_water_piped(self):
        """water with asis trick, output piped to stdout."""
        cline = WaterCommandline(cmd=exes["water"],
                                 asequence="asis:ACCCGGGCGCGGT",
                                 bsequence="asis:ACCCGAGCGCGGT",
                                 gapopen=10,
                                 gapextend=0.5,
                                 auto=True, filter=True)
        self.assertEqual(str(cline),
                         exes["water"] + " -auto -filter" \
                         + " -asequence=asis:ACCCGGGCGCGGT" \
                         + " -bsequence=asis:ACCCGAGCGCGGT" \
                         + " -gapopen=10 -gapextend=0.5")
        #Run the tool,
        child = subprocess.Popen(str(cline),
                                 stdin=subprocess.PIPE,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=(sys.platform!="win32"))
        child.stdin.close()
        #Check we could read it's output
        align = AlignIO.read(child.stdout, "emboss")
        self.assertEqual(len(align), 2)
        self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
        self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
        #Check no error output:
        assert child.stderr.read() == ""
        assert 0 == child.wait()

00439     def test_needle_file(self):
        """needle with the asis trick, output to a file."""
        #Setup,
        cline = NeedleCommandline(cmd=exes["needle"])
        cline.set_parameter("-asequence", "asis:ACCCGGGCGCGGT")
        cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
        cline.set_parameter("-gapopen", "10")
        cline.set_parameter("-gapextend", "0.5")
        #EMBOSS would guess this, but let's be explicit:
        cline.set_parameter("-snucleotide", "True")
        cline.set_parameter("-outfile", "Emboss/temp with space.needle")
        self.assertEqual(str(eval(repr(cline))), str(cline))
        #Run the tool,
        child = subprocess.Popen(str(cline),
                                 stdin=subprocess.PIPE,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=(sys.platform!="win32"))
        out, err = child.communicate()
        return_code = child.returncode
        #Check it worked,
        errors = err.strip()
        self.assert_(err.strip().startswith("Needleman-Wunsch global alignment"), errors)
        self.assertEqual(out.strip(), "")
        if return_code != 0 : print >> sys.stderr, "\n%s"%cline
        self.assertEqual(return_code, 0)
        filename = cline.outfile
        self.assert_(os.path.isfile(filename))
        #Check we can parse the output...
        align = AlignIO.read(open(filename),"emboss")
        self.assertEqual(len(align), 2)
        self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
        self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
        #Clean up,
        os.remove(filename)

00475     def test_needle_piped(self):
        """needle with asis trick, output piped to stdout."""
        cline = NeedleCommandline(cmd=exes["needle"],
                                 asequence="asis:ACCCGGGCGCGGT",
                                 bsequence="asis:ACCCGAGCGCGGT",
                                 gapopen=10,
                                 gapextend=0.5,
                                 auto=True, filter=True)
        self.assertEqual(str(cline),
                         exes["needle"] + " -auto -filter" \
                         + " -asequence=asis:ACCCGGGCGCGGT" \
                         + " -bsequence=asis:ACCCGAGCGCGGT" \
                         + " -gapopen=10 -gapextend=0.5")
        #Run the tool,
        child = subprocess.Popen(str(cline),
                                 stdin=subprocess.PIPE,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=(sys.platform!="win32"))
        child.stdin.close()
        #Check we could read it's output
        align = AlignIO.read(child.stdout, "emboss")
        self.assertEqual(len(align), 2)
        self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
        self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
        #Check no error output:
        assert child.stderr.read() == ""
        assert 0 == child.wait()

00504     def test_water_file2(self):
        """water with the asis trick and nucleotide FASTA file, output to a file."""
        #Setup,
        query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
        out_file = "Emboss/temp_test2.water"
        in_file = "Fasta/f002"
        self.assert_(os.path.isfile(in_file))
        if os.path.isfile(out_file):
            os.remove(out_file)
        cline = WaterCommandline(cmd=exes["water"])
        cline.set_parameter("-asequence", "asis:%s" % query)
        cline.set_parameter("-bsequence", in_file)
        cline.set_parameter("-gapopen", "10")
        cline.set_parameter("-gapextend", "0.5")
        cline.set_parameter("-outfile", out_file)
        self.assertEqual(str(eval(repr(cline))), str(cline))
        #Run the tool,
        self.run_water(cline)
        #Check we can parse the output and it is sensible...
        self.pairwise_alignment_check(query,
                                      SeqIO.parse(open(in_file),"fasta"),
                                      AlignIO.parse(open(out_file),"emboss"),
                                      local=True)
        #Clean up,
        os.remove(out_file)

00530     def test_water_file3(self):
        """water with the asis trick and GenBank file, output to a file."""
        #Setup,
        query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
        out_file = "Emboss/temp_test3.water"
        in_file = "GenBank/cor6_6.gb"
        self.assert_(os.path.isfile(in_file))
        if os.path.isfile(out_file):
            os.remove(out_file)
        cline = WaterCommandline(cmd=exes["water"])
        cline.set_parameter("asequence", "asis:%s" % query)
        cline.set_parameter("bsequence", in_file)
        #TODO - Tell water this is a GenBank file!
        cline.set_parameter("gapopen", "1")
        cline.set_parameter("gapextend", "0.5")
        cline.set_parameter("outfile", out_file)
        self.assertEqual(str(eval(repr(cline))), str(cline))
        #Run the tool,
        self.run_water(cline)
        #Check we can parse the output and it is sensible...
        self.pairwise_alignment_check(query,
                                      SeqIO.parse(open(in_file),"genbank"),
                                      AlignIO.parse(open(out_file),"emboss"),
                                      local=True)
        #Clean up,
        os.remove(out_file)

00557     def test_water_file4(self):
        """water with the asis trick and SwissProt file, output to a file."""
        #Setup,
        query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
        out_file = "Emboss/temp_test4.water"
        in_file = "SwissProt/sp004"
        self.assert_(os.path.isfile(in_file))
        if os.path.isfile(out_file):
            os.remove(out_file)
        cline = WaterCommandline(cmd=exes["water"])
        cline.set_parameter("-asequence", "asis:%s" % query)
        cline.set_parameter("-bsequence", in_file)
        #EMBOSS should work this out, but let's be explicit:
        cline.set_parameter("-sprotein", True)
        #TODO - Tell water this is a SwissProt file!
        cline.set_parameter("-gapopen", "20")
        cline.set_parameter("-gapextend", "5")
        cline.set_parameter("-outfile", out_file)
        self.assertEqual(str(eval(repr(cline))), str(cline))
        #Run the tool,
        self.run_water(cline)
        #Check we can parse the output and it is sensible...
        self.pairwise_alignment_check(query,
                                      SeqIO.parse(open(in_file),"swiss"),
                                      AlignIO.parse(open(out_file),"emboss"),
                                      local=True)
        #Clean up,
        os.remove(out_file)
        
00586     def test_needle_piped2(self):
        """needle with asis trick, and nucleotide FASTA file, output piped to stdout."""
        #TODO - Support needle in Bio.Emboss.Applications
        #(ideally with the -auto and -filter arguments)
        #Setup,
        query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAA"
        cline = exes["needle"]
        cline += " -asequence asis:" + query
        cline += " -bsequence Fasta/f002"
        cline += " -auto" #no prompting
        cline += " -filter" #use stdout
        #Run the tool,
        child = subprocess.Popen(str(cline),
                                 stdin=subprocess.PIPE,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=(sys.platform!="win32"))
        child.stdin.close()
        #Check we can parse the output and it is sensible...
        self.pairwise_alignment_check(query,
                                      SeqIO.parse(open("Fasta/f002"),"fasta"),
                                      AlignIO.parse(child.stdout,"emboss"),
                                      local=False)
        #Check no error output:
        assert child.stderr.read() == ""
        assert 0 == child.wait()

00613     def test_water_needs_output(self):
        """water without output file or stdout/filter should give error."""
        cline = WaterCommandline(cmd=exes["water"],
                                 asequence="asis:ACCCGGGCGCGGT",
                                 bsequence="asis:ACCCGAGCGCGGT",
                                 gapopen=10,
                                 gapextend=0.5,
                                 auto=True)
        self.assert_(cline.auto)
        self.assert_(not cline.stdout)
        self.assert_(not cline.filter)
        self.assertEqual(cline.outfile, None)
        self.assertRaises(ValueError, str, cline)

00627     def test_needle_needs_output(self):
        """needle without output file or stdout/filter should give error."""
        cline = NeedleCommandline(cmd=exes["needle"],
                                 asequence="asis:ACCCGGGCGCGGT",
                                 bsequence="asis:ACCCGAGCGCGGT",
                                 gapopen=10,
                                 gapextend=0.5,
                                 auto=True)
        self.assert_(cline.auto)
        self.assert_(not cline.stdout)
        self.assert_(not cline.filter)
        self.assertEqual(cline.outfile, None)
        self.assertRaises(ValueError, str, cline)
   
00641     def test_seqtmatchall_piped(self):
        """seqmatchall with pair output piped to stdout."""
        cline = SeqmatchallCommandline(cmd=exes["seqmatchall"],
                                       sequence="Fasta/f002",
                                       aformat="pair", wordsize=9,
                                       auto=True, stdout=True)
        self.assertEqual(str(cline),
                         exes["seqmatchall"] + " -auto -stdout" \
                         + " -sequence=Fasta/f002"
                         + " -wordsize=9 -aformat=pair")
        #Run the tool,
        child = subprocess.Popen(str(cline),
                                 stdin=subprocess.PIPE,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=(sys.platform!="win32"))
        child.stdin.close()
        #Check we could read it's output
        for align in AlignIO.parse(child.stdout, "emboss") :
            self.assertEqual(len(align), 2)
            self.assertEqual(align.get_alignment_length(), 9)
        #Check no error output:
        assert child.stderr.read() == ""
        assert 0 == child.wait()
        
#Top level function as this makes it easier to use for debugging:
def emboss_translate(sequence, table=None, frame=None):
    """Call transeq, returns protein sequence as string."""
    #TODO - Support transeq in Bio.Emboss.Applications?
    #(doesn't seem worthwhile as Biopython can do translations)

    if not sequence:
        raise ValueError(sequence)

    #Setup,
    cline = exes["transeq"]

    if len(sequence) < 100:
        filename = None
        cline += " -sequence asis:%s" % sequence
    else:
        #There are limits on command line string lengths...
        #use a temp file instead.
        filename = "Emboss/temp_transeq.txt"
        handle = open(filename,"w")
        SeqIO.write([SeqRecord(sequence, id="Test")], handle, "fasta")
        handle.flush()
        handle.close()
        cline += " -sequence %s" % filename

    cline += " -auto" #no prompting
    cline += " -filter" #use stdout
    if table is not None:
        cline += " -table %s" % str(table)
    if frame is not None:
        cline += " -frame %s" % str(frame)
    #Run the tool,
    child = subprocess.Popen(str(cline),
                             stdin=subprocess.PIPE,
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE,
                             shell=(sys.platform!="win32"))
    child.stdin.close()
    #Check no error output:
    err = child.stderr.read()
    if err != "":
        raise ValueError(str(cline) + "\n" + err)

    #Check we could read it's output
    record = SeqIO.read(child.stdout, "fasta")

    if 0 != child.wait():
        raise ValueError(str(cline))
    
    if filename:
        os.remove(filename)
        if not record.id.startswith("Test"):
            raise ValueError(str(cline))
    else:
        if not record.id.startswith("asis"):
            raise ValueError(str(cline))
    return str(record.seq)

#Top level function as this makes it easier to use for debugging:
def check_translation(sequence, translation, table=None):
    if table is None:
        t = 1
    else:
        t = table
    if translation != str(sequence.translate(t)) \
    or translation != str(translate(sequence,t)) \
    or translation != translate(str(sequence),t):
        #More details...
        for i, amino in enumerate(translation):
            codon = sequence[i*3:i*3+3]
            if amino != str(codon.translate(t)):
                raise ValueError("%s -> %s not %s (table %s)" \
                         % (codon, amino, codon.translate(t), t))
        #Shouldn't reach this line:
        raise ValueError("%s -> %s (table %s)" \
                         % (sequence, translation, t))
    return True

00744 class TranslationTests(unittest.TestCase):
    """Run pairwise alignments with water and needle, and parse them."""

    def tearDown(self):
        clean_up()

00750     def test_simple(self):
        """transeq vs Bio.Seq for simple translations (including alt tables)."""

        examples = [Seq("ACGTGACTGACGTAGCATGCCACTAGG"),
                    #Unamibguous TA? codons:
                    Seq("TAATACTATTAG", generic_dna),
                    #Most of the ambiguous TA? codons:
                    Seq("TANTARTAYTAMTAKTAHTABTADTAV", generic_dna),
                    #Problem cases,
                    #
                    #Seq("TAW", generic_dna),
                    #W = A or T, but EMBOSS does TAW -> X
                    #TAA -> Y, TAT ->Y, so in Biopython TAW -> Y
                    #
                    #Seq("TAS", generic_dna),
                    #S = C or G, but EMBOSS does TAS -> Y
                    #TAG -> *, TAC ->Y, so in Biopython TAS -> X (Y or *)
                    #
                    #Seq("AAS", generic_dna),
                    #On table 9, EMBOSS gives N, we give X.
                    #S = C or G, so according to my reading of
                    #table 9 on the NCBI page, AAC=N, AAG=K
                    #suggesting this is a bug in EMBOSS.
                    #
                    Seq("ACGGGGGGGGTAAGTGGTGTGTGTGTAGT", generic_dna),
                    ]
        
        for sequence in examples:
            #EMBOSS treats spare residues differently... avoid this issue
            if len(sequence) % 3 != 0:
                sequence = sequence[:-(len(sequence)%3)]
            self.assertEqual(len(sequence) % 3, 0)
            self.assert_(len(sequence) > 0)
            self.check(sequence)

00785     def check(self, sequence):
        """Compare our translation to EMBOSS's using all tables.

        Takes a Seq object (and a filename containing it)."""
        translation = emboss_translate(sequence)
        self.assert_(check_translation(sequence, translation))

        for table in [1,2,3,4,5,6,9,10,11,12,13,14,15,16,21,22,23]:
            translation = emboss_translate(sequence, table)
            self.assert_(check_translation(sequence, translation, table))
        return True

    def translate_all_codons(self, letters):
        sequence = Seq("".join([c1+c3+c3 \
                       for c1 in letters \
                       for c2 in letters \
                       for c3 in letters]),
                       generic_nucleotide)
        self.check(sequence)
        
    #def test_all_ambig_dna_codons(self):
    #    """transeq vs Bio.Seq on ambiguous DNA codons (inc. alt tables)."""
    #    self.translate_all_codons(ambiguous_dna_letters)

00809     def test_all_unambig_dna_codons(self):
        """transeq vs Bio.Seq on unambiguous DNA codons (inc. alt tables)."""
        self.translate_all_codons("ATCGatcg")

00813     def test_all_unambig_rna_codons(self):
        """transeq vs Bio.Seq on unambiguous RNA codons (inc. alt tables)."""
        self.translate_all_codons("AUCGaucg")

00817     def test_mixed_unambig_rna_codons(self):
        """transeq vs Bio.Seq on unambiguous DNA/RNA codons (inc. alt tables)."""
        self.translate_all_codons("ATUCGatucg")
        
def clean_up():
    """Fallback clean up method to remove temp files."""
    for filename in os.listdir("Emboss"):
        if filename.startswith("temp_"):
            try:
                os.remove(filename)
            except:
                pass

if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)
    clean_up()

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