<gh_stars>1-10
# Copyright 2009-2012 by <NAME>.  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.

"""Unit tests for Bio.SeqIO.index(...) and index_db() functions."""

try:
    import sqlite3
except ImportError:
    #Try and run what tests we can on Python 2.4 or Jython
    #where we don't expect this to be installed.
    sqlite3 = None

import sys
import os
import unittest
import gzip
from StringIO import StringIO
try:
    #This is in Python 2.6+, but we need it on Python 3
    from io import BytesIO
except ImportError:
    BytesIO = StringIO
from Bio._py3k import _as_bytes, _bytes_to_string


from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.SeqIO._index import _FormatToRandomAccess
from Bio.Alphabet import generic_protein, generic_nucleotide, generic_dna

from seq_tests_common import compare_record

def add_prefix(key):
    """Dummy key_function for testing index code."""
    return "id_" + key

def gzip_open(filename, format):
    #At time of writing, under Python 3.2.2 seems gzip.open(filename, mode)
    #insists on giving byte strings (i.e. binary mode)
    #See http://bugs.python.org/issue13989
    if sys.version_info[0] < 3 or format in SeqIO._BinaryFormats:
        return gzip.open(filename)
    handle = gzip.open(filename)
    data = handle.read() #bytes!
    handle.close()
    return StringIO(_bytes_to_string(data))


if sqlite3:
    class OldIndexTest(unittest.TestCase):
        """Testing a pre-built index (make sure cross platform etc).

        >>> from Bio import SeqIO
        >>> d = SeqIO.index_db("triple_sff.idx", ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"], "sff")
        >>> len(d)
        54
        """
        def test_old(self):
            """Load existing index with no options."""
            d = SeqIO.index_db("Roche/triple_sff.idx")
            self.assertEqual(54, len(d))

        def test_old_format(self):
            """Load existing index with correct format."""
            d = SeqIO.index_db("Roche/triple_sff.idx", format="sff")
            self.assertEqual(54, len(d))

        def test_old_format_wrong(self):
            """Load existing index with wrong format."""
            self.assertRaises(ValueError, SeqIO.index_db,
                              "Roche/triple_sff.idx", format="fasta")

        def test_old_files(self):
            """Load existing index with correct files."""
            d = SeqIO.index_db("Roche/triple_sff.idx",
                               ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"])
            self.assertEqual(54, len(d))

        def test_old_files_wrong(self):
            """Load existing index with wrong files."""
            self.assertRaises(ValueError, SeqIO.index_db,
                              "Roche/triple_sff.idx", ["a.sff", "b.sff", "c.sff"])

        def test_old_files_wrong2(self):
            """Load existing index with wrong number of files."""
            self.assertRaises(ValueError, SeqIO.index_db,
                              "Roche/triple_sff.idx",
                              ["E3MFGYR02_no_manifest.sff", "greek.sff"])


class IndexDictTests(unittest.TestCase):
    """Cunning unit test where methods are added at run time."""
    def simple_check(self, filename, format, alphabet, comp):
        """Check indexing (without a key function)."""
        if comp:
            h = gzip_open(filename, format)
            id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
            h.close()
        else:
            id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]

        rec_dict = SeqIO.index(filename, format, alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict._proxy._handle.close() #TODO - Better solution
        del rec_dict

        if not sqlite3:
            return

        #In memory,
        #note here give filenames as list of strings
        rec_dict = SeqIO.index_db(":memory:", [filename], format,
                                  alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        del rec_dict

        #check error conditions
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", format="dummy")
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", filenames=["dummy"])

        #Saving to file...
        index_tmp = filename + ".idx"
        if os.path.isfile(index_tmp):
            os.remove(index_tmp)

        #To disk,
        #note here we give the filename as a single string
        #to confirm that works too (convience feature).
        rec_dict = SeqIO.index_db(index_tmp, filename, format,
                                  alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload it...
        rec_dict = SeqIO.index_db(index_tmp, [filename], format,
                                  alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload without passing filenames and format
        rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict
        os.remove(index_tmp)
    
    def key_check(self, filename, format, alphabet, comp):
        """Check indexing with a key function."""
        if comp:
            h = gzip_open(filename, format)
            id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
            h.close()
        else:
            id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]

        key_list = [add_prefix(id) for id in id_list]
        rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict._proxy._handle.close() #TODO - Better solution
        del rec_dict

        if not sqlite3:
            return

        #In memory,
        rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet,
                                  add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        #check error conditions
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", format="dummy",
                          key_function=add_prefix)
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", filenames=["dummy"],
                          key_function=add_prefix)
        rec_dict.close()
        del rec_dict

        #Saving to file...
        index_tmp = filename + ".key.idx"
        if os.path.isfile(index_tmp):
            os.remove(index_tmp)
        rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
                                  add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload it...
        rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
                                  add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload without passing filenames and format
        rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet,
                                  key_function=add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict
        os.remove(index_tmp)
        #Done
    
    def check_dict_methods(self, rec_dict, keys, ids):
        self.assertEqual(set(keys), set(rec_dict.keys()))
        #This is redundant, I just want to make sure len works:
        self.assertEqual(len(keys), len(rec_dict))
        #Make sure boolean evaluation works
        self.assertEqual(bool(keys), bool(rec_dict))
        for key,id in zip(keys, ids):
            self.assertTrue(key in rec_dict)
            self.assertEqual(id, rec_dict[key].id)
            self.assertEqual(id, rec_dict.get(key).id)
        #Check non-existant keys,
        assert chr(0) not in keys, "Bad example in test"
        try:
            rec = rec_dict[chr(0)]
            raise ValueError("Accessing a non-existent key should fail")
        except KeyError:
            pass
        self.assertEqual(rec_dict.get(chr(0)), None)
        self.assertEqual(rec_dict.get(chr(0), chr(1)), chr(1))
        if hasattr(dict, "iteritems"):
            #Python 2.x
            for key, rec in rec_dict.iteritems():
                self.assertTrue(key in keys)
                self.assertTrue(isinstance(rec, SeqRecord))
                self.assertTrue(rec.id in ids)
            #Now check non-defined methods...
            self.assertRaises(NotImplementedError, rec_dict.items)
            self.assertRaises(NotImplementedError, rec_dict.values)
        else:
            #Python 3
            assert not hasattr(rec_dict, "iteritems")
            for key, rec in rec_dict.iteritems():
                self.assertTrue(key in keys)
                self.assertTrue(isinstance(rec, SeqRecord))
                self.assertTrue(rec.id in ids)
            for rec in rec_dict.itervalues():
                self.assertTrue(key in keys)
                self.assertTrue(isinstance(rec, SeqRecord))
                self.assertTrue(rec.id in ids)
        #Check the following fail
        self.assertRaises(NotImplementedError, rec_dict.popitem)
        self.assertRaises(NotImplementedError, rec_dict.pop, chr(0))
        self.assertRaises(NotImplementedError, rec_dict.pop, chr(0), chr(1))
        self.assertRaises(NotImplementedError, rec_dict.clear)
        self.assertRaises(NotImplementedError, rec_dict.__setitem__, "X", None)
        self.assertRaises(NotImplementedError, rec_dict.copy)
        self.assertRaises(NotImplementedError, rec_dict.fromkeys, [])

    def get_raw_check(self, filename, format, alphabet, comp):
        #Also checking the key_function here
        if comp:
            h = gzip.open(filename, "rb")
            raw_file = h.read()
            h.close()
            h = gzip_open(filename, format)
            id_list = [rec.id.lower() for rec in \
                       SeqIO.parse(h, format, alphabet)]
            h.close()
        else:
            h = open(filename, "rb")
            raw_file = h.read()
            h.close()
            id_list = [rec.id.lower() for rec in \
                       SeqIO.parse(filename, format, alphabet)]
        rec_dict = SeqIO.index(filename, format, alphabet,
                               key_function = lambda x : x.lower())
        self.assertEqual(set(id_list), set(rec_dict.keys()))
        self.assertEqual(len(id_list), len(rec_dict))
        for key in id_list:
            self.assertTrue(key in rec_dict)
            self.assertEqual(key, rec_dict[key].id.lower())
            self.assertEqual(key, rec_dict.get(key).id.lower())
            raw = rec_dict.get_raw(key)
            self.assertTrue(raw.strip())
            self.assertTrue(raw in raw_file)
            rec1 = rec_dict[key]
            #Following isn't very elegant, but it lets me test the
            #__getitem__ SFF code is working.
            if format in SeqIO._BinaryFormats:
                handle = BytesIO(raw)
            else:
                handle = StringIO(_bytes_to_string(raw))
            if format == "sff":
                rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
                            rec_dict._proxy._flows_per_read,
                            rec_dict._proxy._flow_chars,
                            rec_dict._proxy._key_sequence,
                            rec_dict._proxy._alphabet,
                            trim=False)
            elif format == "sff-trim":
                rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
                            rec_dict._proxy._flows_per_read,
                            rec_dict._proxy._flow_chars,
                            rec_dict._proxy._key_sequence,
                            rec_dict._proxy._alphabet,
                            trim=True)
            elif format == "uniprot-xml":
                self.assertTrue(raw.startswith(_as_bytes("<entry ")))
                self.assertTrue(raw.endswith(_as_bytes("</entry>")))
                #Currently the __getitem__ method uses this
                #trick too, but we hope to fix that later
                raw = """<?xml version='1.0' encoding='UTF-8'?>
                <uniprot xmlns="http://uniprot.org/uniprot"
                xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                xsi:schemaLocation="http://uniprot.org/uniprot
                http://www.uniprot.org/support/docs/uniprot.xsd">
                %s
                </uniprot>
                """ % _bytes_to_string(raw)
                handle = StringIO(raw)
                rec2 = SeqIO.read(handle, format, alphabet)
            else:
                rec2 = SeqIO.read(handle, format, alphabet)
            self.assertEqual(True, compare_record(rec1, rec2))
        rec_dict._proxy._handle.close() #TODO - Better solution
        del rec_dict

    if sqlite3:
        def test_duplicates_index_db(self):
            """Index file with duplicate identifers with Bio.SeqIO.index_db()"""
            self.assertRaises(ValueError, SeqIO.index_db, ":memory:",
                              ["Fasta/dups.fasta"], "fasta")

    def test_duplicates_index(self):
        """Index file with duplicate identifers with Bio.SeqIO.index()"""
        self.assertRaises(ValueError, SeqIO.index, "Fasta/dups.fasta", "fasta")

    def test_duplicates_to_dict(self):
        """Index file with duplicate identifers with Bio.SeqIO.to_dict()"""
        handle = open("Fasta/dups.fasta", "rU")
        iterator = SeqIO.parse(handle, "fasta")
        self.assertRaises(ValueError, SeqIO.to_dict, iterator)
        handle.close()

tests = [
    ("Ace/contig1.ace", "ace", generic_dna),
    ("Ace/consed_sample.ace", "ace", None),
    ("Ace/seq.cap.ace", "ace", generic_dna),
    ("Quality/wrapping_original_sanger.fastq", "fastq", None),
    ("Quality/example.fastq", "fastq", None),
    ("Quality/example.fastq", "fastq-sanger", generic_dna),
    ("Quality/tricky.fastq", "fastq", generic_nucleotide),
    ("Quality/sanger_faked.fastq", "fastq-sanger", generic_dna),
    ("Quality/solexa_faked.fastq", "fastq-solexa", generic_dna),
    ("Quality/illumina_faked.fastq", "fastq-illumina", generic_dna),
    ("EMBL/epo_prt_selection.embl", "embl", None),
    ("EMBL/U87107.embl", "embl", None),
    ("EMBL/TRBG361.embl", "embl", None),
    ("EMBL/A04195.imgt", "embl", None), #Not a proper EMBL file, an IMGT file
    ("EMBL/A04195.imgt", "imgt", None),
    ("GenBank/NC_000932.faa", "fasta", generic_protein),
    ("GenBank/NC_005816.faa", "fasta", generic_protein),
    ("GenBank/NC_005816.tsv", "tab", generic_protein),
    ("GenBank/NC_005816.ffn", "fasta", generic_dna),
    ("GenBank/NC_005816.fna", "fasta", generic_dna),
    ("GenBank/NC_005816.gb", "gb", None),
    ("GenBank/cor6_6.gb", "genbank", None),
    ("IntelliGenetics/vpu_nucaligned.txt", "ig", generic_nucleotide),
    ("IntelliGenetics/TAT_mase_nuc.txt", "ig", None),
    ("IntelliGenetics/VIF_mase-pro.txt", "ig", generic_protein),
    ("Phd/phd1", "phd", generic_dna),
    ("Phd/phd2", "phd", None),
    ("Phd/phd_solexa", "phd", generic_dna),
    ("Phd/phd_454", "phd", generic_dna),
    ("NBRF/B_nuc.pir", "pir", generic_nucleotide),
    ("NBRF/Cw_prot.pir", "pir", generic_protein),
    ("NBRF/clustalw.pir", "pir", None),
    ("SwissProt/sp001", "swiss", None),
    ("SwissProt/sp010", "swiss", None),
    ("SwissProt/sp016", "swiss", None),
    ("SwissProt/multi_ex.txt", "swiss", None),
    ("SwissProt/multi_ex.xml", "uniprot-xml", None),
    ("SwissProt/multi_ex.fasta", "fasta", None),
    ("Roche/E3MFGYR02_random_10_reads.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_random_10_reads.sff", "sff-trim", generic_dna),
    ("Roche/E3MFGYR02_index_at_start.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_index_in_middle.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_alt_index_at_start.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_alt_index_in_middle.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_alt_index_at_end.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_no_manifest.sff", "sff", generic_dna),
    ("Roche/greek.sff", "sff", generic_nucleotide),
    ("Roche/greek.sff", "sff-trim", generic_nucleotide),
    ("Roche/paired.sff", "sff", None),
    ("Roche/paired.sff", "sff-trim", None),
    ]
for filename, format, alphabet in tests:
    assert format in _FormatToRandomAccess
    tasks = [(filename, None)]
    if os.path.isfile(filename + ".bgz"):
        tasks.append((filename + ".bgz","bgzf"))
    for filename, comp in tasks:

        def funct(fn,fmt,alpha,c):
            f = lambda x : x.simple_check(fn, fmt, alpha, c)
            f.__doc__ = "Index %s file %s defaults" % (fmt, fn)
            return f
        setattr(IndexDictTests, "test_%s_%s_simple" \
                    % (format, filename.replace("/","_").replace(".","_")),
                funct(filename, format, alphabet, comp))
        del funct

        def funct(fn,fmt,alpha,c):
            f = lambda x : x.key_check(fn, fmt, alpha, c)
            f.__doc__ = "Index %s file %s with key function" % (fmt, fn)
            return f
        setattr(IndexDictTests, "test_%s_%s_keyf" \
                    % (format, filename.replace("/","_").replace(".","_")),
                funct(filename, format, alphabet, comp))
        del funct

        def funct(fn,fmt,alpha,c):
            f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
            f.__doc__ = "Index %s file %s get_raw" % (fmt, fn)
            return f
        setattr(IndexDictTests, "test_%s_%s_get_raw" \
                    % (format, filename.replace("/","_").replace(".","_")),
                funct(filename, format, alphabet, comp))
        del funct

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

# Copyright 2009-2012 by <NAME>.  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.

"""Unit tests for Bio.SeqIO.index(...) and index_db() functions."""

try:
    import sqlite3
except ImportError:
    #Try and run what tests we can on Python 2.4 or Jython
    #where we don't expect this to be installed.
    sqlite3 = None

import sys
import os
import unittest
import gzip
from StringIO import StringIO
try:
    #This is in Python 2.6+, but we need it on Python 3
    from io import BytesIO
except ImportError:
    BytesIO = StringIO
from Bio._py3k import _as_bytes, _bytes_to_string


from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.SeqIO._index import _FormatToRandomAccess
from Bio.Alphabet import generic_protein, generic_nucleotide, generic_dna

from seq_tests_common import compare_record

def add_prefix(key):
    """Dummy key_function for testing index code."""
    return "id_" + key

def gzip_open(filename, format):
    #At time of writing, under Python 3.2.2 seems gzip.open(filename, mode)
    #insists on giving byte strings (i.e. binary mode)
    #See http://bugs.python.org/issue13989
    if sys.version_info[0] < 3 or format in SeqIO._BinaryFormats:
        return gzip.open(filename)
    handle = gzip.open(filename)
    data = handle.read() #bytes!
    handle.close()
    return StringIO(_bytes_to_string(data))


if sqlite3:
    class OldIndexTest(unittest.TestCase):
        """Testing a pre-built index (make sure cross platform etc).

        >>> from Bio import SeqIO
        >>> d = SeqIO.index_db("triple_sff.idx", ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"], "sff")
        >>> len(d)
        54
        """
        def test_old(self):
            """Load existing index with no options."""
            d = SeqIO.index_db("Roche/triple_sff.idx")
            self.assertEqual(54, len(d))

        def test_old_format(self):
            """Load existing index with correct format."""
            d = SeqIO.index_db("Roche/triple_sff.idx", format="sff")
            self.assertEqual(54, len(d))

        def test_old_format_wrong(self):
            """Load existing index with wrong format."""
            self.assertRaises(ValueError, SeqIO.index_db,
                              "Roche/triple_sff.idx", format="fasta")

        def test_old_files(self):
            """Load existing index with correct files."""
            d = SeqIO.index_db("Roche/triple_sff.idx",
                               ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"])
            self.assertEqual(54, len(d))

        def test_old_files_wrong(self):
            """Load existing index with wrong files."""
            self.assertRaises(ValueError, SeqIO.index_db,
                              "Roche/triple_sff.idx", ["a.sff", "b.sff", "c.sff"])

        def test_old_files_wrong2(self):
            """Load existing index with wrong number of files."""
            self.assertRaises(ValueError, SeqIO.index_db,
                              "Roche/triple_sff.idx",
                              ["E3MFGYR02_no_manifest.sff", "greek.sff"])


class IndexDictTests(unittest.TestCase):
    """Cunning unit test where methods are added at run time."""
    def simple_check(self, filename, format, alphabet, comp):
        """Check indexing (without a key function)."""
        if comp:
            h = gzip_open(filename, format)
            id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
            h.close()
        else:
            id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]

        rec_dict = SeqIO.index(filename, format, alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict._proxy._handle.close() #TODO - Better solution
        del rec_dict

        if not sqlite3:
            return

        #In memory,
        #note here give filenames as list of strings
        rec_dict = SeqIO.index_db(":memory:", [filename], format,
                                  alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        del rec_dict

        #check error conditions
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", format="dummy")
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", filenames=["dummy"])

        #Saving to file...
        index_tmp = filename + ".idx"
        if os.path.isfile(index_tmp):
            os.remove(index_tmp)

        #To disk,
        #note here we give the filename as a single string
        #to confirm that works too (convience feature).
        rec_dict = SeqIO.index_db(index_tmp, filename, format,
                                  alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload it...
        rec_dict = SeqIO.index_db(index_tmp, [filename], format,
                                  alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload without passing filenames and format
        rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
        self.check_dict_methods(rec_dict, id_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict
        os.remove(index_tmp)
    
    def key_check(self, filename, format, alphabet, comp):
        """Check indexing with a key function."""
        if comp:
            h = gzip_open(filename, format)
            id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
            h.close()
        else:
            id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]

        key_list = [add_prefix(id) for id in id_list]
        rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict._proxy._handle.close() #TODO - Better solution
        del rec_dict

        if not sqlite3:
            return

        #In memory,
        rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet,
                                  add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        #check error conditions
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", format="dummy",
                          key_function=add_prefix)
        self.assertRaises(ValueError, SeqIO.index_db,
                          ":memory:", filenames=["dummy"],
                          key_function=add_prefix)
        rec_dict.close()
        del rec_dict

        #Saving to file...
        index_tmp = filename + ".key.idx"
        if os.path.isfile(index_tmp):
            os.remove(index_tmp)
        rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
                                  add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload it...
        rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
                                  add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict

        #Now reload without passing filenames and format
        rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet,
                                  key_function=add_prefix)
        self.check_dict_methods(rec_dict, key_list, id_list)
        rec_dict.close()
        rec_dict._con.close() #hack for PyPy
        del rec_dict
        os.remove(index_tmp)
        #Done
    
    def check_dict_methods(self, rec_dict, keys, ids):
        self.assertEqual(set(keys), set(rec_dict.keys()))
        #This is redundant, I just want to make sure len works:
        self.assertEqual(len(keys), len(rec_dict))
        #Make sure boolean evaluation works
        self.assertEqual(bool(keys), bool(rec_dict))
        for key,id in zip(keys, ids):
            self.assertTrue(key in rec_dict)
            self.assertEqual(id, rec_dict[key].id)
            self.assertEqual(id, rec_dict.get(key).id)
        #Check non-existant keys,
        assert chr(0) not in keys, "Bad example in test"
        try:
            rec = rec_dict[chr(0)]
            raise ValueError("Accessing a non-existent key should fail")
        except KeyError:
            pass
        self.assertEqual(rec_dict.get(chr(0)), None)
        self.assertEqual(rec_dict.get(chr(0), chr(1)), chr(1))
        if hasattr(dict, "iteritems"):
            #Python 2.x
            for key, rec in rec_dict.iteritems():
                self.assertTrue(key in keys)
                self.assertTrue(isinstance(rec, SeqRecord))
                self.assertTrue(rec.id in ids)
            #Now check non-defined methods...
            self.assertRaises(NotImplementedError, rec_dict.items)
            self.assertRaises(NotImplementedError, rec_dict.values)
        else:
            #Python 3
            assert not hasattr(rec_dict, "iteritems")
            for key, rec in rec_dict.iteritems():
                self.assertTrue(key in keys)
                self.assertTrue(isinstance(rec, SeqRecord))
                self.assertTrue(rec.id in ids)
            for rec in rec_dict.itervalues():
                self.assertTrue(key in keys)
                self.assertTrue(isinstance(rec, SeqRecord))
                self.assertTrue(rec.id in ids)
        #Check the following fail
        self.assertRaises(NotImplementedError, rec_dict.popitem)
        self.assertRaises(NotImplementedError, rec_dict.pop, chr(0))
        self.assertRaises(NotImplementedError, rec_dict.pop, chr(0), chr(1))
        self.assertRaises(NotImplementedError, rec_dict.clear)
        self.assertRaises(NotImplementedError, rec_dict.__setitem__, "X", None)
        self.assertRaises(NotImplementedError, rec_dict.copy)
        self.assertRaises(NotImplementedError, rec_dict.fromkeys, [])

    def get_raw_check(self, filename, format, alphabet, comp):
        #Also checking the key_function here
        if comp:
            h = gzip.open(filename, "rb")
            raw_file = h.read()
            h.close()
            h = gzip_open(filename, format)
            id_list = [rec.id.lower() for rec in \
                       SeqIO.parse(h, format, alphabet)]
            h.close()
        else:
            h = open(filename, "rb")
            raw_file = h.read()
            h.close()
            id_list = [rec.id.lower() for rec in \
                       SeqIO.parse(filename, format, alphabet)]
        rec_dict = SeqIO.index(filename, format, alphabet,
                               key_function = lambda x : x.lower())
        self.assertEqual(set(id_list), set(rec_dict.keys()))
        self.assertEqual(len(id_list), len(rec_dict))
        for key in id_list:
            self.assertTrue(key in rec_dict)
            self.assertEqual(key, rec_dict[key].id.lower())
            self.assertEqual(key, rec_dict.get(key).id.lower())
            raw = rec_dict.get_raw(key)
            self.assertTrue(raw.strip())
            self.assertTrue(raw in raw_file)
            rec1 = rec_dict[key]
            #Following isn't very elegant, but it lets me test the
            #__getitem__ SFF code is working.
            if format in SeqIO._BinaryFormats:
                handle = BytesIO(raw)
            else:
                handle = StringIO(_bytes_to_string(raw))
            if format == "sff":
                rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
                            rec_dict._proxy._flows_per_read,
                            rec_dict._proxy._flow_chars,
                            rec_dict._proxy._key_sequence,
                            rec_dict._proxy._alphabet,
                            trim=False)
            elif format == "sff-trim":
                rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
                            rec_dict._proxy._flows_per_read,
                            rec_dict._proxy._flow_chars,
                            rec_dict._proxy._key_sequence,
                            rec_dict._proxy._alphabet,
                            trim=True)
            elif format == "uniprot-xml":
                self.assertTrue(raw.startswith(_as_bytes("<entry ")))
                self.assertTrue(raw.endswith(_as_bytes("</entry>")))
                #Currently the __getitem__ method uses this
                #trick too, but we hope to fix that later
                raw = """<?xml version='1.0' encoding='UTF-8'?>
                <uniprot xmlns="http://uniprot.org/uniprot"
                xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                xsi:schemaLocation="http://uniprot.org/uniprot
                http://www.uniprot.org/support/docs/uniprot.xsd">
                %s
                </uniprot>
                """ % _bytes_to_string(raw)
                handle = StringIO(raw)
                rec2 = SeqIO.read(handle, format, alphabet)
            else:
                rec2 = SeqIO.read(handle, format, alphabet)
            self.assertEqual(True, compare_record(rec1, rec2))
        rec_dict._proxy._handle.close() #TODO - Better solution
        del rec_dict

    if sqlite3:
        def test_duplicates_index_db(self):
            """Index file with duplicate identifers with Bio.SeqIO.index_db()"""
            self.assertRaises(ValueError, SeqIO.index_db, ":memory:",
                              ["Fasta/dups.fasta"], "fasta")

    def test_duplicates_index(self):
        """Index file with duplicate identifers with Bio.SeqIO.index()"""
        self.assertRaises(ValueError, SeqIO.index, "Fasta/dups.fasta", "fasta")

    def test_duplicates_to_dict(self):
        """Index file with duplicate identifers with Bio.SeqIO.to_dict()"""
        handle = open("Fasta/dups.fasta", "rU")
        iterator = SeqIO.parse(handle, "fasta")
        self.assertRaises(ValueError, SeqIO.to_dict, iterator)
        handle.close()

tests = [
    ("Ace/contig1.ace", "ace", generic_dna),
    ("Ace/consed_sample.ace", "ace", None),
    ("Ace/seq.cap.ace", "ace", generic_dna),
    ("Quality/wrapping_original_sanger.fastq", "fastq", None),
    ("Quality/example.fastq", "fastq", None),
    ("Quality/example.fastq", "fastq-sanger", generic_dna),
    ("Quality/tricky.fastq", "fastq", generic_nucleotide),
    ("Quality/sanger_faked.fastq", "fastq-sanger", generic_dna),
    ("Quality/solexa_faked.fastq", "fastq-solexa", generic_dna),
    ("Quality/illumina_faked.fastq", "fastq-illumina", generic_dna),
    ("EMBL/epo_prt_selection.embl", "embl", None),
    ("EMBL/U87107.embl", "embl", None),
    ("EMBL/TRBG361.embl", "embl", None),
    ("EMBL/A04195.imgt", "embl", None), #Not a proper EMBL file, an IMGT file
    ("EMBL/A04195.imgt", "imgt", None),
    ("GenBank/NC_000932.faa", "fasta", generic_protein),
    ("GenBank/NC_005816.faa", "fasta", generic_protein),
    ("GenBank/NC_005816.tsv", "tab", generic_protein),
    ("GenBank/NC_005816.ffn", "fasta", generic_dna),
    ("GenBank/NC_005816.fna", "fasta", generic_dna),
    ("GenBank/NC_005816.gb", "gb", None),
    ("GenBank/cor6_6.gb", "genbank", None),
    ("IntelliGenetics/vpu_nucaligned.txt", "ig", generic_nucleotide),
    ("IntelliGenetics/TAT_mase_nuc.txt", "ig", None),
    ("IntelliGenetics/VIF_mase-pro.txt", "ig", generic_protein),
    ("Phd/phd1", "phd", generic_dna),
    ("Phd/phd2", "phd", None),
    ("Phd/phd_solexa", "phd", generic_dna),
    ("Phd/phd_454", "phd", generic_dna),
    ("NBRF/B_nuc.pir", "pir", generic_nucleotide),
    ("NBRF/Cw_prot.pir", "pir", generic_protein),
    ("NBRF/clustalw.pir", "pir", None),
    ("SwissProt/sp001", "swiss", None),
    ("SwissProt/sp010", "swiss", None),
    ("SwissProt/sp016", "swiss", None),
    ("SwissProt/multi_ex.txt", "swiss", None),
    ("SwissProt/multi_ex.xml", "uniprot-xml", None),
    ("SwissProt/multi_ex.fasta", "fasta", None),
    ("Roche/E3MFGYR02_random_10_reads.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_random_10_reads.sff", "sff-trim", generic_dna),
    ("Roche/E3MFGYR02_index_at_start.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_index_in_middle.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_alt_index_at_start.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_alt_index_in_middle.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_alt_index_at_end.sff", "sff", generic_dna),
    ("Roche/E3MFGYR02_no_manifest.sff", "sff", generic_dna),
    ("Roche/greek.sff", "sff", generic_nucleotide),
    ("Roche/greek.sff", "sff-trim", generic_nucleotide),
    ("Roche/paired.sff", "sff", None),
    ("Roche/paired.sff", "sff-trim", None),
    ]
for filename, format, alphabet in tests:
    assert format in _FormatToRandomAccess
    tasks = [(filename, None)]
    if os.path.isfile(filename + ".bgz"):
        tasks.append((filename + ".bgz","bgzf"))
    for filename, comp in tasks:

        def funct(fn,fmt,alpha,c):
            f = lambda x : x.simple_check(fn, fmt, alpha, c)
            f.__doc__ = "Index %s file %s defaults" % (fmt, fn)
            return f
        setattr(IndexDictTests, "test_%s_%s_simple" \
                    % (format, filename.replace("/","_").replace(".","_")),
                funct(filename, format, alphabet, comp))
        del funct

        def funct(fn,fmt,alpha,c):
            f = lambda x : x.key_check(fn, fmt, alpha, c)
            f.__doc__ = "Index %s file %s with key function" % (fmt, fn)
            return f
        setattr(IndexDictTests, "test_%s_%s_keyf" \
                    % (format, filename.replace("/","_").replace(".","_")),
                funct(filename, format, alphabet, comp))
        del funct

        def funct(fn,fmt,alpha,c):
            f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
            f.__doc__ = "Index %s file %s get_raw" % (fmt, fn)
            return f
        setattr(IndexDictTests, "test_%s_%s_get_raw" \
                    % (format, filename.replace("/","_").replace(".","_")),
                funct(filename, format, alphabet, comp))
        del funct

if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)
# Copyright 2009-2012 by <NAME>.  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. Unit tests for Bio.SeqIO.index(...) and index_db() functions. #Try and run what tests we can on Python 2.4 or Jython #where we don't expect this to be installed. #This is in Python 2.6+, but we need it on Python 3 Dummy key_function for testing index code. #At time of writing, under Python 3.2.2 seems gzip.open(filename, mode) #insists on giving byte strings (i.e. binary mode) #See http://bugs.python.org/issue13989 #bytes! Testing a pre-built index (make sure cross platform etc).          >>> from Bio import SeqIO         >>> d = SeqIO.index_db("triple_sff.idx", ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"], "sff")         >>> len(d)         54 Load existing index with no options. Load existing index with correct format. Load existing index with wrong format. Load existing index with correct files. Load existing index with wrong files. Load existing index with wrong number of files. Cunning unit test where methods are added at run time. Check indexing (without a key function). #TODO - Better solution #In memory, #note here give filenames as list of strings #check error conditions #Saving to file... #To disk, #note here we give the filename as a single string #to confirm that works too (convience feature). #hack for PyPy #Now reload it... #hack for PyPy #Now reload without passing filenames and format #hack for PyPy Check indexing with a key function. #TODO - Better solution #In memory, #check error conditions #Saving to file... #hack for PyPy #Now reload it... #hack for PyPy #Now reload without passing filenames and format #hack for PyPy #Done #This is redundant, I just want to make sure len works: #Make sure boolean evaluation works #Check non-existant keys, #Python 2.x #Now check non-defined methods... #Python 3 #Check the following fail #Also checking the key_function here #Following isn't very elegant, but it lets me test the #__getitem__ SFF code is working. #Currently the __getitem__ method uses this #trick too, but we hope to fix that later <?xml version='1.0' encoding='UTF-8'?>                 <uniprot xmlns="http://uniprot.org/uniprot"                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"                 xsi:schemaLocation="http://uniprot.org/uniprot                 http://www.uniprot.org/support/docs/uniprot.xsd">                 %s                 </uniprot> #TODO - Better solution Index file with duplicate identifers with Bio.SeqIO.index_db() Index file with duplicate identifers with Bio.SeqIO.index() Index file with duplicate identifers with Bio.SeqIO.to_dict() #Not a proper EMBL file, an IMGT file