def test_build_ensembl_transcript_index(self):
"""Build the gtf portion of the ensembl transcript db
"""
# cat ~/oncotator_pycharm/oncotator/test/testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf | cut -f 9 | cut -f 5 --delimiter=" " | sort | uniq | sed -r "s/;//g" | sed -r "s/\"//g"
# snR84, tK(UUU)K, YAL067C, YAL067W-A, YAL068C, YAL068W-A, YAL069W, YBR278W, YBR279W, YBR280C, YBR281C, YDR528W, YDR529C, YKR074W,
#
# grep -Pzo ">(snR84|tK\(UUU\)K|YAL067C|YAL067W-A|YAL068C|YAL068W-A|YAL069W|YBR278W|YBR279W|YBR280C|YBR281C|YDR528W|YDR529C|YKR074W)([A-Za-z_0-9 \:\-\n]+)" Saccharomyces_cerevisiae.EF4.71.cdna.all.fa >Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa
#
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
output_filename = "out/test_ensembl_gtf.db"
protocol = "file"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], output_filename, protocol=protocol)
self.assertTrue(os.path.exists(output_filename))
shove = Shove(protocol + "://" + output_filename, "memory://")
self.assertTrue(len(shove.keys()) > 0)
self.assertTrue("YDR529C" in shove.keys())
t = shove["YDR529C"]
self.assertTrue(t.get_seq() is not None)
self.assertTrue(t.get_seq() is not "")
self.assertTrue(len(t.get_cds()) > 0)
self.assertTrue(len(t.get_exons()) > 0)
MutUtils.removeDir(output_filename)
def test_gencode_small(self):
"""Test that we can create Transcript instances from a small gencode gtf and fasta."""
gencode_input_gtf = "testdata/gencode/MAPK1.gencode.v19.annotation.gtf"
gencode_input_fasta = "testdata/gencode/MAPK1.gencode.v19.pc_transcripts.fa"
base_output_filename = "out/test_small_gencode"
shutil.rmtree(base_output_filename + ".transcript.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gene.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gp_bin.idx", ignore_errors=True)
genome_build_factory = GenomeBuildFactory()
genome_build_factory.construct_ensembl_indices([gencode_input_gtf], [gencode_input_fasta], base_output_filename)
seq_index = Shove("file://" + base_output_filename + ".transcript_by_gene.idx", "memory://", optimize=False)
transcripts = seq_index["MAPK1"]
self.assertTrue(len(transcripts) == 4)
seq_index_gp = Shove("file://" + base_output_filename + ".transcript_by_gp_bin.idx", "memory://", optimize=False)
transcripts = seq_index_gp["22_753"]
self.assertTrue(transcripts[0].get_strand() == "-")
self.assertTrue(len(transcripts) == 1)
for tx in transcripts:
if tx.get_transcript_id() != "ENST00000215832.6":
continue
self.assertTrue(tx.get_seq().startswith("AGGCAATCGGTCCGAG"))
def test_build_ensembl_transcript_index(self):
"""Build the gtf portion of the ensembl transcript db
"""
# cat ~/oncotator_pycharm/oncotator/test/testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf | cut -f 9 | cut -f 5 --delimiter=" " | sort | uniq | sed -r "s/;//g" | sed -r "s/\"//g"
# snR84, tK(UUU)K, YAL067C, YAL067W-A, YAL068C, YAL068W-A, YAL069W, YBR278W, YBR279W, YBR280C, YBR281C, YDR528W, YDR529C, YKR074W,
#
# grep -Pzo ">(snR84|tK\(UUU\)K|YAL067C|YAL067W-A|YAL068C|YAL068W-A|YAL069W|YBR278W|YBR279W|YBR280C|YBR281C|YDR528W|YDR529C|YKR074W)([A-Za-z_0-9 \:\-\n]+)" Saccharomyces_cerevisiae.EF4.71.cdna.all.fa >Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa
#
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
output_filename = "out/test_ensembl_gtf.db"
protocol = "file"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], output_filename, protocol=protocol)
self.assertTrue(os.path.exists(output_filename))
shove = Shove(protocol + "://" + output_filename, "memory://")
self.assertTrue(len(shove.keys()) > 0)
self.assertTrue("YDR529C" in shove.keys())
t = shove["YDR529C"]
self.assertTrue(t.get_seq() is not None)
self.assertTrue(t.get_seq() is not "")
self.assertTrue(len(t.get_cds()) > 0)
self.assertTrue(len(t.get_exons()) > 0)
MutUtils.removeDir(output_filename)
def build_ensembl_transcript_index(self, ensembl_input_gtfs, ensembl_input_fastas, output_filename, protocol="file", protein_id_mapping_file=None):
"""Create the transcript index (using shove) for ensembl. Key is transcript ID.
Note: This method will hold the entire transcript index in RAM.
:param ensembl_input_gtfs: (list)
:param ensembl_input_fastas: (list) sequence data for transcripts corresponding to what is in the gtfs
:param output_filename:
:param protocol: shove protocol. Usually "file" or "sqlite"
"""
# Example code taken from http://biopython.org/wiki/GFF_Parsing
shove = Shove(protocol + "://" + output_filename, "memory://")
logging.getLogger(__name__).info("Transcript index being created: " + protocol + "://" + output_filename)
# Get the transcript ID to protein ID mapping
tx_to_protein_mapping = self._create_tx_id_to_protein_id_mapping(protein_id_mapping_file)
seq_dict = {}
for in_seq_file in ensembl_input_fastas:
in_seq_handle = open(in_seq_file)
seq_dict.update(self._create_seq_dict(in_seq_handle))
in_seq_handle.close()
logging.getLogger(__name__).info("Parsed fasta file: " + in_seq_file)
for file_ctr, in_file in enumerate(ensembl_input_gtfs):
in_handle = open(in_file)
seq_dict_keys = seq_dict.keys()
ctr = 0
for rec in GFF.parse_simple(in_file): #(in_handle, base_dict=seq_dict):
# transcript id seems to always be a list of length 1
if len(rec['quals']['transcript_id']) > 1:
logging.getLogger(__name__).warn("ensembl records had more than one transcript id: " + str(rec['quals']['transcript_id']))
self._convertGFFRecordToTranscript(rec, seq_dict, seq_dict_keys, tx_to_protein_mapping)
ctr += 1
if (ctr % 10000) == 0:
logging.getLogger(__name__).info("Added " + str(ctr) + " lines of gtf " + str(file_ctr+1) + " of " + str(len(ensembl_input_gtfs)) + " (" + in_file + ") into internal transcript index.")
in_handle.close()
logging.getLogger(__name__).info("Finished " + str(ctr) + " lines of gtf (" + in_file + ")")
logging.getLogger(__name__).info("Populating final db with internal transcript index.")
transcript_index_keys = self._transcript_index.keys()
for i,k in enumerate(transcript_index_keys):
# Populate the protein sequence
protein_sequence = self._determine_protein_seq(self._transcript_index[k])
self._transcript_index[k].set_protein_seq(protein_sequence)
shove[k] = self._transcript_index[k]
if i % 10000 == 0:
logging.getLogger(__name__).info("Saved %0.1f%% of transcript index to disk with protein sequence." % (float(i*100)/float(len(transcript_index_keys))))
logging.getLogger(__name__).info("Transcript index created " + str(len(shove.keys())) + " transcripts: " + protocol + "://" + output_filename)
shove.close()
def build_ensembl_transcripts_by_genomic_location_index(
self,
ensembl_transcript_index_fname,
output_filename,
protocol="file"):
"""Create an index for genomic position to transcripts index, using a transcript index created in
build_ensembl_transcript_index
"""
transcript_db = Shove(protocol + "://" +
ensembl_transcript_index_fname)
output_db = Shove(protocol + "://" + output_filename, optimize=False)
transcript_keys = transcript_db.keys()
for i, tx_id in enumerate(transcript_keys):
tx = transcript_db[tx_id]
start = tx.get_start()
end = tx.get_end()
genomic_location_bin = region2bin(start, end)
key = tx.get_contig() + "_" + str(genomic_location_bin)
try:
tmpList = output_db[key]
except KeyError:
output_db[key] = []
tmpList = output_db[key]
tmpList.append(tx)
output_db[key] = tmpList
if (i + 1) % 10000 == 0:
logging.getLogger(
__name__).info("Genomic position index added " + str(i) +
" transcripts so far.")
output_db.close()
transcript_db.close()
def build_ensembl_transcripts_by_gene_index(self, ensembl_transcript_index_fname, output_filename, protocol="file"):
""" Create an index for gene --> transcripts using a transcript index created in build_ensembl_transcript_index
:param ensembl_transcript_index_fname: file/dir location for ensembl transcript db
:return:
"""
#TODO: This may need to be moved to the init of the transcript datasource as that may be faster.
transcript_db = Shove(protocol + "://" + ensembl_transcript_index_fname, "memory://")
output_db = Shove(protocol + "://" + output_filename, "memory://", optimize=False)
transcript_keys = transcript_db.keys()
for i,tx_id in enumerate(transcript_keys):
tx = transcript_db[tx_id]
gene = tx.get_gene()
try:
tmpList = output_db[gene]
except KeyError:
output_db[gene] = []
tmpList = output_db[gene]
tmpList.append(tx)
output_db[gene] = tmpList
if (i+1) % 10000 == 0:
logging.getLogger(__name__).info("Gene index added " + str(i) + " transcripts so far.")
logging.getLogger(__name__).info("Finished gene index with " + str(len(output_db.keys())) + " genes.")
output_db.close()
transcript_db.close()
def build_ensembl_transcripts_by_genomic_location_index(self, ensembl_transcript_index_fname, output_filename, protocol="file"):
"""Create an index for genomic position to transcripts index, using a transcript index created in
build_ensembl_transcript_index
"""
transcript_db = Shove(protocol + "://" + ensembl_transcript_index_fname)
output_db = Shove(protocol + "://" + output_filename, optimize=False)
transcript_keys = transcript_db.keys()
for i,tx_id in enumerate(transcript_keys):
tx = transcript_db[tx_id]
start = tx.get_start()
end = tx.get_end()
genomic_location_bin = region2bin(start, end)
key = tx.get_contig() + "_" + str(genomic_location_bin)
try:
tmpList = output_db[key]
except KeyError:
output_db[key] = []
tmpList = output_db[key]
tmpList.append(tx)
output_db[key] = tmpList
if (i+1) % 10000 == 0:
logging.getLogger(__name__).info("Genomic position index added " + str(i) + " transcripts so far.")
output_db.close()
transcript_db.close()
def parse_with_shove(fname, callableParsingFunction, pickleDir=""):
''' Pickle dir MUST include appended "/" '''
shoveFilename = pickleDir + os.path.basename(fname) + ".shv"
if os.path.exists(shoveFilename):
logging.getLogger(__name__).info("Loading shove structure: " +
str(shoveFilename))
g = Shove("file://" + shoveFilename, "simple://")
else:
logging.getLogger(__name__).info("Parsing...")
tmpStruct = callableParsingFunction(file(fname, 'r'))
logging.getLogger(__name__).info("Writing shove db: " +
str(shoveFilename))
ks = tmpStruct.keys()
g = Shove("file://" + shoveFilename)
for k in ks:
del tmpStruct[
k].references # May be causing an error later down the road.
g[k] = tmpStruct[k]
return g
def test_retrieving_sequence(self):
"""Ensure we can retrieve a sequence from an ensembl transcript given a gene. """
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
base_output_filename = "out/test_retrieving_full_indices_ensembl"
shutil.rmtree(base_output_filename + ".transcript.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gene.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gp_bin.idx", ignore_errors=True)
genome_build_factory = GenomeBuildFactory()
genome_build_factory.construct_ensembl_indices([ensembl_input_gtf], [ensembl_input_fasta], base_output_filename)
seq_index = Shove("file://" + base_output_filename + ".transcript_by_gene.idx", optimize=False)
transcripts = seq_index['SEO1']
transcript = transcripts[0]
for i in xrange(len(transcripts)):
transcript = transcripts[i]
if transcript._transcript_id == "YAL067C":
break
self.assertTrue(transcript.get_seq().startswith('ATGTATTCAATTGTTAAAGAGATTATTGTAGATCCTTACAAAAGACTAAAATGGGGTTTT'))
transcripts = seq_index['PAU8']
transcript = transcripts[0]
for i in xrange(len(transcripts)):
transcript = transcripts[i]
if transcript._transcript_id == "YAL068C":
break
self.assertTrue(transcript.get_strand() == "-")
seq_index_gp = Shove("file://" + base_output_filename + ".transcript_by_gp_bin.idx", "memory://")
transcripts = seq_index_gp["I_585"]
self.assertTrue(len(transcripts) == 5, "There should be 5 transcripts.")
transcript = transcripts[0]
for i in xrange(len(transcripts)):
transcript = transcripts[i]
if transcript._transcript_id == "YAL069W":
break
self.assertTrue(transcript.get_strand() == "+")
def test_build_ensembl_transcripts_by_genomic_location_index(self):
"""Test that we can get an ensembl transcript from a genomic position"""
protocol = "file"
transcript_index_filename = "out/test_ensemble_gtf_for_gp.db"
output_filename = "out/test_ensemble_gtf_for_gp.db.idx"
shutil.rmtree(output_filename, ignore_errors=True)
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], transcript_index_filename, protocol=protocol)
genome_build_factory.build_ensembl_transcripts_by_genomic_location_index(transcript_index_filename, output_filename, protocol=protocol)
# Now load the index and look something up.
gp_index = Shove(protocol + "://" + output_filename)
gt_transcript_id = "YAL067C"
bins = region2bins(1496172, 1496400)
for bin in bins:
key = 'I_' + str(bin)
if key in gp_index.keys():
self.assertTrue(gp_index[key] == gt_transcript_id)
def test_build_ensembl_transcripts_by_genomic_location_index(self):
"""Test that we can get an ensembl transcript from a genomic position"""
protocol = "file"
transcript_index_filename = "out/test_ensemble_gtf_for_gp.db"
output_filename = "out/test_ensemble_gtf_for_gp.db.idx"
shutil.rmtree(output_filename, ignore_errors=True)
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], transcript_index_filename, protocol=protocol)
genome_build_factory.build_ensembl_transcripts_by_genomic_location_index(transcript_index_filename, output_filename, protocol=protocol)
# Now load the index and look something up.
gp_index = Shove(protocol + "://" + output_filename)
gt_transcript_id = "YAL067C"
bins = region2bins(1496172, 1496400)
for bin in bins:
key = 'I_' + str(bin)
if key in gp_index.keys():
self.assertTrue(gp_index[key] == gt_transcript_id)
def build_ensembl_transcripts_by_gene_index(self,
ensembl_transcript_index_fname,
output_filename,
protocol="file"):
""" Create an index for gene --> transcripts using a transcript index created in build_ensembl_transcript_index
:param ensembl_transcript_index_fname: file/dir location for ensembl transcript db
:return:
"""
#TODO: This may need to be moved to the init of the transcript datasource as that may be faster.
transcript_db = Shove(
protocol + "://" + ensembl_transcript_index_fname, "memory://")
output_db = Shove(protocol + "://" + output_filename,
"memory://",
optimize=False)
transcript_keys = transcript_db.keys()
for i, tx_id in enumerate(transcript_keys):
tx = transcript_db[tx_id]
gene = tx.get_gene()
try:
tmpList = output_db[gene]
except KeyError:
output_db[gene] = []
tmpList = output_db[gene]
tmpList.append(tx)
output_db[gene] = tmpList
if (i + 1) % 10000 == 0:
logging.getLogger(__name__).info("Gene index added " + str(i) +
" transcripts so far.")
logging.getLogger(__name__).info("Finished gene index with " +
str(len(output_db.keys())) +
" genes.")
output_db.close()
transcript_db.close()
def test_multiple_gtf_initialization(self):
"""Test that we can create a datasource from multiple gtf & fastas"""
gencode_input_gtfs = ["testdata/gencode/CP.gencode.v19.annotation.gtf", "testdata/gencode/MAPK1.gencode.v19.annotation.gtf"]
gencode_input_fastas = ["testdata/gencode/CP.gencode.v19.pc_transcripts.fa", "testdata/gencode/MAPK1.gencode.v19.pc_transcripts.fa"]
base_output_filename = "out/test_multi_gencode"
shutil.rmtree(base_output_filename + ".transcript.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gene.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gp_bin.idx", ignore_errors=True)
genome_build_factory = GenomeBuildFactory()
genome_build_factory.construct_ensembl_indices(gencode_input_gtfs, gencode_input_fastas, base_output_filename)
seq_index = Shove("file://" + base_output_filename + ".transcript_by_gene.idx", "memory://", optimize=False)
transcripts = seq_index["CP"]
self.assertTrue(len(transcripts) == 15)
transcripts = seq_index["MAPK1"]
self.assertTrue(len(transcripts) == 4)
for tx in transcripts:
self.assertTrue(tx.get_transcript_id() == "ENST00000491588.1" or len(tx.get_seq()) > 100, "No seq data for " + tx.get_transcript_id() )
def test_build_ensembl_transcripts_by_gene_index(self):
"""Test building an index for getting a transcript given a gene."""
protocol = "file"
transcript_index_filename = "out/test_ensembl_gtf_for_gene.db"
output_filename = "out/test_ensembl_gtf_for_gene.db.gene.idx"
shutil.rmtree(output_filename,ignore_errors=True)
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], transcript_index_filename, protocol=protocol)
genome_build_factory.build_ensembl_transcripts_by_gene_index(transcript_index_filename, output_filename)
# Now load the index and look something up.
gene_index = Shove(protocol + "://" + output_filename, optimize=False)
self.assertTrue(len(gene_index['SEO1']) == 1)
tx = gene_index['SEO1'][0]
self.assertTrue(tx.get_transcript_id()=="YAL067C")
def test_gencode_cp(self):
"""Test the indexing of a gene that was causing problems and make sure that it can be indexed."""
gencode_input_gtf = "testdata/gencode/CP.gencode.v19.annotation.gtf"
gencode_input_fasta = "testdata/gencode/CP.gencode.v19.pc_transcripts.fa"
base_output_filename = "out/test_cp_gencode"
shutil.rmtree(base_output_filename + ".transcript.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gene.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gp_bin.idx", ignore_errors=True)
genome_build_factory = GenomeBuildFactory()
genome_build_factory.construct_ensembl_indices([gencode_input_gtf], [gencode_input_fasta], base_output_filename)
seq_index = Shove("file://" + base_output_filename + ".transcript_by_gene.idx", "memory://", optimize=False)
transcripts = seq_index["CP"]
self.assertTrue(len(transcripts) == 15)
troubled_transcript = "ENST00000474204.1"
is_troubled_transcript_seen = False
for tx in transcripts:
if tx.get_transcript_id() == troubled_transcript:
is_troubled_transcript_seen = True
break
self.assertTrue(is_troubled_transcript_seen)
def build_ensembl_transcript_index(self,
ensembl_input_gtfs,
ensembl_input_fastas,
output_filename,
protocol="file",
protein_id_mapping_file=None):
"""Create the transcript index (using shove) for ensembl. Key is transcript ID.
Note: This method will hold the entire transcript index in RAM.
:param ensembl_input_gtfs: (list)
:param ensembl_input_fastas: (list) sequence data for transcripts corresponding to what is in the gtfs
:param output_filename:
:param protocol: shove protocol. Usually "file" or "sqlite"
"""
# Example code taken from http://biopython.org/wiki/GFF_Parsing
shove = Shove(protocol + "://" + output_filename, "memory://")
logging.getLogger(__name__).info("Transcript index being created: " +
protocol + "://" + output_filename)
# Get the transcript ID to protein ID mapping
tx_to_protein_mapping = self._create_tx_id_to_protein_id_mapping(
protein_id_mapping_file)
seq_dict = {}
for in_seq_file in ensembl_input_fastas:
in_seq_handle = open(in_seq_file)
seq_dict.update(self._create_seq_dict(in_seq_handle))
in_seq_handle.close()
logging.getLogger(__name__).info("Parsed fasta file: " +
in_seq_file)
for file_ctr, in_file in enumerate(ensembl_input_gtfs):
in_handle = open(in_file)
seq_dict_keys = seq_dict.keys()
ctr = 0
for rec in GFF.parse_simple(
in_file): #(in_handle, base_dict=seq_dict):
# transcript id seems to always be a list of length 1
if len(rec['quals']['transcript_id']) > 1:
logging.getLogger(__name__).warn(
"ensembl records had more than one transcript id: " +
str(rec['quals']['transcript_id']))
self._convertGFFRecordToTranscript(rec, seq_dict,
seq_dict_keys,
tx_to_protein_mapping)
ctr += 1
if (ctr % 10000) == 0:
logging.getLogger(__name__).info(
"Added " + str(ctr) + " lines of gtf " +
str(file_ctr + 1) + " of " +
str(len(ensembl_input_gtfs)) + " (" + in_file +
") into internal transcript index.")
in_handle.close()
logging.getLogger(__name__).info("Finished " + str(ctr) +
" lines of gtf (" + in_file + ")")
logging.getLogger(__name__).info(
"Populating final db with internal transcript index.")
transcript_index_keys = self._transcript_index.keys()
for i, k in enumerate(transcript_index_keys):
# Populate the protein sequence
protein_sequence = self._determine_protein_seq(
self._transcript_index[k])
self._transcript_index[k].set_protein_seq(protein_sequence)
shove[k] = self._transcript_index[k]
if i % 10000 == 0:
logging.getLogger(__name__).info(
"Saved %0.1f%% of transcript index to disk with protein sequence."
% (float(i * 100) / float(len(transcript_index_keys))))
logging.getLogger(__name__).info("Transcript index created " +
str(len(shove.keys())) +
" transcripts: " + protocol + "://" +
output_filename)
shove.close()