def test_tophat_paired(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_1_fpath = os.path.join(TEST_DATA_DIR, 'reads_1.fastq')
reads_2_fpath = os.path.join(TEST_DATA_DIR, 'reads_2.fastq')
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath,
directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath])
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
self.fail('runtimeError expected')
except RuntimeError:
pass
finally:
directory.close()
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath,
directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath],
mate_inner_dist=350,
mate_std_dev=50)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
finally:
directory.close()
def test_tophat_paired(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_1_fpath = os.path.join(TEST_DATA_DIR, 'reads_1.fastq')
reads_2_fpath = os.path.join(TEST_DATA_DIR, 'reads_2.fastq')
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath, directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath])
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
self.fail('runtimeError expected')
except RuntimeError:
pass
finally:
directory.close()
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath, directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath],
mate_inner_dist=350, mate_std_dev=50)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
finally:
directory.close()
def test_rev_compl_fragmented_reads(self):
reference_seq = GENOME
#with unpaired_reads
query_f = '>seq1\nAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCCTG'
query_f += 'AGGACACCCAGTCTCCCGGGAGTCTTTTCCAAGGTGTGCTCCTGATCGCCGTGTTA\n'
query_r = '>seq2\nTAACACGGCGATCAGGAGCACACCTTGGAAAAGACTCCCGGGAGACTGGGTG'
query_r += 'TCCTCAGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT\n'
query = query_f + query_r
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
ref_fhand = NamedTemporaryFile()
ref_fhand.write(reference_seq)
ref_fhand.flush()
index_fpath = get_or_create_bowtie2_index(ref_fhand.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, extra_params=['-a', '-f'],
unpaired_fpaths=[in_fhand.name])
map_process_to_bam(bowtie2, bam_fhand.name)
samfile = pysam.Samfile(bam_fhand.name)
#for aligned_read in samfile:
# print aligned_read
#with paired_reads.
#f is reversed r is direct
query1 = '>seq10 f\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT'
query1 += '\n'
query2 = '>seq10 r\nATGTAATACGGGCTAGCCGGGGATGCCGACGATTAAACACGCTGTCATA'
query2 += 'GTAGCGTCTTCCTAGGGTTTTCCCCATGGAATCGGTTATCGTGATACGTTAAATTT\n'
#f is direct, r is reversed
query3 = '>seq11 f\nAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCC'
query3 += '\n'
query4 = '>seq11 r\nAAATTTAACGTATCACGATAACCGATTCCATGGGGAAAACCCTAGGAAG'
query4 += 'ACGCTACTATGACAGCGTGTTTAATCGTCGGCATCCCCGGCTAGCCCGTATTACAT\n'
query_f = query1 + query3
query_r = query2 + query4
f_fhand = NamedTemporaryFile()
f_fhand.write(query_f)
f_fhand.flush()
r_fhand = NamedTemporaryFile()
r_fhand.write(query_r)
r_fhand.flush()
paired_fpaths = [[f_fhand.name], [r_fhand.name]]
ref_fhand = NamedTemporaryFile()
ref_fhand.write(reference_seq)
ref_fhand.flush()
index_fpath = get_or_create_bowtie2_index(ref_fhand.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, extra_params=['-a', '-f'],
paired_fpaths=paired_fpaths)
map_process_to_bam(bowtie2, bam_fhand.name)
samfile = pysam.Samfile(bam_fhand.name)
def test_get_or_create_index(self):
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
assert _bowtie2_index_exists(seq_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(seq_fpath, directory.name)
expected_index = os.path.join(directory.name,
os.path.basename(db_name))
assert index_fpath == expected_index
assert _bowtie2_index_exists(index_fpath)
# already exists
index_fpath = get_or_create_bowtie2_index(seq_fpath, directory.name)
assert index_fpath == expected_index
assert _bowtie2_index_exists(index_fpath)
directory.close()
def test_get_or_create_index(self):
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
assert not _bowtie2_index_exists(seq_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(seq_fpath, directory.name)
expected_index = os.path.join(directory.name,
os.path.basename(db_name))
assert index_fpath == expected_index
assert _bowtie2_index_exists(index_fpath)
# already exists
index_fpath = get_or_create_bowtie2_index(seq_fpath, directory.name)
assert index_fpath == expected_index
assert _bowtie2_index_exists(index_fpath)
directory.close()
def test_tophat(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath, directory.name,
unpaired_fpath=reads_fpath)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
directory.close()
def test_tophat(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath,
directory.name,
unpaired_fpath=reads_fpath)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
directory.close()
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_with_bowtie2(index_fpath, bam_fhand.name,
unpaired_fpaths=[reads_fpath])
directory.close()
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_with_bowtie2(index_fpath,
bam_fhand.name,
unpaired_fpaths=[reads_fpath])
directory.close()
def _setup_checks(self, filterpacket):
index_fpath = self._index_fpath
get_or_create_bowtie2_index(index_fpath)
seqs = [s for seqs in filterpacket[SEQS_PASSED]for s in seqs]
seq_class = seqs[0].kind
extra_params = []
# Which format do we need for the bowtie2 input read file fasta or
# fastq?
if seq_class == SEQRECORD:
if 'phred_quality' in seqs[0].object.letter_annotations.viewkeys():
file_format = 'fastq'
else:
extra_params.append('-f')
file_format = 'fasta'
elif seq_class == SEQITEM:
file_format = get_file_format(seqs[0])
if 'illumina' in file_format:
extra_params.append('--phred64')
elif 'fasta' in file_format:
extra_params.append('-f')
elif 'fastq' in file_format:
pass
else:
msg = 'For FilterBowtie2Match and SeqItems fastq or fasta '
msg += 'files are required'
raise RuntimeError(msg)
else:
raise NotImplementedError()
reads_fhand = NamedTemporaryFile(suffix=file_format)
write_seqs(seqs, reads_fhand, file_format=file_format)
reads_fhand.flush()
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_process = map_with_bowtie2(index_fpath,
unpaired_fpaths=[reads_fhand.name],
extra_params=extra_params)
map_process_to_bam(map_process, bam_fhand.name)
self.mapped_reads = _get_mapped_reads(bam_fhand.name, self.min_mapq)
def _setup_checks(self, filterpacket):
index_fpath = self._index_fpath
get_or_create_bowtie2_index(index_fpath)
seqs = [s for seqs in filterpacket[SEQS_PASSED] for s in seqs]
seq_class = seqs[0].kind
extra_params = []
# Which format do we need for the bowtie2 input read file fasta or
# fastq?
if seq_class == SEQRECORD:
if 'phred_quality' in seqs[0].object.letter_annotations.viewkeys():
file_format = 'fastq'
else:
extra_params.append('-f')
file_format = 'fasta'
elif seq_class == SEQITEM:
file_format = get_file_format(seqs[0])
if 'illumina' in file_format:
extra_params.append('--phred64')
elif 'fasta' in file_format:
extra_params.append('-f')
elif 'fastq' in file_format:
pass
else:
msg = 'For FilterBowtie2Match and SeqItems fastq or fasta '
msg += 'files are required'
raise RuntimeError(msg)
else:
raise NotImplementedError()
reads_fhand = NamedTemporaryFile(suffix=file_format)
write_seqs(seqs, reads_fhand, file_format=file_format)
reads_fhand.flush()
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_with_bowtie2(index_fpath,
bam_fhand.name,
unpaired_fpaths=[reads_fhand.name],
extra_params=extra_params)
self.mapped_reads = _get_mapped_reads(bam_fhand.name, self.min_mapq)
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, unpaired_fpath=reads_fpath)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
#With paired_fpahts option
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
forward_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
reverse_fpath = NamedTemporaryFile().name
paired_fpaths = (forward_fpath, reverse_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, paired_fpaths=paired_fpaths)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, unpaired_fpath=reads_fpath)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
# With paired_fpahts option
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
forward_fpath = os.path.join(TEST_DATA_DIR, 'arabreads_1.fastq')
reverse_fpath = os.path.join(TEST_DATA_DIR, 'arabreads_2.fastq')
paired_fpaths = (forward_fpath, reverse_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, paired_fpaths=paired_fpaths)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
def test_filter_by_bowtie2_bin():
filter_bin = os.path.join(BIN_DIR, 'filter_by_bowtie2')
assert 'usage' in check_output([filter_bin, '-h'])
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(TEST_DATA_DIR,
'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
for reads_fpath in [fastq_fpath, fasta_fpath]:
out_fhand = NamedTemporaryFile(suffix='.seqs')
filtered_fhand = NamedTemporaryFile(suffix='.seqs')
cmd = [filter_bin, '-i', index_fpath, '-o', out_fhand.name,
'-e', filtered_fhand.name, reads_fpath]
check_output(cmd)
assert 'no_arabi' in open(out_fhand.name).read()
assert 'read1' in open(filtered_fhand.name).read()
directory.close()
def test_filter_by_bowtie2_bin():
filter_bin = os.path.join(BIN_DIR, 'filter_by_bowtie2')
assert 'usage' in check_output([filter_bin, '-h'])
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(
TEST_DATA_DIR, 'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
for reads_fpath in [fastq_fpath, fasta_fpath]:
out_fhand = NamedTemporaryFile(suffix='.seqs')
filtered_fhand = NamedTemporaryFile(suffix='.seqs')
cmd = [
filter_bin, '-i', index_fpath, '-o', out_fhand.name, '-e',
filtered_fhand.name, reads_fpath
]
check_output(cmd)
assert 'no_arabi' in open(out_fhand.name).read()
assert 'read1' in open(filtered_fhand.name).read()
directory.close()
def test_filter_by_bowtie2():
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(TEST_DATA_DIR,
'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
passed = ['no_arabi']
for preffered_classes in [[SEQITEM], [SEQRECORD]]:
for reads_fpath in [fastq_fpath, fasta_fpath]:
seq_packets = read_seq_packets([open(reads_fpath)],
prefered_seq_classes=preffered_classes)
filter_packets = seq_to_filterpackets(seq_packets)
filter_ = FilterBowtie2Match(index_fpath)
filter_packet = list(filter_packets)[0]
filter_packets = filter_(filter_packet)
assert _seqs_to_names(filter_packets[SEQS_PASSED]) == passed
assert _seqs_to_names(filter_packets[SEQS_FILTERED_OUT]) == [
'read1', 'read2', 'read3']
directory.close()
def test_filter_by_bowtie2():
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(
TEST_DATA_DIR, 'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
passed = ['no_arabi']
for preffered_classes in [[SEQITEM], [SEQRECORD]]:
for reads_fpath in [fastq_fpath, fasta_fpath]:
seq_packets = read_seq_packets(
[open(reads_fpath)],
prefered_seq_classes=preffered_classes)
filter_packets = seq_to_filterpackets(seq_packets)
filter_ = FilterBowtie2Match(index_fpath)
filter_packet = list(filter_packets)[0]
filter_packets = filter_(filter_packet)
assert _seqs_to_names(filter_packets[SEQS_PASSED]) == passed
assert _seqs_to_names(filter_packets[SEQS_FILTERED_OUT]) == [
'read1', 'read2', 'read3'
]
directory.close()
