def test_add_rg_to_bam(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_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
lib_name = 'aa'
log_fhand = NamedTemporaryFile()
readgroup = {
'ID': lib_name,
'PL': 'illumina',
'LB': lib_name,
'SM': '{0}_illumina_pe'.format(lib_name),
'PU': '0'
}
bwa = map_with_bwamem(index_fpath,
unpaired_fpath=reads_fpath,
readgroup=readgroup,
log_fpath=log_fhand.name)
map_process_to_bam(bwa, bam_fhand.name)
out = subprocess.check_output(
[get_binary_path('samtools'), 'view', '-h', bam_fhand.name],
stderr=log_fhand)
assert '@RG\tID:aa' in out
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
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_rev_compl_fragmented_reads(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
# 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()
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath,
extra_params=['-a', '-f'],
unpaired_fpath=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)
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_map_with_bwa(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_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bwa = map_with_bwamem(index_fpath, unpaired_fpath=reads_fpath)
map_process_to_bam(bwa, bam_fhand.name)
out = subprocess.check_output([get_binary_path('samtools'), 'view',
bam_fhand.name])
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
directory.close()
def test_map_with_bwa(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_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bwa = map_with_bwamem(index_fpath, unpaired_fpath=reads_fpath)
map_process_to_bam(bwa, bam_fhand.name)
out = subprocess.check_output(
[get_binary_path('samtools'), 'view', bam_fhand.name])
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
directory.close()
def test_add_rg_to_bam(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_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
lib_name = 'aa'
log_fhand = NamedTemporaryFile()
readgroup = {'ID': lib_name, 'PL': 'illumina', 'LB': lib_name,
'SM': '{0}_illumina_pe'.format(lib_name), 'PU': '0'}
bwa = map_with_bwamem(index_fpath, unpaired_fpath=reads_fpath,
readgroup=readgroup, log_fpath=log_fhand.name)
map_process_to_bam(bwa, bam_fhand.name)
out = subprocess.check_output([get_binary_path('samtools'), 'view',
'-h', bam_fhand.name], stderr=log_fhand)
assert '@RG\tID:aa' in out
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
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 test_rev_compl_fragmented_reads(self):
reference_seq = GENOME
#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'
#f is fragmented in two reference sequences. r mapps completely
query7 = '>seq4 f\nCAAATCATCACCAGACCATGTCCGATCCCGGGAGTCTTTTCCAAGGTGTGC'
query7 += 'TCTTTATCCGGCCCTTGCTCAAGGGTATGTTAAAACGGCAAGAGCTGCCTGAGCGCG\n'
query8 = '>seq4 r\nTGTTCTGCAATCGATACAACGATCGAATTTAATCTGAGTAACTGCCAATTC'
query8 += 'TGAGTAATATTATAGAAAGT\n'
query_f = query1 + query3 + query7
query_r = query2 + query4 + query8
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_bwa_index(ref_fhand.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bwa = map_with_bwamem(index_fpath, paired_fpaths=paired_fpaths)
map_process_to_bam(bwa, bam_fhand.name)
samfile = pysam.Samfile(bam_fhand.name)
def _setup_checks(self, filterpacket):
index_fpath = self._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_fpath=reads_fhand.name,
extra_params=extra_params,
threads=self.threads)
map_process_to_bam(map_process, bam_fhand.name)
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_rev_compl_fragmented_reads(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
# 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'
# f is fragmented in two reference sequences. r mapps completely
query7 = '>seq4 f\nCAAATCATCACCAGACCATGTCCGATCCCGGGAGTCTTTTCCAAGGTGTGC'
query7 += 'TCTTTATCCGGCCCTTGCTCAAGGGTATGTTAAAACGGCAAGAGCTGCCTGAGCGCG\n'
query8 = '>seq4 r\nTGTTCTGCAATCGATACAACGATCGAATTTAATCTGAGTAACTGCCAATTC'
query8 += 'TGAGTAATATTATAGAAAGT\n'
query_f = query1 + query3 + query7
query_r = query2 + query4 + query8
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)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bwa = map_with_bwamem(index_fpath, paired_fpaths=paired_fpaths)
map_process_to_bam(bwa, bam_fhand.name)
samfile = pysam.Samfile(bam_fhand.name)
