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_get_or_create_index(self):
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
assert not _bwa_index_exists(seq_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bwa_index(seq_fpath, directory.name)
expected_index = os.path.join(directory.name,
os.path.basename(db_name))
assert index_fpath == expected_index
assert _bwa_index_exists(index_fpath)
# already exists
index_fpath = get_or_create_bwa_index(seq_fpath, directory.name)
assert index_fpath == expected_index
assert _bwa_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 _bwa_index_exists(seq_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bwa_index(seq_fpath, directory.name)
expected_index = os.path.join(directory.name,
os.path.basename(db_name))
assert index_fpath == expected_index
assert _bwa_index_exists(index_fpath)
# already exists
index_fpath = get_or_create_bwa_index(seq_fpath, directory.name)
assert index_fpath == expected_index
assert _bwa_index_exists(index_fpath)
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')
map_with_bwasw(index_fpath, bam_fhand.name, unpaired_fpath=reads_fpath)
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')
map_with_bwasw(index_fpath, bam_fhand.name, unpaired_fpath=reads_fpath)
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 _sorted_mapped_reads(ref_fpath, paired_fpaths=None,
unpaired_fpaths=None, directory=None,
file_format=None, min_seed_len=None):
fhand = open(paired_fpaths[0]) if paired_fpaths else open(unpaired_fpaths[0])
if file_format is not None:
set_format(fhand, file_format)
else:
file_format = get_format(fhand)
index_fpath = get_or_create_bwa_index(ref_fpath, directory)
extra_params = ['-a', '-M']
if min_seed_len is not None:
extra_params.extend(['-k', min_seed_len])
bwa = map_with_bwamem(index_fpath, paired_fpaths=paired_fpaths,
unpaired_fpath=unpaired_fpaths,
extra_params=extra_params)
bam_fhand = NamedTemporaryFile(dir='/home/carlos/tmp')
sort_mapped_reads(bwa, bam_fhand.name, key='queryname')
bamfile = pysam.Samfile(bam_fhand.name)
return bamfile
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)
