def main():
'The script itself'
#set parameters
work_dir, output, reference = set_parameters()
# make a working tempfir
temp_dir = NamedTemporaryDir()
# add readgroup tag to each alignment in bam
add_header_and_tags_bams(work_dir, temp_dir.name)
# Prepare files to merge
sams = get_opened_sams_from_dir(temp_dir.name)
temp_sam = NamedTemporaryFile()
# merge all the sam in one
merge_sam(sams, temp_sam, reference)
# Convert sam into a bam,(Temporary)
temp_bam = NamedTemporaryFile(suffix='.bam')
sam2bam(temp_sam.name, temp_bam.name)
# finally we need to order the bam
sort_bam_sam(temp_bam.name, output)
# and make and index of the bam
call(['samtools', 'index', output], raise_on_error=True)
temp_dir.close()
def test_blast_seq_against_bad_db(self):
'We can blast a seq file against a database'
test_dir = NamedTemporaryDir()
project_name = 'backbone'
create_project(directory=test_dir.name,
name=project_name)
project_dir = join(test_dir.name, project_name)
#some query fasta file
query = '>seq1\nGATCGGCCTTCTTGCGCATCTCACGCGCTCCTGCGGCGGCCTGTAGGGCAGGCT'
query += 'CATACCCCTGCCGAACCGCTTTTGTCA|n'
query_fhand = NamedTemporaryFile(mode='w')
query_fhand.write(query)
query_fhand.flush()
#the blast db
blast_db_fname = 'uni'
blast_db = join(TEST_DATA_DIR, 'blast', blast_db_fname)
blast_program = 'blastn'
try:
backbone_blast_runner(query_fpath=query_fhand.name,
project_dir=project_dir,
blast_program=blast_program,
blast_db=blast_db)
self.fail('RuntimeError expected')
except RuntimeError:
pass
test_dir.close()
def test_blast_seq_against_db():
'We can blast a seq file against a database'
test_dir = NamedTemporaryDir()
project_name = 'backbone'
create_project(directory=test_dir.name,
name=project_name)
project_dir = join(test_dir.name, project_name)
#some query fasta file
query = '>seq1\nGATCGGCCTTCTTGCGCATCTCACGCGCTCCTGCGGCGGCCTGTAGGGCAGGCT'
query += 'CATACCCCTGCCGAACCGCTTTTGTCA|n'
query_fhand = NamedTemporaryFile(mode='w')
query_fhand.write(query)
query_fhand.flush()
#the blast db
blast_db_fname = 'univec+'
blast_db = join(TEST_DATA_DIR, 'blast', blast_db_fname)
blast_program = 'blastn'
backbone_blast_runner(query_fpath=query_fhand.name,
project_dir=project_dir,
blast_program=blast_program,
blast_db=blast_db)
#is the blast ok?
blast_fpath = join(project_dir,
BACKBONE_DIRECTORIES['blast_dir'],
_get_basename(query_fhand.name),
blast_db_fname,
'%s.%s.xml' % (BACKBONE_BASENAMES['blast_basename'],
blast_program))
assert '<Hit_def>vec1</Hit_def>' in open(blast_fpath).read()
test_dir.close()
def test_orf_annotation_analysis():
"We can annotate orfs"
test_dir = NamedTemporaryDir()
project_name = "backbone"
matrix = os.path.join(TEST_DATA_DIR, "At.smat")
config = {
"Annotation": {"orf_annotation": {"estscan_matrix": matrix}},
"General_settings": {"threads": THREADS},
}
settings_path = create_project(directory=test_dir.name, name=project_name, configuration=config)
project_dir = join(test_dir.name, project_name)
seq = "CTACTTACTAGCTTTAGTAAATCCTTCTAACCCTCGGTAAAAAAAAAAAAGAGGCATCAAATG"
seq += "GCTTCATCCATTCTCTCATCCGCCGNTGTGGCCTTTGNCAACAGGGCTTCCCCTGCTCAAGCT"
seq += "AGCATGGGGGCACCATTCACTGGCCTAAAATCCGCCGCTGCTTTCCCNGTNACTCGCANGACC"
seq += "AACGACATCACCACTTTGGTTAGCAATGGGGGAAGAGTTCAGGGCNTGAAGGTGTGCCCACCA"
seq += "CTTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCTGATATGAGTAACGAGCAATTGGGA"
seq += "AAGGAAGTTGACTACCTTCTCAGGAAGGGATGGATTCCCTGCATTGAATTCGACATTCACAGT"
seq += "GGATTCGTTTACCGTGAGACCCACAGGTCACCAGGATACTTCGATGGACGCTACTGGACCATG"
seq += "TGGAAGCTGCCCATGTTTGGCTGCACCGAT"
annot_input_dir = join(project_dir, "annotations", "input")
os.makedirs(annot_input_dir)
# create some seqs to annotate
fasta = ">seq\n%s\n" % seq
fhand = open(os.path.join(annot_input_dir, "seqs.fasta"), "w")
fhand.write(fasta)
fhand.close()
do_analysis(project_settings=settings_path, kind="annotate_orfs", silent=True)
repr_fpath = join(project_dir, BACKBONE_DIRECTORIES["annotation_dbs"], "seqs.0.pickle")
result = open(repr_fpath).read()
assert "orf" in result
do_analysis(project_settings=settings_path, kind="write_annotations", silent=True)
seq_fpath = join(project_dir, "annotations", "features", "seqs.orf_seq.fasta")
pep_fpath = join(project_dir, "annotations", "features", "seqs.orf_pep.fasta")
assert "ATCCGCCGNTGTGGCCTTTGNCAACAGGGCTTCCCCT" in open(seq_fpath).read()
assert "QASMGAPFTGLKSAAAFPVTRXTNDITTLVSNG" in open(pep_fpath).read()
do_analysis(project_settings=settings_path, kind="annotation_stats", silent=True)
stats_fpath = join(project_dir, "annotations", "features", "stats", "seqs.txt")
result = open(stats_fpath).read()
expected = """Sequences with ORF: 1
Number of ORFs: 1"""
assert expected in result
test_dir.close()
def test_simple_named_temporary_dir():
'It test temporay named dir'
temp_dir = NamedTemporaryDir()
dir_name = temp_dir.name
assert os.path.exists(dir_name) == True
temp_dir.close()
assert os.path.exists(dir_name) == False
temp_dir = NamedTemporaryDir()
dir_name = temp_dir.name
fhand = open(os.path.join(dir_name, 'peio'), 'w')
assert os.path.exists(fhand.name) == True
assert os.path.exists(dir_name) == True
del(temp_dir)
assert os.path.exists(dir_name) == False
def test_create_project():
'We can create a project'
test_dir = NamedTemporaryDir()
settings_path = create_project(directory=test_dir.name,
name='backbone')
assert settings_path == join(test_dir.name,
'backbone', BACKBONE_DIRECTORIES['config_file'])
settings = create_configuration(settings_path)
assert settings['General_settings']['project_name'] == 'backbone'
project_path = join(test_dir.name, 'backbone')
assert settings['General_settings']['project_path'] == project_path
assert settings['Cleaning']['strip_n_percent'] == 2.0
content = open(settings_path).read()
assert 'strip_n_percent' in content
test_dir.close()
def test_microsatellite_annoation_analysis():
"We can annotate introns"
test_dir = NamedTemporaryDir()
project_name = "backbone"
settings_path = create_project(
directory=test_dir.name, name=project_name, configuration={"General_settings": {"threads": THREADS}}
)
project_dir = join(test_dir.name, project_name)
seq = "GAAAAGATGTGATTGGTGAAATAAGTTTGCCTCAATTCTCTTGTGCCGAAGTTCCAAAGAAGC"
seq += "AGTTGGTGAATGAGCAGCCAGTACCCGAAAAATCGAGCAAAGATTTTGTGATGTATGTTGGAG"
seq += "GTCTAGCATGGGGGATGGACTGGTGTCCCCAAGCTCATGAAAATAGGGATGCTCCTATGAAAA"
seq += "GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA"
seq += "GTGAGTTTGTCGCAATTGCTCCTCATCCTCCTGATTCATCATATCACAAGACTGATGCCTCAC"
seq += "TTACAGGCAGAGGTGTAATTCAGATATGGTGCCTGCCAGATCTCATTCAAAAAGATATAATTG"
seq += "TGAAAGAAGATTATTTTGCTCAGGTTAACAAAAAACCGTATAGAAATTTGACAAGAAGTGAAG"
seq += "CAGGTACGGGAGAAGTATCTGGACCTCAAAAACCAAGAGGAAGACCAAAAAAGAACCCTGGTA"
seq += "AAGCAGTCCAGGCAAAAGCATCTAGACCACAAAATCCAAGAGGAAGACCGAGAAAGAAGCCTG"
seq += "TTACTGAATCTTTAGGTGATAGAGATAGTGAAGACCACAGTTTACAACCTCTTGCTATAGAGT"
seq += "GGTCGCTGCAATCAACAGAACTTTCTGTAGATTTGTCTTGTGGAAATATGAATAAAGCCCAAG"
seq += "TAGATATTGCGCTGAGTCAAGAAAGATGTATTAATGCGGCAT"
annot_input_dir = join(project_dir, "annotations", "input")
os.makedirs(annot_input_dir)
# create some seqs to annotate
fasta = ">seq\n%s\n" % seq
fhand = open(os.path.join(annot_input_dir, "seqs.fasta"), "w")
fhand.write(fasta)
fhand.close()
do_analysis(project_settings=settings_path, kind="annotate_microsatellites", silent=True)
pickle_fpath = join(project_dir, BACKBONE_DIRECTORIES["annotation_dbs"], "seqs.0.pickle")
result = open(pickle_fpath).read()
assert "microsatellite" in result
do_analysis(project_settings=settings_path, kind="write_annotations", silent=True)
ssr_fpath = join(project_dir, "annotations", "features", "seqs.ssr")
assert os.path.exists(ssr_fpath)
assert "Seqname" in open(ssr_fpath).read()
do_analysis(project_settings=settings_path, kind="annotation_stats", silent=True)
stats_fpath = join(project_dir, "annotations", "features", "stats", "seqs.txt")
result = open(stats_fpath).read()
expected = "Sequences with microsatellites: 1"
assert expected in result
test_dir.close()
def test_basic_functionality(self):
'VersionedPath basic functionality'
tempdir = NamedTemporaryDir()
tempdir_name = tempdir.name
fnames = ['hola.txt', 'hola.0.txt', 'hola.1.txt',
'adios.txt', 'adios.1.txt',
'foo.txt']
[open(os.path.join(tempdir.name, fname), 'w') for fname in fnames]
path_str = os.path.join(tempdir.name, 'hola.txt')
path = VersionedPath(path_str)
assert str(path) == path_str
path_str_0 = os.path.join(tempdir.name, 'hola.0.txt')
path = VersionedPath(path_str_0)
assert str(path) == path_str
assert path.basename == 'hola'
assert path.directory == tempdir.name
assert path.extension == 'txt'
assert path.last_version == VersionedPath(os.path.join(tempdir_name,
'hola.1.txt'))
assert path.next_version == VersionedPath(os.path.join(tempdir_name,
'hola.2.txt'))
fpaths = [os.path.join(tempdir_name, fname) for fname in ('hola.1.txt',
'adios.1.txt',
'foo.txt')]
expected_paths = set(fpaths)
versioned_paths = set(path.list_fpaths_versioned())
assert versioned_paths == expected_paths
path = VersionedPath(tempdir_name)
versioned_paths = set(path.list_fpaths_versioned())
assert versioned_paths == expected_paths
tempdir.close()
#in an empty dir
path = VersionedPath('hola.txt')
assert path.last_version.endswith('hola.txt')
assert path.next_version.endswith('hola.0.txt')
path = VersionedPath('pl_illumina.sm_rp_75_59_uc82.sfastq')
assert path.last_version.endswith('pl_illumina.sm_rp_75_59_uc82.sfastq')
def b2gpipe_runner(blast, annot_fpath, b2gpipe_bin, prop_fpath, dat_fpath=None, java_conf=None):
"It runs b2gpipe"
tempdir = NamedTemporaryDir()
out_basename = os.path.join(tempdir.name, "out")
cmd = java_cmd(java_conf)
cmd.extend(["-jar", b2gpipe_bin, "-in", blast.name, "-out", out_basename, "-a", "-prop", prop_fpath])
if dat_fpath:
cmd.append("-d")
logger = logging.getLogger("franklin")
logger.info("Running blast2go: %s" % " ".join(cmd))
call(cmd, raise_on_error=True, add_ext_dir=False)
shutil.move(out_basename + ".annot", annot_fpath)
if dat_fpath:
shutil.move(out_basename + ".dat", dat_fpath)
tempdir.close()
def test_cdna_intron_annoation_analysis():
"We can annotate introns"
test_dir = NamedTemporaryDir()
project_name = "backbone"
blast_db_path = os.path.join(TEST_DATA_DIR, "blast")
genomic_db = os.path.join(blast_db_path, "tomato_genome2+")
config = {
"Annotation": {"Cdna_intron_annotation": {"genomic_db": genomic_db, "genomic_seq_file": genomic_db}},
"General_settings": {"threads": THREADS},
}
settings_path = create_project(directory=test_dir.name, name=project_name, configuration=config)
project_dir = join(test_dir.name, project_name)
seq = "GAAAAGATGTGATTGGTGAAATAAGTTTGCCTCAATTCTCTTGTGCCGAAGTTCCAAAGAAGC"
seq += "AGTTGGTGAATGAGCAGCCAGTACCCGAAAAATCGAGCAAAGATTTTGTGATGTATGTTGGAG"
seq += "GTCTAGCATGGGGGATGGACTGGTGTCCCCAAGCTCATGAAAATAGGGATGCTCCTATGAAAA"
seq += "GTGAGTTTGTCGCAATTGCTCCTCATCCTCCTGATTCATCATATCACAAGACTGATGCCTCAC"
seq += "TTACAGGCAGAGGTGTAATTCAGATATGGTGCCTGCCAGATCTCATTCAAAAAGATATAATTG"
seq += "TGAAAGAAGATTATTTTGCTCAGGTTAACAAAAAACCGTATAGAAATTTGACAAGAAGTGAAG"
seq += "CAGGTACGGGAGAAGTATCTGGACCTCAAAAACCAAGAGGAAGACCAAAAAAGAACCCTGGTA"
seq += "AAGCAGTCCAGGCAAAAGCATCTAGACCACAAAATCCAAGAGGAAGACCGAGAAAGAAGCCTG"
seq += "TTACTGAATCTTTAGGTGATAGAGATAGTGAAGACCACAGTTTACAACCTCTTGCTATAGAGT"
seq += "GGTCGCTGCAATCAACAGAACTTTCTGTAGATTTGTCTTGTGGAAATATGAATAAAGCCCAAG"
seq += "TAGATATTGCGCTGAGTCAAGAAAGATGTATTAATGCGGCAT"
annot_input_dir = join(project_dir, "annotations", "input")
os.makedirs(annot_input_dir)
# create some seqs to annotate
fasta = ">seq\n%s\n" % seq
fhand = open(os.path.join(annot_input_dir, "seqs.fasta"), "w")
fhand.write(fasta)
fhand.close()
do_analysis(project_settings=settings_path, kind="annotate_introns", silent=True)
pickle_fpath = join(project_dir, BACKBONE_DIRECTORIES["annotation_dbs"], "seqs.0.pickle")
assert "intron" in open(pickle_fpath).read()
do_analysis(project_settings=settings_path, kind="annotation_stats", silent=True)
stats_fpath = join(project_dir, "annotations", "features", "stats", "seqs.txt")
result = open(stats_fpath).read()
expected = """Sequences with intron: 1
Number of introns: 3"""
assert expected in result
test_dir.close()
def test_description_annotation_analysis():
"We can annotate with description"
test_dir = NamedTemporaryDir()
project_name = "backbone"
arab_blastdb = join(TEST_DATA_DIR, "blast", "arabidopsis_genes+")
config = {
"blast": {"arabidopsis": {"path": arab_blastdb, "species": "arabidopsis"}},
"Annotation": {"description_annotation": {"description_databases": ["arabidopsis"]}},
"General_settings": {"threads": THREADS},
}
settings_path = create_project(directory=test_dir.name, name=project_name, configuration=config)
project_dir = join(test_dir.name, project_name)
# some melon file to annotate
input_dir = join(project_dir, BACKBONE_DIRECTORIES["annotation_input"])
os.makedirs(input_dir)
seq_ = "AGGTGTCACCGTTCACGAGGGCGACTGGGACTCCCACGGGGCCATCAAGTCCTGGAACTACA"
seq_ += "CATGCGGTCCTCTATCTCATTCTCTATTTGTATGAATATGTGTTTATTACTAGCTAGGGTTT"
seq_ += "CTATTAATGAAAGGTTCATGTAAATATATGAAGATGGGAAGCAAGAGGTGTTCAAGGAGAAG"
seq_ += "AGGGAGTTAGACGACCAGAAGAT"
seq1 = SeqWithQuality(Seq(seq_), id="CUTC021854")
seq2 = SeqWithQuality(Seq("Atagtagcatcagatgagcatcgacttctagctagctagct"), id="CUTC021853")
write_seqs_in_file([seq1, seq2], open(join(input_dir, "melon.st_nucl.pl_454.fasta"), "a"))
do_analysis(project_settings=settings_path, kind="annotate_descriptions", silent=True)
repr_fpath = join(project_dir, BACKBONE_DIRECTORIES["annotation_dbs"], "melon.st_nucl.pl_454.0.pickle")
result = open(repr_fpath).read()
# print result
assert "yet another one" in result
do_analysis(project_settings=settings_path, kind="annotation_stats", silent=True)
stats_fpath = join(project_dir, "annotations", "features", "stats", "melon.st_nucl.pl_454.txt")
result = open(stats_fpath).read()
expected = """Annotation statistics
---------------------
Number of sequences: 2
Sequences with description: 1"""
assert expected in result
test_dir.close()
def b2gpipe_runner(blast, annot_fpath, b2gpipe_bin, prop_fpath, dat_fpath=None,
java_conf=None, ):
'It runs b2gpipe'
tempdir = NamedTemporaryDir()
out_basename = os.path.join(tempdir.name, 'out')
cmd = java_cmd(java_conf)
cmd.extend(['-jar', b2gpipe_bin, '-in', blast.name, '-out', out_basename,
'-a', '-prop', prop_fpath])
if dat_fpath:
cmd.append('-d')
logger = logging.getLogger('franklin')
logger.info('Running blast2go: %s' % ' '.join(cmd))
call(cmd, raise_on_error=True, add_ext_dir=False)
shutil.move(out_basename + '.annot', annot_fpath)
if dat_fpath:
shutil.move(out_basename + '.dat', dat_fpath)
tempdir.close()
def test_gmap_mapper():
'It test the gmap mapper'
mappers_dir = join(TEST_DATA_DIR, 'mappers')
gmap_dir = join(TEST_DATA_DIR, 'mappers', 'gmap')
work_dir = NamedTemporaryDir()
temp_genome = join(work_dir.name, 'genome.fa')
os.symlink(join(mappers_dir, 'genome.fa'), temp_genome)
reads_fpath = join(gmap_dir, 'lb_lib1.pl_sanger.sm_sam1.fa')
out_bam_fhand = NamedTemporaryFile(suffix='.bam')
parameters = {'threads':None, 'kmer':13}
map_reads_with_gmap(temp_genome, reads_fpath, out_bam_fhand.name,
parameters)
sam_fhand = NamedTemporaryFile(suffix='.sam')
bam2sam(out_bam_fhand.name, sam_fhand.name, header=True)
result = open(sam_fhand.name).read()
assert exists(out_bam_fhand.name)
assert '36M2I204M' in result
assert 'SN:SL2.30ch00' in result
assert 'seq9_rev_MOD' in result
work_dir.close()
out_bam_fhand.close()
sam_fhand.close()
work_dir = NamedTemporaryDir()
temp_genome = join(work_dir.name, 'genome.fa')
os.symlink(join(mappers_dir, 'genome.fa'), temp_genome)
reads_fpath = join(gmap_dir, 'lb_lib1.pl_sanger.sm_sam1.sfastq')
out_bam_fhand = NamedTemporaryFile(suffix='.bam')
unmapped_fhand = StringIO.StringIO()
parameters = {'threads':None, 'kmer':13,
'unmapped_fhand':unmapped_fhand}
map_reads_with_gmap(temp_genome, reads_fpath, out_bam_fhand.name,
parameters)
sam_fhand = NamedTemporaryFile(suffix='.sam')
bam2sam(out_bam_fhand.name, sam_fhand.name, header=True)
result = open(sam_fhand.name).read()
assert exists(out_bam_fhand.name)
assert '36M2I204M' in result
assert 'SN:SL2.30ch00' in result
assert 'seq9_rev_MOD' in result
assert '?????????????????' in result
work_dir.close()
out_bam_fhand.close()
sam_fhand.close()
def test_cleaning_analysis():
'We can clean the reads'
test_dir = NamedTemporaryDir()
project_name = 'backbone'
project_dir = join(test_dir.name, project_name)
adaptors_dir = join(project_dir, 'config_data', 'adaptors')
adaptors_path_454 = join(adaptors_dir, '454_adaptors')
words = ['^ATGAAC', 'TTGATTTGGT']
univec = os.path.join(TEST_DATA_DIR, 'blast', 'univec+')
configuration = {'Cleaning': {'vector_database': univec,
'adaptors_file_454': adaptors_path_454,
'short_adaptors_454': words,
'edge_removal': {'454_left': 3,
'454_right': 3}},
'General_settings': {'threads': THREADS}}
settings_path = create_project(directory=test_dir.name,
name=project_name,
configuration=configuration)
#setup the original reads
reads_dir = join(project_dir, 'reads')
original_reads_dir = join(reads_dir, 'raw')
os.mkdir(reads_dir)
os.mkdir(original_reads_dir)
os.makedirs(adaptors_dir)
adap_fhand = open(adaptors_path_454, 'w')
adap_fhand.write('''>smart_5_cds_primer_1
GGTTCAAGGTTTGAGAAAGGATGGGAAG\n''')
adap_fhand.close()
#print original_reads_dir
fpath_454 = join(original_reads_dir, 'pl_454.lb_a.sfastq')
fpath_ill = join(original_reads_dir, 'pl_illumina.lb_b.sfastq')
fpath_solid = join(original_reads_dir, 'pl_solid.lb_prueba.sfastq')
open(fpath_solid, 'w').write(READS_SOLID)
open(fpath_454, 'w').write(READS_454)
open(fpath_ill, 'w').write(READS_ILL)
do_analysis(project_settings=settings_path, kind='clean_reads',
silent=True)
cleaned_dir = join(project_dir, 'reads', 'cleaned')
assert exists(cleaned_dir)
cleaned_454 = join(cleaned_dir, os.path.basename(fpath_454))
assert exists(cleaned_454)
seqs = list(seqs_in_file(open(cleaned_454)))
# It means thar the adaptor has been removed
seq = seqs[0].seq
assert 'GGTTCAAGGTTTGAGAAAGGATGGGAAG' not in seq
seq = seqs[2].seq
# It means that the starting word has been removed
assert seq.startswith('TTCCAAGATTCTTCCCACAT')
# solid
cleaned_solid = join(cleaned_dir, os.path.basename(fpath_solid))
clean_seqs = open(cleaned_solid).read()
assert '10_1824_570_F3' not in clean_seqs
do_analysis(project_settings=settings_path,
kind='prepare_mira_assembly', silent=True)
assembly_input = join(project_dir, 'assembly', 'input')
assert exists(assembly_input)
mira_in_454 = join(assembly_input, 'backbone_in.454.fasta')
mira_in_qul = join(assembly_input, 'backbone_in.454.fasta.qual')
assert exists(mira_in_454)
assert exists(mira_in_qul)
do_analysis(project_settings=settings_path, kind='mira_assembly',
silent=True)
assembly_dir = join(project_dir, 'assembly')
sorted(os.listdir(assembly_dir))
test_dir.close()
def test_backbone(analysis=None, analysis_dir=None):
'''It tests the backbone infrastructure.
If no analysis is given it will run all of them.
If no analysis_dir is given a temporary one will be used.
'''
logger = logging.getLogger('franklin')
if analysis_dir:
analysis_fhand = None
analysis_fpath = analysis_dir
else:
analysis_fhand = NamedTemporaryDir()
analysis_fpath = analysis_fhand.name
project_dir = analysis_fpath
repository_dir = join(TEST_DATA_DIR, 'acceptance')
settings_path = prepare_conf(project_dir, repository_dir)
choice = analysis
#choice = 'snvs'
if choice in ('cleaning', None):
original_reads = join(project_dir, 'reads/raw')
if exists(original_reads):
os.remove(original_reads)
reads = join(project_dir, 'reads')
if not exists(reads):
os.mkdir(reads)
shutil.copytree(join(repository_dir, 'cleaning'),
join(project_dir, 'reads/raw'))
analyses = ['clean_reads', 'read_stats']
run_analysis(analyses, settings_path)
if choice in ('assembling', None):
clean_reads_dir = join(project_dir, 'reads', 'cleaned')
if os.path.exists(clean_reads_dir):
shutil.rmtree(join(project_dir, 'reads'))
os.mkdir(join(project_dir, 'reads'))
shutil.copytree(join(repository_dir, 'assembling'),
join(project_dir, 'reads/cleaned'))
analyses = [ 'prepare_mira_assembly', 'mira_assembly']
run_analysis(analyses, settings_path)
if choice in ('mapping', None):
clean_reads_dir = join(project_dir, 'reads', 'cleaned')
if os.path.exists(clean_reads_dir):
shutil.rmtree(join(project_dir, 'reads'))
os.mkdir(join(project_dir, 'reads'))
shutil.copytree(join(repository_dir, 'assembling'),
join(project_dir, 'reads/cleaned'))
if exists(join(project_dir, 'mapping')):
shutil.rmtree(join(project_dir, 'mapping'))
os.makedirs(join(project_dir, 'mapping', 'reference'))
shutil.copy(join(repository_dir, 'mapping', 'reference.fasta'),
join(project_dir, 'mapping', 'reference',
'reference.fasta'))
analyses = ['mapping', 'merge_bams', 'realign_bam']
run_analysis(analyses, settings_path)
if choice in ('snvs', None):
annot_dir = join(project_dir, 'annotations')
create_dir(annot_dir)
annot_res = join(annot_dir, 'repr')
os.mkdir(join(annot_dir, 'input'))
os.mkdir(annot_res)
shutil.copy(join(repository_dir, 'snvs', 'reference.fasta'),
join(annot_dir, 'input', 'reference.fasta'))
mapping_dir = join(project_dir, 'mapping')
create_dir(mapping_dir)
os.mkdir(join(mapping_dir, 'reference'))
shutil.copy(join(repository_dir, 'snvs', 'merged.bam'),
join(project_dir, 'mapping', 'merged.bam'))
shutil.copy(join(repository_dir, 'snvs', 'reference.fasta'),
join(project_dir, 'mapping', 'reference', 'reference.fasta'))
analyses = ['annotate_snvs', 'filter_snvs', 'annotation_stats',
'write_annotations']
run_analysis(analyses, settings_path)
stats_fpath = join(project_dir, 'annotations', 'features', 'stats',
'reference.txt')
result = open(stats_fpath).read()
#print result
expected = '''Sequences with SNVs: 47
SNVs found: 186
SNV types:
\tinsertion: 2
\tdeletion: 12
\tcomplex: 1
\ttransition: 45
\ttransversion: 14
\tunknown: 112
SNV locations:
\tunknown: 186'''
assert expected in result
if choice in ('annotation', None):
annot_dir = join(project_dir, 'annotations')
if exists(join(annot_dir)):
shutil.rmtree(annot_dir)
os.mkdir(annot_dir)
shutil.copytree(join(repository_dir, 'annotation', 'input'),
join(annot_dir, 'input'))
shutil.copytree(join(repository_dir, 'annotation', 'blast'),
join(annot_dir, 'blast'))
analyses = ['annotate_orfs', 'annotate_microsatellites',
'annotate_gos', 'annotate_descriptions',
'annotate_orthologs', 'annotate_introns',
'annotate_prot_change',
'write_annotations', 'annotation_stats']
run_analysis(analyses, settings_path)
stats_fpath = join(project_dir, 'annotations', 'features', 'stats',
'tair7_cdna.st_nucl.txt')
result = open(stats_fpath).read()
expected = '''Number of sequences: 4
Sequences with description: 4
Sequences with ORF: 4
Number of ORFs: 4
Sequences with intron: 2
Number of introns: 3'''
assert expected in result
if not analysis_dir:
analysis_fhand.close()
def test_mapping_color():
'It test the mapping of the mapper with color space'
test_dir = NamedTemporaryDir()
project_name = 'backbone'
blastdb_seq = os.path.join(TEST_DATA_DIR, 'blast', 'arabidopsis_genes+')
snv_filters = {'filter1':{'name':'uniq_contiguous', 'use':True,
'genomic_db':blastdb_seq,
'genomic_seqs_fpath':blastdb_seq},
'filter7':{'name':'by_kind', 'use':True,
'kind':'SNP'},
'filter12':{'name':'ref_not_in_list', 'use':True,
'list_path':os.path.join(TEST_DATA_DIR, 'cos_list')},
'filter10':{'unique_name': 'variable_in_sm',
'name': 'is_variable', 'use':True,
'group_kind':'libraries',
'groups':['hola']},
'filter11':{'unique_name': 'variable_in_adios',
'name': 'is_variable', 'use':True,
'group_kind':'libraries',
'groups':['adios']},
'filter13':{'unique_name': 'variable_in_caracola',
'name': 'is_variable', 'use':True,
'group_kind':'libraries',
'groups':['caracola']}, }
configuration = {'Snvs':{'min_quality':20},
'Sam_processing':{'add_default_qualities':True},
'snv_filters':snv_filters,
'General_settings':{'threads':THREADS}}
settings_path = create_project(directory=test_dir.name,
name=project_name,
configuration=configuration)
project_dir = join(test_dir.name, project_name)
#setup the original reads
reads_dir = join(project_dir, 'reads')
clean_reads_dir = join(reads_dir, 'cleaned')
os.mkdir(reads_dir)
os.mkdir(clean_reads_dir)
shutil.copy(os.path.join(TEST_DATA_DIR, 'solid.fastq'),
os.path.join(clean_reads_dir, 'pl_solid.lb_hola.sm_hola.sfastq'))
#the reference
reference_dir = join(project_dir, 'mapping/reference')
os.makedirs(reference_dir)
reference_fpath = join(reference_dir, 'reference.fasta')
out = open(reference_fpath, 'w')
for line in open(join(TEST_DATA_DIR, 'samtools_color/reference')):
out.write(line)
do_analysis(project_settings=settings_path, kind='mapping', silent=True)
mapping_dir = join(project_dir, 'mapping')
singular_mapping_dir = sorted(os.listdir(mapping_dir))[0]
singular_mapping_dir = join(mapping_dir, singular_mapping_dir)
assert exists(join(singular_mapping_dir, 'bams',
'by_readgroup', 'pl_solid.lb_hola.sm_hola.bam'))
result_dir = join(mapping_dir, 'bams')
assert exists(result_dir)
result_dir_by_lib = join(result_dir, 'by_readgroup')
assert exists(result_dir_by_lib)
do_analysis(project_settings=settings_path, kind='merge_bams',
silent=True)
assert exists(join(result_dir, 'merged.0.bam'))
assert exists(join(result_dir, 'merged.0.bam.bai'))
#we realign the mapping using GATK
do_analysis(project_settings=settings_path, kind='realign_bam',
silent=True)
assert exists(join(result_dir, 'merged.1.bam'))
test_dir.close()
def test_ortholog_annotation_analysis():
"We can annotate orthologs"
test_dir = NamedTemporaryDir()
project_name = "backbone"
config = {
"blast": {
"arabidopsis": {"path": "/path/to/tair", "species": "arabidopsis", "kind": "nucl"},
"arabidopsis2": {"path": "/path/to/tair2", "species": "arabidopsis2", "kind": "nucl"},
},
"Annotation": {"ortholog_annotation": {"ortholog_databases": ["arabidopsis", "arabidopsis2"]}},
"General_settings": {"threads": THREADS},
}
settings_path = create_project(directory=test_dir.name, name=project_name, configuration=config)
project_dir = join(test_dir.name, project_name)
# create blast results
melon_tair_blastdir = join(project_dir, "annotations", "blast", "melon.st_nucl.pl_454", "tair")
melon_tair2_blastdir = join(project_dir, "annotations", "blast", "melon.st_nucl.pl_454", "tair2")
os.makedirs(melon_tair_blastdir)
os.makedirs(melon_tair2_blastdir)
tair_melon_blastdir = join(project_dir, "annotations", "blast", "tair", "melon.st_nucl.pl_454")
tair2_melon_blastdir = join(project_dir, "annotations", "blast", "tair2", "melon.st_nucl.pl_454")
os.makedirs(tair_melon_blastdir)
os.makedirs(tair2_melon_blastdir)
blast_fname = BACKBONE_BASENAMES["blast_basename"] + ".tblastx.xml"
shutil.copy(join(TEST_DATA_DIR, "melon_tair.xml"), join(melon_tair_blastdir, blast_fname))
shutil.copy(join(TEST_DATA_DIR, "melon_tair.xml"), join(melon_tair2_blastdir, blast_fname))
shutil.copy(join(TEST_DATA_DIR, "tair_melon.xml"), join(tair_melon_blastdir, blast_fname))
shutil.copy(join(TEST_DATA_DIR, "tair_melon.xml"), join(tair2_melon_blastdir, blast_fname))
# some melon file to annotate
input_dir = join(project_dir, BACKBONE_DIRECTORIES["annotation_input"])
os.makedirs(input_dir)
seq1 = SeqWithQuality(Seq("A"), id="melon1")
seq2 = SeqWithQuality(Seq("A"), id="melon2")
write_seqs_in_file([seq1, seq2], open(join(input_dir, "melon.st_nucl.pl_454.fasta"), "a"))
do_analysis(project_settings=settings_path, kind="annotate_orthologs", silent=True)
pickle_fpath = join(project_dir, BACKBONE_DIRECTORIES["annotation_dbs"], "melon.st_nucl.pl_454.0.pickle")
pickle = open(pickle_fpath).read()
assert "arabidopsis-orthologs" in pickle
assert "arabidopsis2-orthologs" in pickle
do_analysis(project_settings=settings_path, kind="write_annotations", silent=True)
orf_fpath = join(project_dir, "annotations", "features", "melon.st_nucl.pl_454.orthologs")
assert os.path.exists(orf_fpath)
assert "tair1" in open(orf_fpath).read()
orf_fpath = join(project_dir, "annotations", "features", "melon.st_nucl.pl_454.orf")
assert not os.path.exists(orf_fpath)
do_analysis(project_settings=settings_path, kind="annotation_stats", silent=True)
stats_fpath = join(project_dir, "annotations", "features", "stats", "melon.st_nucl.pl_454.txt")
result = open(stats_fpath).read()
expected = """Orthologs
_________
Sequences with arabidopsis orthologs: 2
Number of arabidopsis orthologs: 2
Sequences with arabidopsis2 orthologs: 2
Number of arabidopsis2 orthologs: 2"""
assert expected in result
test_dir.close()
def test_protein_change_annotation_analysis():
"We can annotate protein changes"
test_dir = NamedTemporaryDir()
project_name = "backbone"
matrix = os.path.join(TEST_DATA_DIR, "At.smat")
configuration = {
"Snvs": {"min_quality": 20},
"Sam_processing": {"add_default_qualities": True},
"Annotation": {"orf_annotation": {"estscan_matrix": matrix}},
"General_settings": {"threads": THREADS},
}
settings_path = create_project(directory=test_dir.name, name=project_name, configuration=configuration)
project_dir = join(test_dir.name, project_name)
# setup the original reads
reads_dir = join(project_dir, "reads")
clean_reads_dir = join(reads_dir, "cleaned")
os.mkdir(reads_dir)
os.mkdir(clean_reads_dir)
solexa = "@seq1\n"
solexa += "TCATTGAAAGTTGAAACTGATAGTAGCAGAGTTTTTTCCTCTGTTTGG\n"
solexa += "+\n"
solexa += "IIIIIIHIIIIIIIIIIIIIIIIIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa = "@seq2\n"
solexa += "ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n"
solexa += "+\n"
solexa += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa = "@seq14\n"
solexa += "ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n"
solexa += "+\n"
solexa += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa = "@seq15\n"
solexa += "ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n"
solexa += "+\n"
solexa += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa = "@seq12\n"
solexa += "ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n"
solexa += "+\n"
solexa += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa = "@seq13\n"
solexa += "ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n"
solexa += "+\n"
solexa += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa = "@seq16\n"
solexa += "ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n"
solexa += "+\n"
solexa += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 = "@seq18\n"
solexa2 += "TCATTGAAAGTTGAAACTGATAGTAGCAGAGTTTTTTCCTCTGTTTGG\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIIIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 += "@seq19\n"
solexa2 += "ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 += "@seq20\n"
solexa2 += "ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 += "@seq21\n"
solexa2 += "ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 += "@seq22\n"
solexa2 += "ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 += "@seq23\n"
solexa2 += "ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 += "@seq24\n"
solexa2 += "ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
solexa2 += "@seq25\n"
solexa2 += "ATGTACTAGCAGTACGATCACACACTGGACAGTACAGACCAGAATGAC\n"
solexa2 += "+\n"
solexa2 += "IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n"
sanger = ">seq3\n"
sanger += "GATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATAGGAGATACTGA"
sanger += "GATTCTGGAATCTCTGAGTTTCTGGGTTCAAGTTGCACTGACCATTGTTGGATTTGTAGA"
sanger += "TTGTTTCTTCTTTCATTAGGCATTGATTATGGGTAAATGCGTGGGTACATATAATATATA"
sanger += "TCTGTTGAATGCAATTTACACATTGACTGAGGAACAACATGAACATGGCAGCTTTCTCAA"
sanger += "AATTGAACCACAGAAGGCTTAAAAGCAAAGTCTTTGGAGAATCAGACTAAGCTTGAGA\n"
sanger += ">seq4\n"
sanger += "TCCATACTTTACTCTATCTCTTTCTGTGTTTGGTAACACGCGAGGATTGGATGATAT"
sanger += "CTATATATTCTAATGTGGACTAAAAATGTGTGTGTGTGTATGAAGATGGGAAGCCGGAAG"
sanger += "TCATCAAGGAGAAAAGAGAGATAGACGACGAGAAGATGGCGTTGACGTTCAGAGGACTAG"
sanger += "AGGGTCATGTGATGGAGAAGTACAAGAAGTATGAGGTTATCTTACAGTTCATTCCCAAGT"
sanger += "CGAACGAAGGCTGCGTCTGCAAAGTCACTCTGATATGGGAGAATCGCAACGAAGACTCCC"
sanger += ">seq5\n"
sanger += "TCCATACTTTACTCTATCTCTTTCTGTGTTTGGTAACACGCGAGGATTGGATGATAT"
sanger += "CTATATATTCTAAAGTGGACTAAAAATGTGTGTGTGTGTATGAAGATGGGAAGCCGGAAG"
sanger += "TCATCAAGGAGAAAAGAGAGATAGACGACGAGAAGATGGCGTTGACGTTCAGAGGACTAG"
sanger += "AGGGTCATGTGATGGAGAAGTACAAGAAGTATGAGGTTATCTTACAGTTCATTCCCAAGT"
sanger += "CGAACGAAGGCTGCGTCTGCAAAGTCACTCTGATATGGGAGAATCGCAACGAAGACTCCC"
sange2 = ">seq6\n"
sange2 += "GATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATAGGAGATACTGA"
sange2 += "GATTCTGGAATCTCTGAGTTTCTGGGTTCAAGTTGCACTGACCATTGTTGGATTTGTAGA"
sange2 += "TTGTTTCTTCTTTCATTAGGCATTGATTATGGGTAAATGCGTGGGTACATATAATATATA"
sange2 += "TCTGTTGAATGCAATTTACACATTGACTGAGGAACAACATGAACATGGCAGCTTTCTCAA"
sange2 += "AATTGAACCACAGAAGGCTTAAAAGCAAAGTCTTTGGAGAATCAGACTAAGCTTGAGA\n"
sange2 += ">seq7\n"
sange2 += "TCCATACTTTACTCTATCTCTTTCTGTGTTTGGTAACACGCGAGGATTGGATGATAT"
sange2 += "CTATATATTCTAATGTGGACTAAAAATGTGTGTGTGTGTATGAAGATGGGAAGCCGGAAG"
sange2 += "TCATCAAGGAGAAAAGAGAGATAGACGACGAGAAGATGGCGTTGACGTTCAGAGGACTAG"
sange2 += "AGGGTCATGTGATGGAGAAGTACAAGAAGTATGAGGTTATCTTACAGTTCATTCCCAAGT"
sange2 += "CGAACGAAGGCTGCGTCTGCAAAGTCACTCTGATATGGGAGAATCGCAACGAAGACTCCC"
sange2 += ">seq8\n"
sange2 += "TCCATACTTTACTCTATCTCTTTCTGTGTTTGGTAACACGCGAGGATTGGATGATAT"
sange2 += "CTATATATTCTAAAGTGGACTAAAAATGTGTGTGTGTGTATGAAGATGGGAAGCCGGAAG"
sange2 += "TCATCAAGGAGAAAAGAGAGATAGACGACGAGAAGATGGCGTTGACGTTCAGAGGACTAG"
sange2 += "AGGGTCATGTGATGGAGAAGTACAAGAAGTATGAGGTTATCTTACAGTTCATTCCCAAGT"
sange2 += "CGAACGAAGGCTGCGTCTGCAAAGTCACTCTGATATGGGAGAATCGCAACGAAGACTCCC"
fpath_sanger = join(clean_reads_dir, "lb_hola1.pl_sanger.sm_hola.fasta")
fpath_solexa = join(clean_reads_dir, "lb_hola2.pl_illumina.sm_hola.sfastq")
open(fpath_sanger, "w").write(sanger)
open(fpath_solexa, "w").write(solexa)
fpath_sanger2 = join(clean_reads_dir, "lb_adios.pl_sanger.fasta")
fpath_solexa2 = join(clean_reads_dir, "lb_adios.pl_illumina.sfastq")
open(fpath_sanger2, "w").write(sange2)
open(fpath_solexa2, "w").write(solexa2)
# the reference
reference_dir = join(project_dir, "mapping/reference")
os.makedirs(reference_dir)
reference_fpath = join(reference_dir, "reference.fasta")
out = open(reference_fpath, "w")
for line in open(join(TEST_DATA_DIR, "blast/arabidopsis_genes")):
out.write(line)
do_analysis(project_settings=settings_path, kind="mapping", silent=True)
mapping_dir = join(project_dir, "mapping")
singular_mapping_dir = sorted(os.listdir(mapping_dir))[0]
singular_mapping_dir = join(mapping_dir, singular_mapping_dir)
assert exists(join(singular_mapping_dir, "bams", "by_readgroup", "lb_hola2.pl_illumina.sm_hola.bam"))
result_dir = join(mapping_dir, "bams")
assert exists(result_dir)
result_dir_by_lib = join(result_dir, "by_readgroup")
assert exists(result_dir_by_lib)
do_analysis(project_settings=settings_path, kind="merge_bams", silent=True)
assert exists(join(result_dir, "merged.0.bam"))
assert exists(join(result_dir, "merged.0.bam.bai"))
# we realign the mapping using GATK
do_analysis(project_settings=settings_path, kind="realign_bam", silent=True)
assert exists(join(result_dir, "merged.1.bam"))
annot_input_dir = join(project_dir, "annotations", "input")
os.makedirs(annot_input_dir)
os.symlink(reference_fpath, join(annot_input_dir, "reference.fasta"))
do_analysis(project_settings=settings_path, kind="annotate_snvs", silent=True)
do_analysis(project_settings=settings_path, kind="annotate_orfs", silent=True)
do_analysis(project_settings=settings_path, kind="annotate_prot_change", silent=True)
result_file = join(project_dir, "annotations", "db", "reference.2.pickle")
seqs = list(seqs_in_file(open(result_file)))
snv = seqs[2].features[0]
assert snv.qualifiers["protein_change"]["kind"] == "substitution"
assert snv.qualifiers["protein_change"]["location"] == "codon_1"
test_dir.close()
def test_mapping_analysis():
'We can map the reads'
test_dir = NamedTemporaryDir()
project_name = 'backbone'
bed_fhand = NamedTemporaryFile(suffix='.bed')
bed_fhand.write('AT1G14930.1\t200\t400\nAT1G55265.1\t100\t300\n')
bed_fhand.flush()
blastdb_seq = os.path.join(TEST_DATA_DIR, 'blast', 'arabidopsis_genes+')
snv_filters = {'filter1':{'name':'uniq_contiguous', 'use':True,
'genomic_db':blastdb_seq,
'genomic_seqs_fpath':blastdb_seq},
'filter7':{'name':'by_kind', 'use':True,
'kind':'SNP'},
'filter12':{'name':'ref_not_in_list', 'use':True,
'list_path':os.path.join(TEST_DATA_DIR, 'cos_list')},
'filter10':{'unique_name': 'variable_in_sm',
'name': 'is_variable', 'use':True,
'group_kind':'libraries',
'groups':['hola1']},
'filter11':{'unique_name': 'variable_in_adios',
'name': 'is_variable', 'use':True,
'group_kind':'libraries',
'groups':['adios']},
'filter13':{'unique_name': 'variable_in_caracola',
'name': 'is_variable', 'use':True,
'group_kind':'libraries',
'groups':['hola2']},
'filter14':{'name': 'in_segment_bed', 'use':True,
'bed_fpath':bed_fhand.name,
'edge_avoidance':10}}
configuration = {'Snvs':{'min_quality':20},
'Sam_processing':{'add_default_qualities':True},
'snv_filters':snv_filters,
'General_settings':{'threads':THREADS},
'Mappers':{'keep_unmapped_reads_in_bam':False}}
settings_path = create_project(directory=test_dir.name,
name=project_name,
configuration=configuration)
project_dir = join(test_dir.name, project_name)
#setup the original reads
reads_dir = join(project_dir, 'reads')
clean_reads_dir = join(reads_dir, 'cleaned')
os.mkdir(reads_dir)
os.mkdir(clean_reads_dir)
solexa = '@seq1\n'
solexa += 'TCATTGAAAGTTGAAACTGATAGTAGCAGAGTTTTTTCCTCTGTTTGG\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIIIIUJUAUGJUUJUDFAOUDJOFSUD\n'
solexa += '@seq2\n'
solexa += 'ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n'
solexa += '@seq14\n'
solexa += 'ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n'
solexa += '@seq15\n'
solexa += 'ATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATA\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n'
solexa += '@seq12\n'
solexa += 'ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n'
solexa += '@seq13\n'
solexa += 'ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n'
solexa += '@seq16\n'
solexa += 'ATATGATTGAAGATATTTCTGGACTTTAAGGGTTCTTGAGGATTTATA\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n'
solexa += '@seq17\n'
solexa += 'ATGTACTAGCAGTACGATCACACACTGGACAGTACAGACCAGAATGAC\n'
solexa += '+\n'
solexa += 'IIIIIIHIIIIIIIIIIIIIIIZIIUJUAUGJUUJUDFAOUDJOFSUD\n'
sanger = '>seq3\n'
sanger += 'GATATGATTGAAGATATTTCTGGGCTTTAAGGGTTCTTGAGGATTTATAGGAGATACTGA'
sanger += 'GATTCTGGAATCTCTGAGTTTCTGGGTTCAAGTTGCACTGACCATTGTTGGATTTGTAGA'
sanger += 'TTGTTTCTTCTTTCATTAGGCATTGATTATGGGTAAATGCGTGGGTACATATAATATATA'
sanger += 'TCTGTTGAATGCAATTTACACATTGACTGAGGAACAACATGAACATGGCAGCTTTCTCAA'
sanger += 'AATTGAACCACAGAAGGCTTAAAAGCAAAGTCTTTGGAGAATCAGACTAAGCTTGAGA\n'
sanger += '>seq4\n'
sanger += 'TCCATACTTTACTCTATCTCTTTCTGTGTTTGGTAACACGCGAGGATTGGATGATAT'
sanger += 'CTATATATTCTAATGTGGACTAAAAATGTGTGTGTGTGTATGAAGATGGGAAGCCGGAAG'
sanger += 'TCATCAAGGAGAAAAGAGAGATAGACGACGAGAAGATGGCGTTGACGTTCAGAGGACTAG'
sanger += 'AGGGTCATGTGATGGAGAAGTACAAGAAGTATGAGGTTATCTTACAGTTCATTCCCAAGT'
sanger += 'CGAACGAAGGCTGCGTCTGCAAAGTCACTCTGATATGGGAGAATCGCAACGAAGACTCCC'
sanger += '>seq5\n'
sanger += 'TCCATACTTTACTCTATCTCTTTCTGTGTTTGGTAACACGCGAGGATTGGATGATAT'
sanger += 'CTATATATTCTAAAGTGGACTAAAAATGTGTGTGTGTGTATGAAGATGGGAAGCCGGAAG'
sanger += 'TCATCAAGGAGAAAAGAGAGATAGACGACGAGAAGATGGCGTTGACGTTCAGAGGACTAG'
sanger += 'AGGGTCATGTGATGGAGAAGTACAAGAAGTATGAGGTTATCTTACAGTTCATTCCCAAGT'
sanger += 'CGAACGAAGGCTGCGTCTGCAAAGTCACTCTGATATGGGAGAATCGCAACGAAGACTCCC'
fpath_sanger = join(clean_reads_dir, 'lb_hola1.pl_sanger.sm_hola.fasta')
fpath_solexa = join(clean_reads_dir,
'lb_hola2.pl_illumina.sm_hola.sfastq')
open(fpath_sanger, 'w').write(sanger)
open(fpath_solexa, 'w').write(solexa)
fpath_sanger2 = join(clean_reads_dir, 'lb_adios.pl_sanger.fasta')
fpath_solexa2 = join(clean_reads_dir,
'lb_adios.pl_illumina.sfastq')
open(fpath_sanger2, 'w').write(sanger)
open(fpath_solexa2, 'w').write(solexa)
#the reference
reference_dir = join(project_dir, 'mapping/reference')
os.makedirs(reference_dir)
reference_fpath = join(reference_dir, 'reference.fasta')
out = open(reference_fpath, 'w')
for line in open(join(TEST_DATA_DIR, 'blast/arabidopsis_genes')):
out.write(line)
do_analysis(project_settings=settings_path, kind='mapping', silent=True)
mapping_dir = join(project_dir, 'mapping')
singular_mapping_dir = sorted(os.listdir(mapping_dir))[0]
singular_mapping_dir = join(mapping_dir, singular_mapping_dir)
assert exists(join(singular_mapping_dir, 'bams',
'by_readgroup', 'lb_hola2.pl_illumina.sm_hola.bam'))
result_dir = join(mapping_dir, 'bams')
assert exists(result_dir)
result_dir_by_lib = join(result_dir, 'by_readgroup')
assert exists(result_dir_by_lib)
unmapped_fpath = join(mapping_dir, 'unmapped_reads.gz')
assert exists(unmapped_fpath)
unmappeds = GzipFile(unmapped_fpath).read()
assert 'seq17' in unmappeds
do_analysis(project_settings=settings_path, kind='merge_bams',
silent=True)
assert exists(join(result_dir, 'merged.0.bam'))
assert exists(join(result_dir, 'merged.0.bam.bai'))
#we realign the mapping using GATK
do_analysis(project_settings=settings_path, kind='realign_bam',
silent=True)
assert exists(join(result_dir, 'merged.1.bam'))
#we calculate BAQ
do_analysis(project_settings=settings_path, kind='calmd_bam',
silent=True)
assert exists(join(result_dir, 'merged.2.bam'))
assert exists(join(result_dir, 'merged.2.bam.bai'))
do_analysis(project_settings=settings_path, kind='mapping_stats',
silent=True)
stats_fname = join(mapping_dir,
BACKBONE_DIRECTORIES['mapping_stats'][1],
BACKBONE_BASENAMES['statistics_file'])
result = open(stats_fname).read()
assert 'Statistics for Coverage for platform sanger' in result
annot_input_dir = join(project_dir, 'annotations', 'input')
os.makedirs(annot_input_dir)
os.symlink(reference_fpath, join(annot_input_dir, 'reference.fasta'))
do_analysis(project_settings=settings_path, kind='annotate_snvs',
silent=True)
json_fpath = join(project_dir, BACKBONE_DIRECTORIES['annotation_dbs'],
'reference.0.pickle')
assert 'snv' in open(json_fpath).read()
do_analysis(project_settings=settings_path, kind='filter_snvs',
silent=True)
json_fpath = join(project_dir, BACKBONE_DIRECTORIES['annotation_dbs'],
'reference.1.pickle')
result = open(json_fpath).read()
#print result
assert 'snv' in result
assert 'adios_sanger' in result
do_analysis(project_settings=settings_path, kind='write_annotations',
silent=True)
vcf_fpath = join(project_dir, 'annotations', 'features',
'reference.vcf')
vcf = open(vcf_fpath).read()
assert 'VLB1' in vcf
assert 'VLB2' in vcf
assert 'VLB3' in vcf
assert 'AT1G14930.1' in vcf
assert 'IS10' in vcf
do_analysis(project_settings=settings_path, kind='mapping_stats',
silent=True)
stats_dir = join(project_dir, 'mapping', 'bams', 'stats')
assert exists(join(stats_dir, 'backbone.coverage_illumina.dat'))
stats_fpath = join(stats_dir, BACKBONE_BASENAMES['statistics_file'])
result = open(stats_fpath).read()
expected = '''average: 0.4542
variance: 1.3050
total sequence length: 3941'''
assert expected in result
test_dir.close()
