def flow_control():
today = dt.datetime.now().strftime("%Y-%m-%d")
args = get_args().parse_args()
if args.local:
config_dict = helpers.process_config("local_config")
else:
config_dict = helpers.process_config("config")
if args.analysis == 'test':
print(workflow_test(args.analysis, args.input, args.out_dir))
elif args.analysis == 'qc':
print(workflow_qc(args.input, config_dict, args.local))
elif args.analysis == 'mqc':
print(workflow_mqc(args.input, config_dict, args.local))
elif args.analysis == 'trim':
print(workflow_trim_and_qc(args.input, config_dict, args.local))
elif args.analysis == 'align': # tested locally
print(
workflow_align(args.input, args.reference_genome, args.gff,
config_dict, today, args.local))
elif args.analysis == 'bam-stats':
print(workflow_bam_stats(args.input, today, args.local))
elif args.analysis == 'count': # todo test
assert args.gff
workflow_count(args.gff, args.input, config_dict, today, args.local)
def flux_mqc_dir():
data_dir = "/scratch/hmobley_fluxod/annasint/code/data/mqc_dir/"
mqc_dir = "/scratch/hmobley_fluxod/annasint/code/test_data"
shutil.copytree(data_dir, mqc_dir)
config_dict = helpers.process_config(config_file="config")
local = False
yield (mqc_dir, config_dict, local)
def local_sam(tmpdir, day):
sam_file = "/Users/annasintsova/git_repos/code/data/alignments/SRR1051490.sam"
s_file = tmpdir.mkdir("alignments").join("align.sam")
shutil.copy(sam_file, str(s_file))
config_dict = helpers.process_config(config_file="local_config")
local = True
today = day
yield (str(s_file), today, config_dict, local)
def local_fastq_ref(tmpdir, day):
fastq_file = "/Users/annasintsova/git_repos/code/data/reads/SRR1051490.fastq"
reference_genome = "/Users/annasintsova/git_repos/code/data/ref/MG1655.fna"
f_file = tmpdir.join("test.fastq")
r_file = tmpdir.mkdir("ref").join("genome.fna")
shutil.copy(fastq_file, str(f_file))
shutil.copy(reference_genome, str(r_file))
config_dict = helpers.process_config(config_file="local_config")
local = True
yield (str(f_file), str(r_file), config_dict, local)
def count_keep_output():
data_dir = "/scratch/hmobley_fluxod/annasint/code/data/"
test_dir = "/scratch/hmobley_fluxod/annasint/code/test_data"
os.mkdir(test_dir)
cnts = os.path.join(data_dir, "counts/SRR1051490_sorted_counts_st.csv")
test_cnts = os.path.join(test_dir, "SRR1051490_sorted_counts_st.csv")
shutil.copy(cnts, test_cnts)
config_dict = helpers.process_config(config_file="config")
local = False
return test_cnts, config_dict, local
def flux_fastq_ref(tmpdir):
fastq_file = "/scratch/hmobley_fluxod/annasint/code/data/reads/SRR1051490.fastq"
reference_genome = "/scratch/hmobley_fluxod/annasint/code/data/ref/MG1655.fna"
#f_file = tmpdir.join("test.fastq")
#r_file = tmpdir.mkdir("ref").join("genome.fna")
test_dir = "/scratch/hmobley_fluxod/annasint/code/test_data"
os.mkdir(test_dir)
f_file = os.path.join(test_dir, "test.fastq")
r_file = os.path.join(test_dir, "genome.fna")
shutil.copy(fastq_file, f_file)
shutil.copy(reference_genome, r_file)
config_dict = helpers.process_config(config_file="config")
local = False
yield (f_file, r_file, config_dict, local)
def local_bam(tmpdir, day):
gff_file = "/Users/annasintsova/git_repos/code/data/ref/MG1655.gff"
bam_file = "/Users/annasintsova/git_repos/code/data/alignments/SRR1051490_sorted.bam"
bai_file = bam_file + ".bai"
b_file = tmpdir.mkdir("alignments").join("align.bam")
bi_file = tmpdir.join("alignments/align.bam.bai")
g_file = tmpdir.mkdir("ref").join("annotation.gff")
shutil.copy(bam_file, str(b_file))
shutil.copy(bai_file, str(bi_file))
shutil.copy(gff_file, str(g_file))
config_dict = helpers.process_config(config_file="local_config")
local = True
today = day
yield (str(b_file), str(g_file), today, config_dict, local)
def flux_bam_keep_output():
data_dir = "/scratch/hmobley_fluxod/annasint/code/data/"
test_dir = "/scratch/hmobley_fluxod/annasint/code/test_data"
os.mkdir(test_dir)
gff = os.path.join(data_dir, "ref/MG1655.gff")
test_gff = os.path.join(test_dir, "MG1655.gff")
shutil.copy(gff, test_gff)
bam = os.path.join(data_dir, "alignments/SRR1051490_sorted.bam")
test_bam = os.path.join(test_dir, "SRR1051490_sorted.bam")
shutil.copy(bam, test_bam)
bai = os.path.join(data_dir, "alignments/SRR1051490_sorted.bam.bai")
test_bai = os.path.join(test_dir, "SRR1051490_sorted.bam.bai")
shutil.copy(bai, test_bai)
config_dict = helpers.process_config(config_file="config")
local = False
return test_bam, test_gff, config_dict, local
def flux_fastq_dir_ref_PE(day): # todo refactor
data_dir = "/scratch/hmobley_fluxod/annasint/code/data2/"
test_dir = "/scratch/hmobley_fluxod/annasint/code/test_data/"
shutil.copytree(data_dir, test_dir)
ref_genome = os.path.join(test_dir, 'ref/MG1655.fna')
gff = os.path.join(test_dir, 'ref/MG1655.gff')
fastq_file_dir = os.path.join(test_dir, "reads")
today = day
config_dict = helpers.process_config(config_file="config")
local = False
return fastq_file_dir, ref_genome, gff, today, config_dict, local
# @pytest.fixture()
# def remove_test_data():
# yield
# os.remove()
# todo finish fixture that would remove all data from test_data directory in the end
def flux_sam_bam(tmpdir, day):
data_dir = "/scratch/hmobley_fluxod/annasint/code/data/"
gff = os.path.join(data_dir, "ref/MG1655.gff")
gff_name = "MG1655.gff"
test_gff = str(tmpdir.join(gff_name))
shutil.copy(gff, test_gff)
sam = os.path.join(data_dir, "alignments/SRR1051490.sam")
sam_name = "SRR1051490.sam"
test_sam = str(tmpdir.join(sam_name))
shutil.copy(sam, test_sam)
bam = os.path.join(data_dir, "alignments/SRR1051490_sorted.bam")
bam_name = "SRR1051490_sorted.bam"
test_bam = str(tmpdir.join(bam_name))
shutil.copy(bam, test_bam)
config_dict = helpers.process_config(config_file="config")
local = False
return test_sam, test_bam, test_gff, config_dict, local
def test_process_config():
output = helpers.process_config(config_file="tests/test_config")
actual_output = output['bin_path']['binbase']
expected_output = '/home/annasint/'
assert actual_output == expected_output