def test_batch():
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
with TempFile(suffix=".tt") as tempfile:
import sys
sys.argv = ["bioconvert", "fastq2fasta", infile, tempfile.name,
"--force", "-m"]
converter.main()
def test_converter2():
infile = bioconvert_data("test_measles.sorted.bam")
with TempFile(suffix=".bed") as tempfile:
import sys
sys.argv = ["bioconvert", "bam2cov", infile, tempfile.name,
"--method", "bedtools", "--force"]
converter.main()
def test_converter_show_methods():
import sys
sys.argv = ["bioconvert", "fastq2fasta", "--show-methods"]
try:
converter.main()
except SystemExit as e:
assert e.code == 0
def test_converter_no_outfile_without_srs_argv():
import shutil
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
with TempFile(suffix=".fastq") as tempfile:
shutil.copy(infile, tempfile.name)
args = ["bioconvert", "fastq2fasta", tempfile.name, "--force", "--raise-exception"]
converter.main(args[1:])
def test_conversion_graph_error():
import sys
sys.argv = ["bioconvert", "--conversion-graph", "toto"]
try:
converter.main()
except SystemExit as e:
assert e.code > 0
def test_converter_no_outfile():
infile = bioconvert_data("test_measles.sorted.bam")
try:
sys.argv = ["bioconvert", infile]
converter.main()
except:
pass
def test_converter_compression():
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
with TempFile(suffix=".fasta.gz") as tempfile:
sys.argv = [
"bioconvert", "fastq2fasta", infile, tempfile.name, "--force"
]
converter.main()
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
with TempFile(suffix=".fasta.bz2") as tempfile:
sys.argv = [
"bioconvert", "fastq2fasta", infile, tempfile.name, "--force"
]
converter.main()
infile = bioconvert_data("test_fastq2fasta_v1.fasta")
with TempFile(suffix=".fastq.gz") as tempfile:
sys.argv = [
"bioconvert", "fasta2fastq", infile, tempfile.name, "--force"
]
converter.main()
infile = bioconvert_data("test_fastq2fasta_v1.fasta")
with TempFile(suffix=".fastq.bz2") as tempfile:
sys.argv = [
"bioconvert", "fasta2fastq", infile, tempfile.name, "--force"
]
converter.main()
infile = bioconvert_data("test_fastq2fasta_v1.fasta")
with TempFile(suffix=".fastq.dsrc") as tempfile:
sys.argv = [
"bioconvert", "fasta2fastq", infile, tempfile.name, "--force"
]
converter.main()
def test_plink_no_extension():
infile = bioconvert_data("plink_toy.ped")
infile = infile.replace(".ped", "")
with TempFile(suffix="") as outfile:
import sys, os
sys.argv = ["bioconvert", "plink2bplink", infile, outfile.name, "--force"]
converter.main()
def test_converter_without_converter():
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
with TempFile(suffix=".fasta") as tempfile1, TempFile(suffix=".fasta") as tempfile2:
cmd = "bioconvert {} {} --force".format(infile, tempfile1.name)
p = subprocess.Popen(cmd, shell=True)
assert p.wait() == 0
import sys
sys.argv = ["bioconvert", infile, tempfile2.name, "--force"]
converter.main()
assert md5(tempfile1.name) == md5(tempfile2.name)
def test_verbose():
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
with TempFile(suffix=".tt") as tempfile:
import sys
sys.argv = ["bioconvert", "fastq2fasta", infile, tempfile.name,
"--force", "-v", "CRITICAL"]
converter.main()
sys.argv = ["bioconvert","fastq2fasta", infile, tempfile.name,
"--force","--verbosity", "CRITICAL"]
converter.main()
def test_converter_output_format():
infile = bioconvert_data("test_measles.sorted.bam")
with TempFile() as tempfile:
import sys
sys.argv = ["bioconvert", infile, tempfile.name,
"--output-format", "bed", "--force"]
try:
converter.main()
except SystemExit:
pass
def test_not_existing_param():
import sys
sys.argv = ["bioconvert", "--tagada"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 2
except:
assert False
def test_converter_formats():
import sys
sys.argv = ["bioconvert", "--formats"]
try:
converter.main()
assert False
except SystemExit:
assert True
except:
assert False
def test_dependency_report():
import sys
sys.argv = ["bioconvert", "--dependency-report"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
def test_converter_with_nothing():
import sys
sys.argv = ["bioconvert", "fastq2fasta"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code > 0
except:
assert False
def test_version():
import sys
sys.argv = ["bioconvert", "--version"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
def test_not_existing_subcommand():
import sys
sys.argv = ["bioconvert", "bam2tagada", "--help"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code in [1, 2]
except:
assert False
def test_indirect_conversion():
import sys
infile = bioconvert_data("fastqutils_1.fastq")
with TempFile(suffix=".clustal") as tempfile:
sys.argv = ["bioconvert", "fastq2clustal", infile, tempfile.name,
"--force", "--allow-indirect-conversion", "-v", "DEBUG"]
converter.main()
sys.argv = ["bioconvert", "fastq2clustal", infile, tempfile.name,
"--force", "-a", "-v", "DEBUG"]
converter.main()
def test_converter_show_methods():
infile = bioconvert_data("test_measles.sorted.bam")
with TempFile(suffix=".bed") as tempfile:
import sys
sys.argv = [
"bioconvert", infile, tempfile.name, "--show-methods", "--force"
]
try:
converter.main()
except SystemExit:
pass
def test_conversion_graph():
import sys
sys.argv = ["bioconvert", "--conversion-graph", "cytoscape"]
try:
converter.main()
except SystemExit as e:
assert e.code == 0
sys.argv = ["bioconvert", "--conversion-graph", "cytoscape-all"]
try:
converter.main()
except SystemExit as e:
assert e.code == 0
def test_converter_wrong_input_file():
with TempFile(suffix=".fasta") as tempfile1, TempFile(suffix=".fasta") as tempfile2:
cmd = "bioconvert fastq2fasta {} {} --force".format("missing.fastq", tempfile1.name)
p = subprocess.Popen(cmd, shell=True)
assert p.wait() == 1
import sys
sys.argv = ["bioconvert", "fastq2fasta", "missing.fastq", tempfile2.name, "--force"]
try:
converter.main()
assert False
except:
assert True
def test_indirect_conversion_without_argument():
import sys
infile = bioconvert_data("fastqutils_1.fastq")
with TempFile(suffix=".clustal") as tempfile:
sys.argv = ["bioconvert", "fastq2clustal", infile, tempfile.name, "--force"]
# For now we want the user to explicitly indicate that (s)he agrees with an indirect conversion
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 2
except:
assert False
def test_close_match():
infile = bioconvert_data("test_fastq2fasta_v1.fastq")
with TempFile(suffix=".tt") as tempfile:
import sys
sys.argv = ["bioconvert", "fastq2fastpp", infile, tempfile.name,
"--force"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 2
except:
assert False
def test_allow_indirect_conversion():
import sys
sys.argv = ["bioconvert", "-a", "--help"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
sys.argv = ["bioconvert", "--allow-indirect-conversion", "--help"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
def test_no_converter_specified():
import sys
try:
sys.argv = ["bioconvert"]
converter.main()
assert False
except SystemExit as e:
assert e.code == 1
except Exception as e:
assert type(e) == SystemExit
try:
sys.argv = ["bioconvert", '--verbosity', 'DEBUG']
converter.main()
assert False
except SystemExit as e:
assert e.code == 2
except Exception as e:
assert type(e) == SystemExit and e.code == 2
def test_help_works():
import sys
sys.argv = ["bioconvert", "--help"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
sys.argv = ["bioconvert", "-v", "DEBUG", "--help"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
sys.argv = ["bioconvert", "--help", "-v", "DEBUG"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
sys.argv = ["bioconvert", "fastq2fasta", "--help"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
sys.argv = ["bioconvert", "fastq2fasta", "--help", "-v", "DEBUG"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 0
except:
assert False
def compute_job(pk):
job = BioConvertJob.objects.get(pk=pk)
job.status = 2
job.error_message = ""
job.started = timezone.now()
job.save()
try:
os.chdir(job.get_absolute_local_dir())
converter.main(job.command)
job.status = 4
except SystemExit as e:
if e.code == 0:
job.status = 4
else:
job.status = 5
job.error_message = traceback.format_exc()
except Exception as e:
job.status = 5
job.error_message = traceback.format_exc()
job.ended = timezone.now()
job.save()
def test_wrong_verbose():
import sys
sys.argv = ["bioconvert", "--version", "-v" "INFO "]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 2
except:
assert False
import sys
sys.argv = ["bioconvert", "--version", "-v" "TRALALA"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 2
except:
assert False
sys.argv = ["bioconvert", "fastq2fasta", "--show-methods", "-v", "TRALALA"]
try:
converter.main()
assert False
except SystemExit as e:
assert e.code == 2
except:
assert False
def test_converter_no_infile_ext():
try:
sys.argv = ["bioconvert", "test_without_ext", "--input-format", "bam"]
converter.main()
except:
pass