def test_srnabench(self):
"""testing reading seqbuster files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import srnabench
annotate("data/examples/srnabench", srnabench.read_file, create=False)
def test_srnabench(self):
"""testing reading seqbuster files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import srnabench
annotate("data/examples/srnabench", srnabench.read_file, create=False)
def test_collapse(self):
"""testing GFF function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.bam import bam
bam_fn = "data/aligments/collapsing-isomirs.sam"
annotate(bam_fn, bam.read_bam)
return True
def test_collapse(self):
"""testing GFF function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.bam import bam
bam_fn = "data/aligments/collapsing-isomirs.sam"
annotate(bam_fn, bam.read_bam)
return True
def test_optimir(self):
"""testing reading optimir files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import optimir
annotate("data/examples/optimir/synthetic_100_full.gff3",
optimir.read_file,
create=False)
def test_seqbuster(self):
"""testing reading seqbuster files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import seqbuster
print("\nperfect\n")
annotate("data/examples/seqbuster/reads20.mirna", seqbuster.read_file)
print("\naddition\n")
annotate("data/examples/seqbuster/readsAdd.mirna", seqbuster.read_file)
def test_seqbuster(self):
"""testing reading seqbuster files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import seqbuster
print("\nperfect\n")
annotate("data/examples/seqbuster/reads20.mirna", seqbuster.read_file)
print("\naddition\n")
annotate("data/examples/seqbuster/readsAdd.mirna", seqbuster.read_file)
def test_prost(self):
"""testing reading prost files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.mirna import fasta
precursors = fasta.read_precursor("data/examples/annotate/hairpin.fa",
"hsa")
fn = "data/examples/prost/prost.example.txt"
from mirtop.importer import prost
reads = prost.read_file(fn, precursors, "miRBasev21",
"data/examples/annotate/hsa.gff3")
annotate("data/example/prost/prost.example.txt", reads, True)
def test_prost(self):
"""testing reading prost files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.mirna import fasta
precursors = fasta.read_precursor("data/examples/annotate/hairpin.fa",
"hsa")
fn = "data/examples/prost/prost.example.txt"
from mirtop.importer import prost
reads = prost.read_file(
fn, precursors, "miRBasev21", "data/examples/annotate/hsa.gff3")
annotate("data/example/prost/prost.example.txt", reads, True)
def test_alignment(self):
"""testing alignments function"""
from mirtop.bam import bam
from mirtop.gff.classgff import feature
fns = {
"let7-last1D.sam": {
56: "iso_add3p:1,iso_snv"
},
"let7-1D.sam": {
5: "iso_snv,iso_3p:-5"
},
"let7-last7M1I.sam": {
5: "iso_add3p:1,iso_snv_seed"
},
"let7-middle1D.sam": {
5: "iso_snv_central_supp,iso_3p:-2"
},
"let7-perfect.sam": {
5: "NA"
},
"let7-triming.sam": {
5: "iso_3p:+2",
4: "iso_5p:-1",
6: "iso_5p:+1,iso_3p:-3"
}
}
#import pdb; pdb.set_trace()
for fn in fns:
gff = annotate("data/aligments/%s" % fn, bam.read_bam)
for pos in gff['hsa-let-7a-1']:
f = feature(gff['hsa-let-7a-1'][pos][0][4])
if not set(f.attributes['Variant'].split(",")) == set(
fns[fn][pos].split(",")):
raise ValueError("Error in %s" % fn)
def test_keep_name(self):
from mirtop.bam import bam
line = annotate("data/aligments/let7-perfect.sam",
bam.read_bam,
keep_name=True)
print(line)
if line["hsa-let-7a-1"][5][0][4].find("seq_perfect_x2") < 0:
raise ValueError("Keep name failed: %s" % line)
def test_alignment(self):
"""testing alignments function"""
from mirtop.bam import bam
print("\nlast1D\n")
print(annotate("data/aligments/let7-last1D.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq AGAGGTAGTAGGTTGTA
print("\n1D\n")
print(annotate("data/aligments/let7-1D.sam", bam.read_bam))
# mirna TGAGGTAG-TAGGTTGTATAGTT
# seq TGAGGTAGGTAGGTTGTATAGTTA
print("\nlast7M1I\n")
print(annotate("data/aligments/let7-last7M1I.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq TGAGGTAGTAGGTTGTA-AGT
print("\nmiddle1D\n")
print(annotate("data/aligments/let7-middle1D.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq TGAGGTAGTAGGTTGTATAGTT
print("\nperfect\n")
print(annotate("data/aligments/let7-perfect.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq TGAGGTAGTAGGTTGTATAG (3tt 3TT)
print("\ntriming\n")
print(annotate("data/aligments/let7-triming.sam", bam.read_bam))
def test_alignment(self):
"""testing alignments function"""
from mirtop.bam import bam
print("\nlast1D\n")
print(annotate("data/aligments/let7-last1D.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq AGAGGTAGTAGGTTGTA
print("\n1D\n")
print(annotate("data/aligments/let7-1D.sam", bam.read_bam))
# mirna TGAGGTAG-TAGGTTGTATAGTT
# seq TGAGGTAGGTAGGTTGTATAGTTA
print("\nlast7M1I\n")
print(annotate("data/aligments/let7-last7M1I.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq TGAGGTAGTAGGTTGTA-AGT
print("\nmiddle1D\n")
print(annotate("data/aligments/let7-middle1D.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq TGAGGTAGTAGGTTGTATAGTT
print("\nperfect\n")
print(annotate("data/aligments/let7-perfect.sam", bam.read_bam))
# mirna TGAGGTAGTAGGTTGTATAGTT
# seq TGAGGTAGTAGGTTGTATAG (3tt 3TT)
print("\ntriming\n")
print(annotate("data/aligments/let7-triming.sam", bam.read_bam))
def test_alignment_genomic(self):
"""testing alignments function"""
from mirtop.bam import bam
from mirtop.libs import logger
logger.initialize_logger("test_read_files", True, True)
# print(annotate("data/examples/annotate/hsa-let-7a-5ploss1_neg.sam",
# bam.read_bam,
# gtf="data/db/hsa.gff3", genomic=True))
print("\ngenomic\n")
with make_workdir():
for example in [
"hsa-let-7a-nm", "hsa-let-7a-5ploss1",
"hsa-let-7a-3ploss1", "hsa-let-7a-5ploss1_neg"
]:
print(
annotate("data/examples/annotate/%s.sam" % example,
bam.read_bam,
gtf="data/db/mirbase/hsa.gff3",
genomic=True))