def test_collapse(self):
"""testing GFF function"""
from mirtop.libs import logger
from mirtop.mirna import mapper, fasta
from mirtop.gff import body, header
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
precursors = fasta.read_precursor("data/examples/annotate/hairpin.fa",
"hsa")
# depend on https://github.com/miRTop/mirtop/issues/6
matures = mapper.read_gtf_to_precursor(
"data/examples/annotate/hsa.gff3")
# matures = mirtop.mirna.read_mature("data/examples/annotate/mirnas.gff", "hsa")
from mirtop.bam import bam
bam_fn = "data/aligments/collapsing-isomirs.sam"
reads = bam.read_bam(bam_fn, precursors)
ann = bam.annotate(reads, matures, precursors)
fn = bam_fn + ".gff"
h = header.create(bam_fn, ["example"], "miRBase21")
gff = body.create(ann, "miRBase21", "example", fn, header)
print gff
return True
def reader(args):
"""
Realign BAM hits to miRBAse to get better accuracy and annotation
"""
database = mapper.guess_database(args.gtf)
# hairpin, mirna = download_mirbase(args)
precursors = fasta.read_precursor(args.hairpin, args.sps)
matures = mapper.read_gtf_to_precursor(args.gtf)
# check numnbers of miRNA and precursors read
# print message if numbers mismatch
out_dts = dict()
for fn in args.files:
sample = op.splitext(op.basename(fn))[0]
fn_out = op.join(args.out, sample + ".gff")
if args.format == "BAM":
reads = _read_bam(fn, precursors)
elif args.format == "seqbuster":
reads = seqbuster.read_file(fn, precursors)
custom = seqbuster.header()
elif args.format == "srnabench":
reads = srnabench.read_gile(fn, precursors)
h = header.create([sample], database, "")
ann = annotate(reads, matures, precursors)
out_dts[fn] = body.create(ann, database, sample, fn_out, h)
def annotate(fn, precursors, matures):
from mirtop.bam import bam
from mirtop.gff import body
reads = bam.read_bam(fn, precursors)
ann = bam.annotate(reads, matures, precursors)
gff = body.create(ann, "miRBase21", "example", fn + ".gff3", "#")
def annotate(fn, precursors, matures):
from mirtop.importer import srnabench
from mirtop.bam import bam
reads = srnabench.read_file(fn, precursors)
ann = bam.annotate(reads, matures, precursors)
return True
def annotate(fn, precursors, matures):
from mirtop.importer import seqbuster
from mirtop.bam import bam
reads = seqbuster.read_file(fn, precursors)
ann = bam.annotate(reads, matures, precursors)
return True