def _read_bam(bam_fn, precursors):
if bam_fn.endswith("bam") or bam_fn.endswith("sam"):
logger.info("Reading %s" % bam_fn)
reads = read_bam(bam_fn, precursors)
else:
raise ValueError("Format not recognized. Only working with BAM/SAM files.")
return reads
def _read_bam(bam_fn, precursors):
if bam_fn.endswith("bam") or bam_fn.endswith("sam"):
logger.info("Reading %s" % bam_fn)
reads = read_bam(bam_fn, precursors)
else:
raise ValueError("Format not recognized."
" Only working with BAM/SAM files.")
return reads
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 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", "#")