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", "#")