def listsamples(methods=['POST', 'GET']):
# If a single file, jump right to the view for that file
BAM = current_app.config['BAM']
BAMDIR = current_app.config['BAMDIR']
if BAM:
if not os.path.exists(BAM) or not pybamview.CheckBam(BAM):
return render_template("error.html",
message="%s not a valid BAM file" % BAM)
try:
samplesToBam = pybamview.GetSamplesFromBamFiles(
[os.path.abspath(BAM)])
except ValueError, e:
return render_template("error.html",
message="Problem parsing BAM file: %s" % e,
title="PyBamView - %s" % BAM)
if not os.path.exists(BAM + ".bai"):
return render_template("error.html",
message="No index found for %s" % BAM)
if len(samplesToBam.keys()) == 0:
return render_template("error.html",
message="No samples found in BAM file",
title="PyBamView - %s" % BAM)
argstring = "&".join([
"samplebams=%s:%s" % (sample, os.path.abspath(BAM))
for sample in samplesToBam
])
return redirect(url_for("display_bam") + "?" + argstring)
argstring = "&".join(["samplebams=%s:%s"%(sample, os.path.abspath(BAM)) for sample in samplesToBam])
return redirect(url_for(".display_bam")+"?"+argstring)
# If given a directory to look for bams, determine which samples are present
else:
bamfiles = request.args.getlist("bamfiles")
samples = request.args.getlist("samples")
if len(bamfiles) > 0 and len(samples) > 0:
return display_bam(samples)
try:
files = os.listdir(BAMDIR)
except OSError: files = []
bamfiles = [f for f in files if re.match(".*.bam$", f) is not None]
bamfiles = [f for f in bamfiles if ((f+".bai") in files or \
f.replace(".bam",".bai") in files)]
try:
samplesToBam = pybamview.GetSamplesFromBamFiles([os.path.join(os.path.abspath(BAMDIR), b) for b in bamfiles])
except ValueError, e:
return render_template("error.html", message="Problem parsing BAM file: %s"%e, title="PyBamView - %s"%BAMDIR)
return render_template("index.html", samplesToBam=samplesToBam, title="PyBamView - %s"%BAMDIR)
@blueprint.route('/bamview', methods=['POST', 'GET'])
def display_bam():
samplebams = request.args.getlist("samplebams")
zoomlevel = request.args.get("zoomlevel")
if len(samplebams) == 0:
samples_toinclude = list(set(request.args.getlist("samples")))
bamfiles_toinclude = list(set(request.args.getlist("bamfiles")))
else:
samples_toinclude = []
bamfiles_toinclude = []
for s in samplebams: