def profile(args):
intervals = [x.strip() for x in args.intervals.split(",")]
datafiles = [x.strip() for x in args.datafiles]
annotation = args.annotation
outfile = args.outfile
colors = parse_colors(args.colors)
for x in args.datafiles:
if '.bam' in x and not os.path.isfile("{0}.bai".format(x)):
print "Data file '{0}' does not have an index file. Creating an index file for {0}.".format(x)
pysam.index(x)
trackgroups = process_groups(args.trackgroups)
if not trackgroups:
trackgroups = [[x] for x in range(1, len(datafiles) + 1)]
scalegroups = process_groups(args.scalegroups)
scale = args.scale
if scale == "auto":
scale = True
elif scale == "off":
scale = False
elif scale:
try:
scale = [int(x) for x in scale.split(",")]
except:
print "Error in scale argument"
sys.exit(1)
if trackgroups and scalegroups:
if len(trackgroups) != sum([len(x) for x in scalegroups]):
sys.stderr.write("Track groups and scales do not match!\n")
sys.exit()
# Group the tracks according to track_groups
tracks = []
for group in trackgroups:
tracks.append([datafiles[i - 1] for i in group])
# Intervals
intervals = [split_interval(x) for x in intervals]
# Create the image
profile_screenshot(outfile, intervals, tracks,
annotation=annotation,
scalegroups=scalegroups,
fontsize=args.textfontsize,
colors=colors,
bgmode=args.background,
fragmentsize=args.fragmentsize,
scale=scale,
rmdup=args.rmdup,
rmrepeats=args.rmrepeats,
reverse=args.reverse
)
def profile(args):
interval = args.interval
datafiles = [x.strip() for x in args.datafiles]
annotation = args.annotation
outfile = args.outfile
colors = parse_colors(args.colors)
for x in args.datafiles:
if '.bam' in x and not os.path.isfile("{0}.bai".format(x)):
print(
"Data file '{0}' does not have an index file. Creating an index file for {0}."
.format(x))
pysam.index(x)
trackgroups = process_groups(args.trackgroups)
if not trackgroups:
trackgroups = [[x] for x in range(1, len(datafiles) + 1)]
scalegroups = process_groups(args.scalegroups)
scale = args.scale
if scale:
try:
scale = [float(x) for x in scale.split(",")]
except Exception:
print("Error in scale argument")
sys.exit(1)
if trackgroups and scalegroups:
if len(trackgroups) != sum([len(x) for x in scalegroups]):
sys.stderr.write("Track groups and scales do not match!\n")
sys.exit()
# Group the tracks according to track_groups
tracks = []
for group in trackgroups:
tracks.append([datafiles[i - 1] for i in group])
# Create the image
profile_screenshot(outfile,
interval,
tracks,
annotation=annotation,
scalegroups=scalegroups,
fontsize=args.textfontsize,
colors=colors,
bgmode=args.background,
fragmentsize=args.fragmentsize,
scale=scale,
show_scale=args.show_scale,
rmdup=args.rmdup,
rmrepeats=args.rmrepeats,
reverse=args.reverse,
adjscale=args.adjscale)
def test_profile(region, bamfile):
tmp = NamedTemporaryFile(suffix=".png")
profile_screenshot(tmp.name, region, [[bamfile]])
def test_profile(region, bamfile):
tmp = NamedTemporaryFile(suffix=".png")
profile_screenshot(tmp.name, region, [[bamfile]])
