def main():
args = docopt(__doc__)
args = BtPlot.check_input(args)
blobdb_f = args['--infile']
rank = args['--rank']
min_length = int(args['--length'])
max_group_plot = int(args['--plotgroups'])
hide_nohits = args['--nohit']
taxrule = args['--taxrule']
c_index = args['--cindex']
exclude_groups = args['--exclude']
labels = args['--label']
colour_f = args['--colours']
refcov_f = args['--refcov']
catcolour_f = args['--catcolour']
multiplot = args['--multiplot']
out_prefix = args['--out']
sort_order = args['--sort']
sort_first = args['--sort_first']
hist_type = args['--hist']
no_title = args['--notitle']
ignore_contig_length = args['--noscale']
format_plot = args['--format']
no_plot_blobs = args['--noblobs']
no_plot_reads = args['--noreads']
legend_flag = args['--legend']
cumulative_flag = args['--cumulative']
cov_lib_selection = args['--lib']
filelabel = args['--filelabel']
exclude_groups = BtIO.parseCmdlist(exclude_groups)
refcov_dict = BtIO.parseReferenceCov(refcov_f)
user_labels = BtIO.parseCmdLabels(labels)
catcolour_dict = BtIO.parseCatColour(catcolour_f)
colour_dict = BtIO.parseColours(colour_f)
# Load BlobDb
print BtLog.status_d['9'] % blobdb_f
blobDb = BtCore.BlobDb('blobplot')
blobDb.version = blobtools.__version__
blobDb.load(blobdb_f)
# Generate plot data
print BtLog.status_d['18']
data_dict, min_cov, max_cov, cov_lib_dict = blobDb.getPlotData(
rank, min_length, hide_nohits, taxrule, c_index, catcolour_dict)
plotObj = BtPlot.PlotObj(data_dict, cov_lib_dict, cov_lib_selection,
'blobplot', sort_first)
plotObj.exclude_groups = exclude_groups
plotObj.version = blobDb.version
plotObj.format = format_plot
plotObj.max_cov = max_cov
plotObj.min_cov = min_cov
plotObj.no_title = no_title
plotObj.multiplot = multiplot
plotObj.hist_type = hist_type
plotObj.ignore_contig_length = ignore_contig_length
plotObj.max_group_plot = max_group_plot
plotObj.legend_flag = legend_flag
plotObj.cumulative_flag = cumulative_flag
# order by which to plot (should know about user label)
plotObj.group_order = BtPlot.getSortedGroups(data_dict, sort_order,
sort_first)
# labels for each level of stats
plotObj.labels.update(plotObj.group_order)
# plotObj.group_labels is dict that contains labels for each group : all/other/user_label
if (user_labels):
for group, label in user_labels.items():
plotObj.labels.add(label)
plotObj.group_labels = {group: set() for group in plotObj.group_order}
plotObj.relabel_and_colour(colour_dict, user_labels)
plotObj.compute_stats()
plotObj.refcov_dict = refcov_dict
# Plotting
info_flag = 1
out_f = ''
for cov_lib in plotObj.cov_libs:
plotObj.ylabel = "Coverage"
plotObj.xlabel = "GC proportion"
if (filelabel):
plotObj.ylabel = basename(cov_lib_dict[cov_lib]['f'])
out_f = "%s.%s.%s.p%s.%s.%s" % (blobDb.title, taxrule, rank,
max_group_plot, hist_type, min_length)
if catcolour_dict:
out_f = "%s.%s" % (out_f, "catcolour")
if ignore_contig_length:
out_f = "%s.%s" % (out_f, "noscale")
if c_index:
out_f = "%s.%s" % (out_f, "c_index")
if exclude_groups:
out_f = "%s.%s" % (out_f, "exclude_" + "_".join(exclude_groups))
if labels:
out_f = "%s.%s" % (out_f, "userlabel_" + "_".join(
set([name for name in user_labels.values()])))
out_f = "%s.%s" % (out_f, "blobplot")
if (plotObj.cumulative_flag):
out_f = "%s.%s" % (out_f, "cumulative")
if (plotObj.multiplot):
out_f = "%s.%s" % (out_f, "multiplot")
out_f = BtIO.getOutFile(out_f, out_prefix, None)
if not (no_plot_blobs):
plotObj.plotScatter(cov_lib, info_flag, out_f)
info_flag = 0
if not (no_plot_reads) and (
plotObj.cov_libs_total_reads_dict[cov_lib]):
# prevent plotting if --noreads or total_reads == 0
plotObj.plotBar(cov_lib, out_f)
plotObj.write_stats(out_f)
if rank not in RANKS:
BtLog.error('9', rank)
# Are sort_order and hist_type sane?
if not sort_order in ['span', 'count']:
BtLog.error('14', sort_order)
if not hist_type in ['span', 'count']:
BtLog.error('15', hist_type)
# is taxrule provided?
if taxrule not in TAXRULES:
BtLog.error('8', taxrule)
# compute labels if supplied
user_labels = BtPlot.parse_labels(labels)
if (exclude_groups):
if "," in exclude_groups:
exclude_groups = exclude_groups.rsplit(",")
else:
exclude_groups = exclude_groups
refcov_dict = {}
if (refcov_f):
refcov_dict = BtPlot.parseRefCov(refcov_f)
catcolour_dict = {}
if (catcolour_f) and (c_index):
BtLog.error('24')
elif (catcolour_f):
for name in readFasta(infile):
fasta_order.append(name)
fasta_dict[name] = 0.0
return fasta_dict, fasta_order
if __name__ == '__main__':
main_dir = dirname(__file__)
#print data_dir
args = docopt(__doc__)
assembly_f = args['--infile']
cov_fs = args['--cov']
fasta_dict = {}
fasta_order = []
if not isfile(assembly_f):
BtLog.error('0', assembly_f)
else:
fasta_dict, fasta_order = parseFasta(assembly_f)
for cov_f in cov_fs:
if not isfile(cov_f):
BtLog.error('0', cov_f)
else:
lib_cov_dict = BtPlot.parseCovFile(cov_f)
for name in fasta_order:
fasta_dict[name] = fasta_dict.get(name, 0.0) + lib_cov_dict[name]
for name in fasta_order:
print "%s\t%s" % (name, fasta_dict[name])
#exclude_groups = args['--exclude']
format = args['--format']
#no_plot_blobs = args['--noblobs']
#no_plot_reads = args['--noreads']
#refcov_f = args['--refcov']
#catcolour_f = args['--catcolour']
# Does blobdb_f exist ?
if not isfile(blobdb_f):
BtLog.error('0', blobdb_f)
# Does cov_f exist ?
if not isfile(cov_f):
BtLog.error('0', cov_f)
# parse cov file in dict
cov_dict = BtPlot.parseCovFile(cov_f)
# Are ranks sane ?
if rank not in RANKS:
BtLog.error('9', rank)
# Are sort_order and hist_type sane?
if not sort_order in ['span', 'count']:
BtLog.error('14', sort_order)
if not hist_type in ['span', 'count']:
BtLog.error('15', hist_type)
# is taxrule provided?
if taxrule not in TAXRULES:
BtLog.error('8', taxrule)
fasta_order.append(name)
fasta_dict[name] = 0.0
return fasta_dict, fasta_order
if __name__ == '__main__':
main_dir = dirname(__file__)
#print data_dir
args = docopt(__doc__)
assembly_f = args['--infile']
cov_fs = args['--cov']
fasta_dict = {}
fasta_order = []
if not isfile(assembly_f):
BtLog.error('0', assembly_f)
else:
fasta_dict, fasta_order = parseFasta(assembly_f)
for cov_f in cov_fs:
if not isfile(cov_f):
BtLog.error('0', cov_f)
else:
lib_cov_dict = BtPlot.parseCovFile(cov_f)
for name in fasta_order:
fasta_dict[name] = fasta_dict.get(name,
0.0) + lib_cov_dict[name]
for name in fasta_order:
print "%s\t%s" % (name, fasta_dict[name])
if rank not in RANKS:
BtLog.error('9', rank)
# Are sort_order and hist_type sane?
if not sort_order in ['span', 'count']:
BtLog.error('14', sort_order)
if not hist_type in ['span', 'count']:
BtLog.error('15', hist_type)
# is taxrule provided?
if taxrule not in TAXRULES:
BtLog.error('8', taxrule)
# compute labels if supplied
user_labels = BtPlot.parse_labels(labels)
if (exclude_groups):
if "," in exclude_groups:
exclude_groups = exclude_groups.rsplit(",")
else:
exclude_groups = exclude_groups
refcov_dict = {}
if (refcov_f):
refcov_dict = BtPlot.parseRefCov(refcov_f)
catcolour_dict = {}
if (catcolour_f) and (c_index):
BtLog.error('24')
elif (catcolour_f):
#exclude_groups = args['--exclude']
format = args['--format']
#no_plot_blobs = args['--noblobs']
#no_plot_reads = args['--noreads']
#refcov_f = args['--refcov']
#catcolour_f = args['--catcolour']
# Does blobdb_f exist ?
if not isfile(blobdb_f):
BtLog.error('0', blobdb_f)
# Does cov_f exist ?
if not isfile(cov_f):
BtLog.error('0', cov_f)
# parse cov file in dict
cov_dict = BtPlot.parseCovFile(cov_f)
# Are ranks sane ?
if rank not in RANKS:
BtLog.error('9', rank)
# Are sort_order and hist_type sane?
if not sort_order in ['span', 'count']:
BtLog.error('14', sort_order)
if not hist_type in ['span', 'count']:
BtLog.error('15', hist_type)
# is taxrule provided?
if taxrule not in TAXRULES:
BtLog.error('8', taxrule)
