def parse_plot_settings(settings_filename, event=None, chrom=None,
# Float parameters
FLOAT_PARAMS=["intron_scale",
"exon_scale",
"ymax",
"resolution",
"fig_width",
"fig_height",
"font_size",
"junction_log_base"],
# Integer parameters
INT_PARAMS=["posterior_bins",
"gene_posterior_ratio",
"insert_len_bins",
"nyticks",
"nxticks"],
# Boolean parameters
BOOL_PARAMS=["logged",
"show_posteriors",
"number_junctions",
"reverse_minus",
"bar_posteriors",
"show_ylabel",
"show_xlabel",
"sans_serif"],
# Parameters to be interpreted as Python lists or
# data structures
DATA_PARAMS=["miso_files",
"bam_files",
"bf_thresholds",
"bar_color",
"sample_labels"],
no_posteriors=False):
"""
Populate a settings dictionary with the plotting parameters, parsed
as the right datatype.
"""
settings = get_default_settings()
config = ConfigParser.ConfigParser()
#print "Reading settings from: %s" %(settings_filename)
config.read(settings_filename)
for section in config.sections():
for option in config.options(section):
#print "Parsing %s:%s" %(section, option)
if option in FLOAT_PARAMS:
settings[option] = config.getfloat(section, option)
elif option in INT_PARAMS:
settings[option] = config.getint(section, option)
elif option in BOOL_PARAMS:
settings[option] = config.getboolean(section, option)
elif option in DATA_PARAMS:
settings[option] = ast.literal_eval(config.get(section,
option))
else:
settings[option] = config.get(section, option)
# Ensure that bf_thresholds are integers
settings["bf_thresholds"] = [int(t) for t in settings["bf_thresholds"]]
if "colors" in settings:
colors = ast.literal_eval(settings["colors"])
else:
colors = [None for x in settings["bam_files"]]
settings["colors"] = colors
if "bam_prefix" in settings:
bam_files = [os.path.join(settings["bam_prefix"], x) \
for x in settings["bam_files"]]
else:
bam_files = settings["bam_files"]
settings["bam_files"] = bam_files
# Make the sample labels be the BAM files by default
if "sample_labels" not in settings:
settings["sample_labels"] = [os.path.basename(bfile) \
for bfile in settings["bam_files"]]
num_labels = len(settings["sample_labels"])
num_bams = len(settings["bam_files"])
num_colors = len(settings["colors"])
if not (num_labels == num_bams == num_colors):
print "Error: Must provide sample label and color for each entry in bam_files!"
print " - Provided %d labels, %d BAMs, %d colors" \
%(num_labels, num_bams, num_colors)
sys.exit(1)
if no_posteriors:
settings["show_posteriors"] = False
if ("miso_prefix" in settings) and (event != None and chrom != None) \
and settings["show_posteriors"]:
miso_files = miso_utils.get_miso_output_files(event, chrom, settings)
elif "miso_files" in settings:
miso_files = settings["miso_files"]
else:
miso_files = []
settings["miso_files"] = miso_files
if "coverages" in settings:
coverages = ast.literal_eval(settings["coverages"])
coverages = map(float, coverages)
# Normalize coverages per M
coverages = [x / 1e6 for x in coverages]
else:
coverages = [1 for x in settings["bam_files"]]
settings["coverages"] = coverages
if len(settings["coverages"]) != len(settings["sample_labels"]):
print "Error: Must provide a coverage value for each sample or leave coverages unset."
sys.exit(1)
return settings
def parse_plot_settings(
settings_filename,
event=None,
chrom=None,
# Float parameters
FLOAT_PARAMS=[
"intron_scale",
"exon_scale",
"ymax",
"resolution",
"fig_width",
"fig_height",
"font_size",
"junction_log_base",
"min_counts",
],
# Integer parameters
INT_PARAMS=[
"posterior_bins", "gene_posterior_ratio", "insert_len_bins",
"nyticks", "nxticks"
],
# Boolean parameters
BOOL_PARAMS=[
"logged", "show_posteriors", "reverse_minus", "bar_posteriors",
"show_ylabel", "show_xlabel", "number_junctions", "sans_serif",
"text_background", "group_info"
],
# Parameters to be interpreted as Python lists or
# data structures
DATA_PARAMS=[
"miso_files", "bam_files", "bf_thresholds", "bar_color",
"sample_labels"
],
no_posteriors=False):
"""
Populate a settings dictionary with the plotting parameters, parsed
as the right datatype.
"""
settings = get_default_settings()
config = ConfigParser.ConfigParser()
print "Reading settings from: %s" % (settings_filename)
config.read(settings_filename)
for section in config.sections():
for option in config.options(section):
print "Parsing %s:%s" % (section, option)
if option in FLOAT_PARAMS:
settings[option] = config.getfloat(section, option)
elif option in INT_PARAMS:
settings[option] = config.getint(section, option)
elif option in BOOL_PARAMS:
settings[option] = config.getboolean(section, option)
elif option in DATA_PARAMS:
settings[option] = ast.literal_eval(config.get(
section, option))
else:
settings[option] = config.get(section, option)
# Ensure that bf_thresholds are integers
settings["bf_thresholds"] = [int(t) for t in settings["bf_thresholds"]]
if "colors" in settings:
colors = ast.literal_eval(settings["colors"])
else:
colors = [None for x in settings["bam_files"]]
settings["colors"] = colors
if "bam_prefix" in settings:
bam_files = [os.path.join(settings["bam_prefix"], x) \
for x in settings["bam_files"]]
else:
bam_files = settings["bam_files"]
settings["bam_files"] = bam_files
# Make the sample labels be the BAM files by default
if "sample_labels" not in settings:
settings["sample_labels"] = [os.path.basename(bfile) \
for bfile in settings["bam_files"]]
num_labels = len(settings["sample_labels"])
num_bams = len(settings["bam_files"])
num_colors = len(settings["colors"])
if not (num_labels == num_bams ==
num_colors) and not (settings["group_info"]):
print('\033[0;31;m') # change the print color as red
print "Error: Must provide sample label and color for each entry in bam_files!"
print " - Provided %d labels, %d BAMs, %d colors" \
%(num_labels, num_bams, num_colors)
print('\033[0m') # set the color as default value
sys.exit(1)
if no_posteriors:
settings["show_posteriors"] = False
if ("miso_prefix" in settings) and (event != None and chrom != None) \
and settings["show_posteriors"]:
miso_files = miso_utils.get_miso_output_files(event, chrom, settings)
elif "miso_files" in settings:
miso_files = settings["miso_files"]
else:
miso_files = []
settings["miso_files"] = miso_files
if "coverages" in settings:
coverages = ast.literal_eval(settings["coverages"])
coverages = map(float, coverages)
# Normalize coverages per M
coverages = [x / 1e6 for x in coverages]
else:
coverages = [1 for x in settings["bam_files"]]
settings["coverages"] = coverages
if len(settings["coverages"]) != len(settings["sample_labels"]):
print('\033[0;31;m') # change the print color as red
print "Error: Must provide a coverage value for each sample or leave coverages unset."
print('\033[0m') # set the color as default value
sys.exit(1)
return settings
def parse_plot_settings(
settings_filename,
event=None,
chrom=None,
# Float parameters
FLOAT_PARAMS=[
"intron_scale", "exon_scale", "ymax", "resolution", "fig_width",
"fig_height", "font_size", "junction_log_base"
],
# Integer parameters
INT_PARAMS=[
"posterior_bins", "gene_posterior_ratio", "insert_len_bins",
"nyticks", "nxticks"
],
# Boolean parameters
BOOL_PARAMS=[
"logged", "show_posteriors", "number_junctions", "reverse_minus",
"bar_posteriors", "show_ylabel", "show_xlabel", "sans_serif"
],
# Parameters to be interpreted as Python lists or
# data structures
DATA_PARAMS=[
"miso_files", "bam_files", "bf_thresholds", "bar_color",
"sample_labels", "event_title"
],
no_posteriors=False):
"""
Populate a settings dictionary with the plotting parameters, parsed
as the right datatype.
"""
settings = get_default_settings()
config = ConfigParser.ConfigParser()
print "Reading settings from: %s" % (settings_filename)
config.read(settings_filename)
for section in config.sections():
for option in config.options(section):
print "Parsing %s:%s" % (section, option)
if option in FLOAT_PARAMS:
settings[option] = config.getfloat(section, option)
elif option in INT_PARAMS:
settings[option] = config.getint(section, option)
elif option in BOOL_PARAMS:
settings[option] = config.getboolean(section, option)
elif option in DATA_PARAMS:
settings[option] = ast.literal_eval(config.get(
section, option))
else:
settings[option] = config.get(section, option)
if "event_title" not in settings:
settings["event_title"] = None
# Ensure that bf_thresholds are integers
settings["bf_thresholds"] = [int(t) for t in settings["bf_thresholds"]]
if "colors" in settings:
colors = ast.literal_eval(settings["colors"])
else:
colors = [None for x in settings["bam_files"]]
settings["colors"] = colors
if "bam_prefix" in settings:
bam_files = [os.path.join(settings["bam_prefix"], x) \
for x in settings["bam_files"]]
else:
bam_files = settings["bam_files"]
settings["bam_files"] = bam_files
# Make the sample labels be the BAM files by default
if "sample_labels" not in settings:
settings["sample_labels"] = [os.path.basename(bfile) \
for bfile in settings["bam_files"]]
num_labels = len(settings["sample_labels"])
num_bams = len(settings["bam_files"])
num_colors = len(settings["colors"])
if not (num_labels == num_bams == num_colors):
print "Error: Must provide sample label and color for each entry in bam_files!"
print " - Provided %d labels, %d BAMs, %d colors" \
%(num_labels, num_bams, num_colors)
sys.exit(1)
if no_posteriors:
settings["show_posteriors"] = False
if ("miso_prefix" in settings) and (event != None and chrom != None) \
and settings["show_posteriors"]:
if [".h5", ".gz"].count(settings["miso_files"][0][-3:]) == 1:
miso_files = [
settings["miso_prefix"] + x for x in settings["miso_files"]
]
else:
miso_files = miso_utils.get_miso_output_files(
event, chrom, settings)
elif "miso_files" in settings:
miso_files = settings["miso_files"]
else:
miso_files = []
settings["miso_files"] = miso_files
# print settings["miso_files"]
# exit()
if "coverages" in settings:
coverages = ast.literal_eval(settings["coverages"])
coverages = map(float, coverages)
# Normalize coverages per M
coverages = [x / 1e6 for x in coverages]
else:
# coverages = [1 for x in settings["bam_files"]]
coverages = []
for _bam in settings["bam_files"]:
#print(_bam)
coverage = 0
pysam_stats = pysam.idxstats(_bam)
#print(pysam_stats)
if type(pysam_stats) is not list:
pysam_stats = pysam_stats.split("\n")
for tp in pysam_stats:
tmp = tp.strip().split("\t")
if len(tmp) >= 3:
coverage += float(tp.strip().split("\t")[2])
coverage = (coverage + 1.0) / float(10**6)
coverages.append(coverage)
# coverages = [x / np.mean(coverages) for x in coverages]
settings["coverages"] = coverages
if len(settings["coverages"]) != len(settings["sample_labels"]):
print "Error: Must provide a coverage value for each sample or leave coverages unset."
sys.exit(1)
return settings