def run_qc(gid,
uid,
r1,
r2=None,
adapter=None,
contaminants=None,
exclude=[],
kmers=8,
out_dir=".",
threads=1):
"""Creates output directory tree, handles JSON creation and updating when running QC, and
executes FastQC.
Args:
gid (str): group, batch, or experiment ID
uid (str): unique ID to this group, e.g. run ID or sample ID
r1 (str): file path to R1 FASTQ file
r2 (Optional[str]): file path to R2 FASTQ file
adapter (Optional[str]): file path to optional adapters FASTA
contaminants (Optional[str]): file path to optional contaminants FASTA
exclude (Optional[list]): tab name list to exclude from JSON
kmers (Optional[int]): the length of kmer for which to look
out_dir (Optional[str]): parent directory of server; holds 'plot_data' and child folders
threads (Optional[str]): number of threads to use
"""
qc_obj = Fastqc(gid, uid, r1, r2=r2, out_dir=out_dir)
logging.info("Running FastQC")
# executes fastqc and writes data tables
qc_obj.run(adapter=adapter,
contaminants=contaminants,
kmers=kmers,
threads=threads)
# exclude user requested tabs
tabs = []
for filename, web_tab in qc_obj.tabs.items():
if exclude and web_tab.tab_name in exclude:
logging.info("Omitting tab '%s'" % web_tab.tab_name)
else:
tabs.append(web_tab.to_dict())
# writes config for this uid
with open(os.path.join(qc_obj.out_dir, "config.json"), 'w') as fh:
print(json.dumps(tabs, indent=4), file=fh)
# update groups json
group_config = os.path.join(
qc_obj.out_dir.partition(gid)[0], "groups.json")
logging.debug("Updating Group config: %s" % group_config)
group_data = import_json(group_config)
# if existing group
if gid in [i['group_id'] for i in group_data]:
for i in range(len(group_data)):
if group_data[i]['group_id'] == gid:
if uid not in group_data[i]['uids']:
# update UID list
insort_left(group_data[i]['uids'], uid)
else:
group_data.insert(0, {'group_id': gid, 'uids': [uid]})
with open(group_config, 'w') as fh:
print(json.dumps(group_data, indent=4, sort_keys=True), file=fh)
logging.info("Processing of %s complete" % uid)
def run_add(config,
name,
plot_type,
csv,
prepend=False,
status=None,
x_value=None,
y_value=None,
x_label=None,
y_label=None,
subtitle=None,
lower_quartile=None,
upper_quartile=None,
mean=None,
value=None,
label=None,
colors=None,
step=10,
min_value=None,
min_color=None,
mid_color=None,
max_value=None,
max_color=None):
"""Copies the CSV into the directory containing the config file if it does not already exist
there, then either appends an appropriate entry onto the existing config JSON or creates a new
file.
Args:
config (str): file path to config.json
name (str): name being used in the tab on the dashboard
plot_type (str): type of chart being created
csv (str): file path to data file being added to dashboard
prepend (Optional[bool]): add new plot as first tab in dashboard
status (Optional[str]): image icon to be displayed on tab [None, 'warn', 'pass', 'fail']
x_value (Optional[str]): header label in CSV containing the x-values
y_value (Optional[str]): header label in CSV containing the y-values
x_label (Optional[str]): x-label to be drawn on dashboard; defaults to `x_value`
y_label (Optional[str]): y-label to be drawn on dashboard; defaults to `y_value`
subtitle (Optional[str]): subtitle to be drawn on dashboard
lower_quartile (Optional[str]): arearange specific option; header label in CSV for lower
quartile value
upper_quartile (Optional[str]): arearange specific option; header label in CSV for upper
quartile value
mean (Optional[str]): arearange specific option; header label in CSV for mean value
value (Optional[str]): value label in CSV to be plotted in heatmap
label (Optional[str]): optional heatmap label header to mark individual coordinates
colors (Optional[str]): optional color definitions for observable labels
step (Optional[int]): histogram step
min_value (Optional[int]): optional heatmap minimum value threshold for color map
min_color (Optional[str]): optional heatmap minimum color
mid_color (Optional[str]): optional heatmap mid color for color map
max_value (Optional[int]): optional heatmap maximum value threshold for color map
max_color (Optional[str]): optional heatmap maximum color
"""
filename = add_csv_input(csv, os.path.dirname(config))
if colors:
# '(-)CTRL:#1f77b4,(+)CTRL:#d62728'
try:
colors_dict = dict([i.split(":") for i in colors.split(",")])
except ValueError:
logging.warning("Unable to parse colors (%s) in key:value pairs" %
colors)
colors_dict = None
colors = colors_dict
web_tab = WebTab(
filename, name, status,
ChartProperties(plot_type,
subtitle,
x_label,
x_value,
y_label,
y_value,
lower_quartile,
upper_quartile,
mean,
value,
label,
minimum=min_value,
maximum=max_value,
min_color=min_color,
mid_color=mid_color,
max_color=max_color,
colors=colors,
step=step))
# append onto configuration file
if os.path.exists(config):
shutil.copy(config, config + '.bak')
logging.info("Saving backup: %s" % config + '.bak')
tab_data = import_json(config)
if prepend:
tab_data.insert(0, web_tab.to_dict())
else:
tab_data.append(web_tab.to_dict())
try:
with open(config, 'w') as fh:
print(json.dumps(tab_data, indent=4), file=fh)
except Exception:
shutil.move(config + '.bak', config)
logging.exception("The backup config has been restored.")
raise
# create new
else:
with open(config, 'w') as fh:
print(json.dumps([entry], indent=4), file=fh)
logging.info("Added entry into %s\n%s" %
(config, json.dumps(web_tab.to_dict(), indent=4)))