def create_graph_from_data(nodes, edges, output_filename):
pygraphviz = import_pygraphviz()
attrs = dict(strict=True, directed=True)
if len(nodes) > 10:
attrs['rankdir'] = 'LR'
graph = pygraphviz.AGraph(**attrs)
# graph.graph_attr['rankdir'] = 'LR' # Orientation left-right
# graph.node_attr['shape'] = 'plaintext'
# graph.node_attr['shape'] = 'record'
# graph.edge_attr['lblstyle'] = 'above, sloped'
for node, attrs in nodes:
graph.add_node(node, **attrs)
# Edges
for from_node, to_node, attrs in edges:
graph.add_edge(from_node, to_node, **attrs)
# Export
graph.write(output_filename + '.dot')
# prog=neato|dot|twopi|circo|fdp|nop
ps_file = output_filename + '.ps'
graph.draw(ps_file, prog='dot')
ps_viewer = get_settings()['ps_viewer']
if ps_viewer:
os.system(f"{ps_viewer} {ps_file}")
def import_bio_entrez():
from Bio import Entrez
# Set email from settings file
from common_utils.file_utils import get_settings
email = get_settings()['email']
if email:
Entrez.email = email
return Entrez
def run(self, step_data):
from .mvista import create_mvista_data
from common_utils.file_utils import get_settings
email = self.args.email or get_settings()['email']
if self.args.run and not email:
raise ZCItoolsValueError(
'Email address is needed to post mVISTA data!')
return create_mvista_data(step_data, self._input_step(), self.args.run,
email)
def get_workflow(self):
settings = get_settings()
if not (wf := settings.get('workflow')):
raise ZCItoolsValueError("Project doesn't have defined workflow!")
def create_circos_correlation(project, step_data, params):
# Read correlation data
cm = None
if params.input_filename:
cm = CorrelationMatrix.from_file(params.input_filename)
if not cm:
raise ZCItoolsValueError('No correlation input data!')
num_c = cm.num_columns()
if num_c < 2:
raise ZCItoolsValueError('Not much of a matrix!')
step = ImagesStep(project, step_data, remove_data=True)
one_width = params.one_width
gap_correlations = params.gap_correlations
ow_2 = one_width // 2
one_plus_gap = one_width + gap_correlations
# Note: column lowercase names are used as column identifiers
data_dir = step.step_file('data')
etc_dir = step.step_file('etc')
ensure_directory(data_dir)
ensure_directory(etc_dir)
colors = dict(
(lc, 'green') for lc in cm._columns_lower) # ToDo: some defaults
colors['plus_'] = 'blue'
colors['minus_'] = 'red'
for col_def in params.group_color:
col_fields = col_def.split(',', 1)
if len(col_fields) == 2 and cm.check_column(col_fields[0]):
colors[cm.check_column(col_fields[0])] = col_fields[1]
else:
print(f"Warning: '{col_def}' is not column color definition!")
# data directory
# karyotype.txt: defines groups (as chromosomes)
# chr - <name> <label> <start> <end> <color>
# ...
gl = (num_c - 1) * one_width + (num_c -
2) * gap_correlations # group length
write_str_in_file(
os.path.join(data_dir, 'karyotype.txt'),
'\n'.join(f"chr - {lc} {c} 0 {gl} color_{lc}"
for lc, c in zip(cm._columns_lower, cm._columns)))
# tiles.txt: defines abs(correlation) == 1 interval, as tiles
# <name> <start> <end> [options]
with open(os.path.join(data_dir, 'tiles.txt'), 'w') as out:
for idx1, c1 in enumerate(cm._columns_lower):
for idx2, c2 in enumerate(cm._columns_lower):
if idx1 == idx2:
continue
pos = (idx1 - idx2 - 1) if idx1 > idx2 else (idx1 - idx2 +
(num_c - 1))
start = pos * one_plus_gap
out.write(
f"{c1} {start} {start + one_width} fill_color=color_{c2}\n"
)
# cells.txt: defines correlations as links
# <cell_idx> <group_1> <start_1> <end_1> color=color_{plus|minus}_,dist={int}
# <cell_idx> <group_2> <start_2> <end_2> color=color_{plus|minus}_,dist={int}
# ...
with open(os.path.join(data_dir, 'links.txt'), 'w') as out:
cell_idx = 0
for idx1, c1 in enumerate(cm._columns_lower):
rest_c = cm._columns_lower[idx1 + 1:]
for idx2, c2 in enumerate(rest_c):
corr = cm.get(c1, c2)
if corr is not None:
w = round(abs(corr) * one_width)
w_1 = w // 2
w_2 = w - w_1 # - 1?
centar = ow_2 + idx2 * one_plus_gap
color = 'plus_' if corr >= 0 else 'minus_'
dist = min(idx2 + 1, idx1 + (len(rest_c) - idx2))
atts = f"color=color_{color},dist={dist}"
out.write(
f"cell_{cell_idx} {c1} {gl - centar - w_2} {gl - centar + w_1} {atts}\n"
)
out.write(
f"cell_{cell_idx} {c2} {centar - w_1} {centar + w_2} {atts}\n"
)
cell_idx += 1
# etc directory
write_str_in_file(
os.path.join(etc_dir, 'circos.conf'),
_circos_conf.format(colors='\n'.join(f"color_{lc} = {c}"
for lc, c in colors.items())))
subprocess.run(['circos', '-conf', 'etc/circos.conf'], cwd=step.directory)
# View it
if params.show_image:
image_viewer = get_settings().get('image_viewer')
if image_viewer:
subprocess.Popen([image_viewer, step.step_file('circos.png')])
def export_chloroplast_list(table_step, output_filename, num_columns):
outgroup = None
if _set := get_settings():
if wp := _set.get('workflow_parameters'):
outgroup = wp.get('outgroup')