def list_features(self):
"""Print ASCII table with all features.
Examples
--------
>>> from Bio.Seq import Seq
>>> from pydna.seqrecord import SeqRecord
>>> a=SeqRecord(Seq("atgtaa"))
>>> a.add_feature(2,4)
>>> print(a.list_features())
+-----+---------------+-----+-----+-----+-----+------+------+
| Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |
+-----+---------------+-----+-----+-----+-----+------+------+
| 0 | L:ft2 | --> | 2 | 4 | 2 | misc | no |
+-----+---------------+-----+-----+-----+-----+------+------+
"""
x = _PrettyTable([
"Ft#", "Label or Note", "Dir", "Sta", "End", "Len", "type", "orf?"
])
x.align["Ft#"] = "r" # Left align
x.align["Label or Note"] = "l" # Left align
x.align["Len"] = "r"
x.align["Sta"] = "l"
x.align["End"] = "l"
x.align["type"] = "l"
x.padding_width = 1 # One space between column edges and contents
for i, sf in enumerate(self.features):
try:
lbl = sf.qualifiers["label"]
except KeyError:
try:
lbl = sf.qualifiers["note"]
except KeyError:
lbl = "nd"
else:
lbl = "N:{}".format(" ".join(lbl).strip())
else:
lbl = "L:{}".format(" ".join(lbl).strip())
x.add_row([
i,
lbl[:16],
{
1: "-->",
-1: "<--",
0: "---",
None: "---"
}[sf.strand],
sf.location.start,
sf.location.end,
len(sf),
sf.type,
{
True: "yes",
False: "no"
}[self.extract_feature(i).isorf()
or self.extract_feature(i).reverse_complement().isorf()],
])
return _pretty_str(x)
def _format(self, title, key_values):
if len(key_values) == 0:
return ""
tbl = _PrettyTable(header=False)
for k, v in key_values.iteritems():
tbl.add_row([k, v])
tbl.align['Field 1'] = 'l'
tbl.align['Field 2'] = 'l'
s = title + ":\n"
s += tbl.__str__() + '\n'
return s
def _format(self, title, key_values):
if len(key_values) == 0:
return ""
tbl = _PrettyTable(header=False)
for k, v in key_values.iteritems():
tbl.add_row([k, v])
tbl.align['Field 1'] = 'l'
tbl.align['Field 2'] = 'l'
s = title + ":\n"
s += tbl.__str__() + '\n'
return s
def _format(self, title, key_values):
if len(key_values) == 0:
return ""
tbl = _PrettyTable(header=False)
for k, v in six.iteritems(key_values):
tbl.add_row([k, v])
tbl.align["Field 1"] = "l"
tbl.align["Field 2"] = "l"
s = title + ":\n"
s += tbl.__str__() + "\n"
return s
def __str__(self):
"""
Print the tree summary table.
"""
summary = _PrettyTable([
"id", "start_level", "end_level", "start_mass", "end_mass", "size",
"parent", "children"
])
for node_id, v in self.nodes.items():
summary.add_row([
node_id, v.start_level, v.end_level, v.start_mass, v.end_mass,
len(v.members), v.parent, v.children
])
for col in ["start_level", "end_level", "start_mass", "end_mass"]:
summary.float_format[col] = "5.3"
return summary.get_string()
def __str__(self):
"""
Print the tree summary table.
"""
summary = _PrettyTable(["id", "start_level", "end_level", "start_mass",
"end_mass", "size", "parent", "children"])
for node_id, v in self.nodes.items():
summary.add_row([node_id,
v.start_level,
v.end_level,
v.start_mass,
v.end_mass,
len(v.members),
v.parent,
v.children])
for col in ["start_level", "end_level", "start_mass", "end_mass"]:
summary.float_format[col] = "5.3"
return summary.get_string()
def _describe_fields(cls):
"""
Return a pretty table for the class fields description.
"""
dispatch_table = {
'ShortestPathModel': 'sssp_model_fields',
'GraphColoringModel': 'graph_coloring_model_fields',
'PagerankModel': 'pagerank_model_fields',
'ConnectedComponentsModel': 'connected_components_model_fields',
'TriangleCountingModel': 'triangle_counting_model_fields',
'KcoreModel': 'kcore_model_fields'
}
try:
fields_description = _main.run(dispatch_table[cls.__name__], {})
tbl = _PrettyTable(['Field', 'Description'])
for k, v in fields_description.iteritems():
tbl.add_row([k, v])
tbl.align['Field'] = 'l'
tbl.align['Description'] = 'l'
return tbl
except:
raise RuntimeError('Model %s does not have fields description' % cls.__name__)
def _describe_fields(cls):
"""
Return a pretty table for the class fields description.
"""
dispatch_table = {
'ShortestPathModel': 'sssp_model_fields',
'GraphColoringModel': 'graph_coloring_model_fields',
'PagerankModel': 'pagerank_model_fields',
'ConnectedComponentsModel': 'connected_components_model_fields',
'TriangleCountingModel': 'triangle_counting_model_fields',
'KcoreModel': 'kcore_model_fields'
}
try:
fields_description = _main.run(dispatch_table[cls.__name__], {})
tbl = _PrettyTable(['Field', 'Description'])
for k, v in fields_description.iteritems():
tbl.add_row([k, v])
tbl.align['Field'] = 'l'
tbl.align['Description'] = 'l'
return tbl
except:
raise RuntimeError('Model %s does not have fields description' % cls.__name__)