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Package csb :: Package bio :: Package io :: Module clans :: Class Clans
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Class Clans

source code

object --+
         |
        Clans

Class for holding and manipulating data from one CLANS file. Initialization is always done as empty clustermap with default parameters.

Instance Methods
 
__getitem__(self, index) source code
 
__init__(self)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
__len__(self) source code
 
__repr__(self)
str(x)		 source code
 
__setitem__(self, index, data) source code
 
__str__(self)
str(x)		 source code
 
add_entry(self, entry)
Adds an new entry.		 source code
 
add_group(self, group, members=None)
Adds a new group.		 source code
 
append_groups_from(self, other)
Append the ClansSeqgroup-s of other that contain at least one entry that corresponds to an entry in this instance.		 source code
ClansEntry
get_entry(self, name, pedantic=True)
Checks if an entry with name name exists and returns it.		 source code
 
initialize(self)
Initializes the coordinates of all entries with random numbers in [-1, 1].		 source code
 
remove_entry(self, entry)
Removes an entry.		 source code
 
remove_entry_by_name(self, entry_name)
Removes an entry fetched by its name.		 source code
 
remove_group(self, group)
Removes a group.		 source code
 
restrict(self, keep_names)
Removes all entries whose name is not in keep_names		 source code
 
restrict_to_max_pvalue(self, cutoff)
removes all ClansEntrys that have no connections above the cutoff		 source code
 
set_default_rotmtx(self)
Resets the rotation matrix (rotmtx) to no rotation.		 source code
 
sort(self, key=None)
Sorts the ClansEntrys by their name or by a custom comparison function.		 source code
 
write(self, filename)
writes the Clans instance to a file in CLANS format		 source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Properties
list entries
list of clustermap ClansEntrys.
str or None filename
file from which the data was parsed
ClansParams params
ClansParams that contains the parameters set for this Clans instance.
numpy.array rotmtx
3x3 rotation matrix that indicates the rotation state of the clustermap
list seqgroups
list of ClansSeqgroups defined in the clustermap.

Inherited from object: __class__

Method Details

__init__(self)
(Constructor)

source code 

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

__repr__(self)
(Representation operator)

source code 

str(x)

Overrides: object.__repr__
(inherited documentation)

__str__(self)
(Informal representation operator)

source code 

str(x)

Overrides: object.__str__
(inherited documentation)

add_entry(self, entry)

source code 

Adds an new entry.

Parameters:
Raises:

add_group(self, group, members=None)

source code 

Adds a new group.

Parameters:
Raises:
  • ValueError - if group is no ClansSeqgroup instance

append_groups_from(self, other)

source code 

Append the ClansSeqgroup-s of other that contain at least one entry that corresponds to an entry in this instance. Entries are compared by their name only! Groups without any matching members in this instance are not created in the local instance.

Parameters:
  • other (Clans instance) - the source of the new group definitions

get_entry(self, name, pedantic=True)

source code 

Checks if an entry with name name exists and returns it.

Parameters:
  • name (str) - name of the sought entry
  • pedantic (bool) - If True, a ValueError is raised if multiple entries with name name are found. If False, returns the first one.
Returns: ClansEntry
entry with name name
Raises:
  • ValueError - if no entry with name name is found
  • DuplicateEntryNameError - if multiple entries with name name are found and pedantic == True

remove_entry(self, entry)

source code 

Removes an entry.

Parameters:
  • entry (ClansEntry instance) - the entry that shall be removed

remove_entry_by_name(self, entry_name)

source code 

Removes an entry fetched by its name.

Parameters:
  • entry_name (string) - name of the entry that shall be removed

remove_group(self, group)

source code 

Removes a group.

Parameters:

restrict(self, keep_names)

source code 

Removes all entries whose name is not in keep_names

Parameters:
  • keep_names (iterable) - names of entries that shall be kept

restrict_to_max_pvalue(self, cutoff)

source code 

removes all ClansEntrys that have no connections above the cutoff

Parameters:
  • cutoff (float) - the cutoff

sort(self, key=None)

source code 

Sorts the ClansEntrys by their name or by a custom comparison function.

Parameters:
  • key (function) - a custom key function

write(self, filename)

source code 

writes the Clans instance to a file in CLANS format

Parameters:
  • filename (str) - the target file's name

Property Details

entries

list of clustermap ClansEntrys.

Get Method:
unreachable.entries(self) - list of clustermap ClansEntrys.
Type:
list

filename

file from which the data was parsed

Get Method:
unreachable.filename(self) - file from which the data was parsed
Type:
str or None

params

ClansParams that contains the parameters set for this Clans instance.

Get Method:
unreachable.params(self) - ClansParams that contains the parameters set for this Clans instance.
Type:
ClansParams

rotmtx

3x3 rotation matrix that indicates the rotation state of the clustermap

raises ValueError if rotation matrix shape is not 3x3

Get Method:
unreachable.rotmtx(self) - 3x3 rotation matrix that indicates the rotation state of the clustermap
Set Method:
unreachable.rotmtx(self, value)
Type:
numpy.array

seqgroups

list of ClansSeqgroups defined in the clustermap.

Get Method:
unreachable.seqgroups(self) - list of ClansSeqgroups defined in the clustermap.
Type:
list

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