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: `entry` (ClansEntry instance) - the new entry Raises: `ValueError` - if `entry` is no ClansEntry instance

### add_group(self, group, members=None) | source code
Adds a new group. Parameters: `group` (ClansSeqgroup instance) - the new group `members` (list) - ClansEntry instances to be in the new group 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: `group` (ClansSeqgroup instance) - the new group

### 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