conkit.core.sequencefile module¶

SequenceFile container used throughout ConKit

class SequenceFile(id)[source]¶

Bases: conkit.core._entity._Entity

A sequence file object representing a single sequence file

The SequenceFile class represents a data structure to hold Sequence instances in a single sequence file. It contains functions to store and analyze sequences.

Examples

>>> from conkit.core import Sequence, SequenceFile
>>> sequence_file = SequenceFile("example")
>>> sequence_file.add(Sequence("foo", "ABCDEF"))
>>> sequence_file.add(Sequence("bar", "ZYXWVU"))
>>> print(sequence_file)
SequenceFile(id="example" nseq=2)

Attributes

id	The ID of the selected entity
is_alignment	A boolean status for the alignment
meff	The number of effective sequences
nseq	The number of sequences
remark	The SequenceFile-specific remarks
status	An indication of the residue status, i.e true positive, false positive, or unknown
top_sequence	The first Sequence entry in SequenceFile

Methods

add(entity)	Add a child to the Entity
calculate_freq()	Calculate the gap frequency in each alignment column
calculate_meff([identity])	Calculate the number of effective sequences
calculate_meff_with_identity(identity)	Calculate the number of effective sequences with specified sequence identity
calculate_neff_with_identity(identity)	Calculate the number of effective sequences with specified sequence identity
calculate_weights([identity])	Calculate the sequence weights
copy()	Create a shallow copy of Entity
deepcopy()	Create a deep copy of Entity
filter([min_id, max_id, inplace])	Filter sequences from an alignment according to the minimum and maximum identity
filter_gapped([min_prop, max_prop, inplace])	Filter all sequences a gap proportion greater than the limit
remove(id)	Remove a child
sort(kword[, reverse, inplace])	Sort the SequenceFile
to_string()	Return the SequenceFile as str
trim(start, end[, inplace])	Trim the SequenceFile

ascii_matrix¶

The alignment encoded in a 2-D ASCII matrix

calculate_freq()[source]¶

Calculate the gap frequency in each alignment column

This function calculates the frequency of gaps at each position in the Multiple Sequence Alignment.

Returns:	list A list containing the per alignment-column amino acid frequency count
Raises:	MemoryError Too many sequences in the alignment RuntimeError SequenceFile is not an alignment

calculate_meff(identity=0.8)[source]¶

Calculate the number of effective sequences

See also

meff

calculate_meff_with_identity(identity)[source]¶

Calculate the number of effective sequences with specified sequence identity

See also

meff, calculate_weights

calculate_neff_with_identity(identity)[source]¶

Calculate the number of effective sequences with specified sequence identity

See also

neff, calculate_weights

calculate_weights(identity=0.8)[source]¶

Calculate the sequence weights

This function calculates the sequence weights in the the Multiple Sequence Alignment.

The mathematical function used to calculate Meff is

\[M_{eff}=\sum_{i}\frac{1}{\sum_{j}S_{i,j}}\]

Parameters:	identity : float, optional The sequence identity to use for similarity decision [default: 0.8]
Returns:	list A list of the sequence weights in the alignment
Raises:	ImportError Cannot find SciPy package ValueError SequenceFile is not an alignment ValueError Sequence Identity needs to be between 0 and 1

diversity¶

The diversity of an alignment defined by \(\sqrt{N}/L\).

N equals the number of sequences in the alignment and L the sequence length

empty¶

Status of emptiness of sequencefile

encoded_matrix¶

The alignment encoded for contact prediction

filter(min_id=0.3, max_id=0.9, inplace=False)[source]¶

Filter sequences from an alignment according to the minimum and maximum identity between the sequences

Parameters:	min_id : float, optional Minimum sequence identity max_id : float, optional Maximum sequence identity inplace : bool, optional Replace the saved order of sequences [default: False]
Returns:	obj The reference to the SequenceFile, regardless of inplace
Raises:	MemoryError Too many sequences in the alignment for Hamming distance calculation RuntimeError SciPy package not installed ValueError SequenceFile is not an alignment ValueError Minimum sequence identity needs to be between 0 and 1 ValueError Maximum sequence identity needs to be between 0 and 1

filter_gapped(min_prop=0.0, max_prop=0.9, inplace=True)[source]¶

Filter all sequences a gap proportion greater than the limit

Parameters:	min_prop : float, optional Minimum allowed gap proportion [default: 0.0] max_prop : float, optional Maximum allowed gap proportion [default: 0.9] inplace : bool, optional Replace the saved order of sequences [default: False]
Returns:	obj The reference to the SequenceFile, regardless of inplace

is_alignment¶

A boolean status for the alignment

Returns:	bool A boolean status for the alignment

meff¶

The number of effective sequences

neff¶

The number of effective sequences

nseq¶

The number of sequences

remark¶

The SequenceFile-specific remarks

sort(kword, reverse=False, inplace=False)[source]¶

Sort the SequenceFile

Parameters:	kword : str The dictionary key to sort sequences by reverse : bool, optional Sort the sequences in reverse order [default: False] inplace : bool, optional Replace the saved order of sequences [default: False]
Returns:	obj The reference to the SequenceFile, regardless of inplace
Raises:	ValueError kword not in SequenceFile

status¶

An indication of the residue status, i.e true positive, false positive, or unknown

to_string()[source]¶

Return the SequenceFile as str

top_sequence¶

The first Sequence entry in SequenceFile

Returns:	obj The first Sequence entry in SequenceFile

trim(start, end, inplace=False)[source]¶

Trim the SequenceFile

Parameters:	start : int First residue to include end : int Final residue to include inplace : bool, optional Replace the saved order of sequences [default: False]
Returns:	obj The reference to the SequenceFile, regardless of inplace