conkit.core.SequenceFile module¶

Storage space for a sequence file

class SequenceFile(id)[source]¶

Bases: conkit.core.Entity.Entity

A sequence file object representing a single sequence file

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" nseqs=2)

Attributes

id	The ID of the selected entity
is_alignment	A boolean status for the alignment
nseqs	The number of conkit.core.Sequence instances in the conkit.core.SequenceFile
remark	The conkit.core.SequenceFile-specific remarks
status	An indication of the residue status, i.e true positive, false positive, or unknown
top_sequence	The first conkit.core.Sequence entry in conkit.core.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
copy()	Create a shallow copy of conkit.core.Entity
deepcopy()	Create a deep copy of conkit.core.Entity
remove(id)	Remove a child
sort(kword[, reverse, inplace])	Sort the conkit.core.SequenceFile

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

calculate_meff(identity=0.7)[source]¶

Calculate the number of effective sequences

This function calculates the number of effective sequences (Meff) in 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: 0.7]
Returns:	meff : int The number of effective sequences
Raises:	MemoryError Too many sequences in the alignment for Hamming distance calculation RuntimeError SciPy package not installed ValueError conkit.core.SequenceFile is not an alignment ValueError Sequence Identity needs to be between 0 and 1

is_alignment¶

A boolean status for the alignment

Returns:	is_alignment : bool A boolean status for the alignment

nseqs¶

The number of conkit.core.Sequence instances in the conkit.core.SequenceFile

Returns:	nseqs : int The number of sequences in the conkit.core.SequenceFile

remark¶

The conkit.core.SequenceFile-specific remarks

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

Sort the conkit.core.SequenceFile

Parameters:	kword : str The dictionary key to sort contacts by reverse : bool, optional Sort the contact pairs in descending order [default: False] inplace : bool, optional Replace the saved order of contacts [default: False]
Returns:	contact_map : conkit.core.ContactMap The reference to the conkit.core.ContactMap, regardless of inplace
Raises:	ValueError kword not in conkit.core.SequenceFile

status¶

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

top_sequence¶

The first conkit.core.Sequence entry in conkit.core.SequenceFile

Returns:	top_sequence : conkit.core.Sequence, None The first conkit.core.Sequence entry in conkit.core.SequenceFile