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

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" nseqs=2)

Attributes

id	The ID of the selected entity
is_alignment	A boolean status for the alignment
nseqs	The number of Sequence instances
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
copy()	Create a shallow copy of Entity
deepcopy()	Create a deep copy of Entity
remove(id)	Remove a child
sort(kword[, reverse, inplace])	Sort the SequenceFile
trim(start, end[, inplace])	Trim the 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:	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=0.7)[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:	int The number of effective sequences
Raises:	MemoryError Too many sequences in the alignment for Hamming distance calculation RuntimeError SciPy package not installed ValueError SequenceFile is not an alignment ValueError Sequence Identity needs to be between 0 and 1

is_alignment¶

A boolean status for the alignment

Returns:	bool A boolean status for the alignment

nseqs¶

The number of Sequence instances in the SequenceFile

Returns:	int The number of sequences in the SequenceFile

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:	SequenceFile 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

top_sequence¶

The first Sequence entry in SequenceFile

Returns:	Sequence, None 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:	SequenceFile The reference to the SequenceFile, regardless of inplace