MultiFile
#
- class biotite.sequence.io.genbank.MultiFile[source]#
Bases:
TextFile
This class represents a file in GenBank or GenPept format, that contains multiple entries, for more than one UID.
The information for each UID are appended to each other in such a file. Objects of this class can be iterated to obtain a
GenBankFile
for each entry in the file.Examples
>>> import os.path >>> file_name = fetch_single_file( ... ["1L2Y_A", "3O5R_A", "5UGO_A"], ... os.path.join(path_to_directory, "multifile.gp"), ... "protein", "gp" ... ) >>> multi_file = MultiFile.read(file_name) >>> for gp_file in multi_file: ... print(get_accession(gp_file)) 1L2Y_A 3O5R_A 5UGO_A
- copy()#
Create a deep copy of this object.
- Returns:
- copy
A copy of this object.
- classmethod read(file, *args, **kwargs)#
Parse a file (or file-like object).
- Parameters:
- filefile-like object or str
The file to be read. Alternatively a file path can be supplied.
- Returns:
- file_objectFile
An instance from the respective
File
subclass representing the parsed file.
- static read_iter(file)#
Create an iterator over each line of the given text file.
- Parameters:
- filefile-like object or str
The file to be read. Alternatively a file path can be supplied.
- Yields:
- linestr
The current line in the file.
- write(file)#
Write the contents of this object into a file (or file-like object).
- Parameters:
- filefile-like object or str
The file to be written to. Alternatively a file path can be supplied.
- static write_iter(file, lines)#
Iterate over the given lines of text and write each line into the specified file.
In contrast to
write()
, each line of text is not stored in an intermediateTextFile
, but is directly written to the file. Hence, this static method may save a large amount of memory if a large file should be written, especially if the lines are provided as generator.- Parameters:
- filefile-like object or str
The file to be written to. Alternatively a file path can be supplied.
- linesgenerator or array-like of str
The lines of text to be written. Must not include line break characters.
Gallery#
Finding homologs of a gene in a genome
Domains of bacterial sigma factors