biotite.sequence.io.genbank.GenBankFile

class biotite.sequence.io.genbank.GenBankFile[source]

Bases: biotite.file.TextFile

This class represents a file in GenBank format (including GenPept).

A GenBank file annotates a reference sequence with features such as positions of genes, promoters, etc. Additionally, it provides metadata further describing the file.s

A file is divided into separate fields, e.g. the DEFINITION field contains a description of the file. The field name starts at the beginning of a line, followed by the content. A field may contain subfields, whose name is indented. For example, the SOURCE field contains the ORGANISM subfield. Some fields may occur multiple times, e.g. the REFERENCE field. A sample GenBank file can be viewed at https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html.

This class provides a low-level interface for parsing, editing and writing GenBank files. It works like a list of field entries, where a field consists of the field name, the field content and the subfields. The field content is separated into the lines belonging to the content. While the content of metadata fields starts at the standard GenBank indentation of 12, the content of the FEATURES (contains the annotation) and ORIGIN (contains the sequence) fields starts without indentation. The subfields are represented by a dictionary, with subfield names being keys and the corresponding lines being values. The FEATURES and ORIGIN fields have no subfields.

Every entry can be obtained, set and deleted via the index operator.

Notes

This class does not support location identifiers with references to other Entrez database entries, e.g. join(1..100,J00194.1:100..202).

Examples

Create a GenBank file from scratch:

>>> file = GenBankFile()
>>> file.append(
...     "SOMEFIELD", ["One line", "A second line"],
...     subfields={"SUBFIELD1": ["Single Line"], "SUBFIELD2": ["Two", "lines"]}
... )
>>> print(file)
SOMEFIELD   One line
            A second line
  SUBFIELD1 Single Line
  SUBFIELD2 Two
            lines
//
>>> name, content, subfields = file[0]
>>> print(name)
SOMEFIELD
>>> print(content)
['One line', 'A second line']
>>> print(subfields)
OrderedDict([('SUBFIELD1', ['Single Line']), ('SUBFIELD2', ['Two', 'lines'])])

Adding an additional field:

>>> file.insert(0, "OTHERFIELD", ["Another line"])
>>> print(len(file))
2
>>> print(file)
OTHERFIELD  Another line
SOMEFIELD   One line
            A second line
  SUBFIELD1 Single Line
  SUBFIELD2 Two
            lines
//

Overwriting and deleting an existing field:

>>> file[1] = "NEWFIELD", ["Yet another line"]
>>> print(file)
OTHERFIELD  Another line
NEWFIELD    Yet another line
//
>>> file[1] = "NEWFIELD", ["Yet another line"], {"NEWSUB": ["Subfield line"]}
>>> print(file)
OTHERFIELD  Another line
NEWFIELD    Yet another line
  NEWSUB    Subfield line
//
>>> del file[1]
>>> print(file)
OTHERFIELD  Another line
//

Parsing fields from a real GenBank file:

>>> import os.path
>>> file = GenBankFile()
>>> file.read(os.path.join(path_to_sequences, "gg_avidin.gb"))
>>> print(file)
LOCUS       AJ311647                1224 bp    DNA     linear   VRT 14-NOV-2006
DEFINITION  Gallus gallus AVD gene for avidin, exons 1-4.
ACCESSION   AJ311647
VERSION     AJ311647.1  GI:13397825
KEYWORDS    AVD gene; avidin.
SOURCE      Gallus gallus (chicken)
  ORGANISM  Gallus gallus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Phasianinae; Gallus.
REFERENCE   1
  AUTHORS   Wallen,M.J., Laukkanen,M.O. and Kulomaa,M.S.
  TITLE     Cloning and sequencing of the chicken egg-white avidin-encoding
            gene and its relationship with the avidin-related genes Avr1-Avr5
  JOURNAL   Gene 161 (2), 205-209 (1995)
   PUBMED   7665080
REFERENCE   2
  AUTHORS   Ahlroth,M.K., Kola,E.H., Ewald,D., Masabanda,J., Sazanov,A.,
            Fries,R. and Kulomaa,M.S.
  TITLE     Characterization and chromosomal localization of the chicken avidin
            gene family
  JOURNAL   Anim. Genet. 31 (6), 367-375 (2000)
   PUBMED   11167523
REFERENCE   3  (bases 1 to 1224)
  AUTHORS   Ahlroth,M.K.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-MAR-2001) Ahlroth M.K., Department of Biological and
            Environmental Science, University of Jyvaskyla, PO Box 35,
            FIN-40351 Jyvaskyla, FINLAND
FEATURES             Location/Qualifiers
     source          1..1224
                     /organism="Gallus gallus"
                     /mol_type="genomic DNA"
...
>>> name, content, _ = file[3]
>>> print(name)
VERSION
>>> print(content)
['AJ311647.1  GI:13397825']
>>> name, content, subfields = file[5]
>>> print(name)
SOURCE
>>> print(content)
['Gallus gallus (chicken)']
>>> print(dict(subfields))
{'ORGANISM': ['Gallus gallus', 'Eukaryota; Metazoa; Chordata; ...', ...]}
read(self, file)[source]

Parse a file (or file-like object) and store the content in this object.

Parameters
file_namefile-like object or str

The file to be read. Alternatively a file path can be supplied.

get_fields(self, name)[source]

Get all GenBank fields associated with a given field name.

Parameters
namestr

The field name.

Returns
fieldslist of (list of str, OrderedDict of str -> str)

A list containing the fields. For most field names, the list will only contain one element, but fields like REFERENCE are an exception. Each field is represented by a tuple. Each tuple contains as first element the content lines and as second element the subfields as dictionary. If the field has no subfields, the dictionary is empty.

get_indices(self, name)[source]

Get the indices to all GenBank fields associated with a given field name.

Parameters
namestr

The field name.

Returns
fieldslist of int

A list of indices. For most field names, the list will only contain one element, but fields like REFERENCE are an exception.

set_field(self, name, content, subfield_dict=None)[source]

Set a GenBank field with the given content.

If the field already exists in the file, the field is overwritten, otherwise a new field is created at the end of the file.

Parameters
namestr

The field name.

contentlist of str

The content lines.

subfield_dictdict of str -> str, optional

The subfields of the field. The dictionary maps subfield names to the content lines of the respective subfield.

Raises
InvalidFileError

If the field occurs multiple times in the file. In this case it is ambiguous which field to overwrite.

insert(self, index, name, content, subfields=None)[source]

Insert a GenBank field at the given position.

Parameters
indexint

The new field is inserted before the current field at this index. If the index is after the last field, the new field is appended to the end of the file.

namestr

The field name.

contentlist of str

The content lines.

subfield_dictdict of str -> str, optional

The subfields of the field. The dictionary maps subfield names to the content lines of the respective subfield.

append(self, name, content, subfields=None)[source]

Create a new GenBank field at the end of the file.

Parameters
namestr

The field name.

contentlist of str

The content lines.

subfield_dictdict of str -> str, optional

The subfields of the field. The dictionary maps subfield names to the content lines of the respective subfield.

copy(self)

Create a deep copy of this object.

Returns
copy

A copy of this object.

write(self, file)

Write the contents of this object into a file (or file-like object).

Parameters
file_namefile-like object or str

The file to be written to. Alternatively a file path can be supplied.