API Reference¶
Rearrangement Interface¶
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airr.
read_rearrangement
(filename, validate=False, debug=False)¶ Open an iterator to read an AIRR rearrangements file
- Parameters
file (str) – path to the input file.
validate (bool) – whether to validate data as it is read, raising a ValidationError exception in the event of an error.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
iterable reader class.
- Return type
-
airr.
create_rearrangement
(filename, fields=None, debug=False)¶ Create an empty AIRR rearrangements file writer
- Parameters
filename (str) – output file path.
fields (list) – additional non-required fields to add to the output.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
open writer class.
- Return type
-
airr.
derive_rearrangement
(out_filename, in_filename, fields=None, debug=False)¶ Create an empty AIRR rearrangements file with fields derived from an existing file
- Parameters
out_filename (str) – output file path.
in_filename (str) – existing file to derive fields from.
fields (list) – additional non-required fields to add to the output.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
open writer class.
- Return type
-
airr.
load_rearrangement
(filename, validate=False, debug=False)¶ Load the contents of an AIRR rearrangements file into a data frame
- Parameters
filename (str) – input file path.
validate (bool) – whether to validate data as it is read, raising a ValidationError exception in the event of an error.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
Rearrangement records as rows of a data frame.
- Return type
pandas.DataFrame
-
airr.
dump_rearrangement
(dataframe, filename, debug=False)¶ Write the contents of a data frame to an AIRR rearrangements file
- Parameters
dataframe (pandas.DataFrame) – data frame of rearrangement data.
filename (str) – output file path.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
True if the file is written without error.
- Return type
bool
-
airr.
merge_rearrangement
(out_filename, in_filenames, drop=False, debug=False)¶ Merge one or more AIRR rearrangements files
- Parameters
out_filename (str) – output file path.
in_filenames (list) – list of input files to merge.
drop (bool) – drop flag. If True then drop fields that do not exist in all input files, otherwise combine fields from all input files.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
True if files were successfully merged, otherwise False.
- Return type
bool
-
airr.
validate_rearrangement
(filename, debug=False)¶ Validates an AIRR rearrangements file
- Parameters
filename (str) – path of the file to validate.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
True if files passed validation, otherwise False.
- Return type
bool
Repertoire Interface¶
-
airr.
load_repertoire
(filename, validate=False, debug=False)¶ Load an AIRR repertoire metadata file
- Parameters
filename (str) – path to the input file.
validate (bool) – whether to validate data as it is read, raising a ValidationError exception in the event of an error.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
list of Repertoire dictionaries.
- Return type
list
-
airr.
write_repertoire
(filename, repertoires, info=None, debug=False)¶ Write an AIRR repertoire metadata file
- Parameters
file (str) – path to the output file.
repertoires (list) – array of repertoire objects.
info (object) – info object to write. Will write current AIRR Schema info if not specified.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
True if the file is written without error.
- Return type
bool
-
airr.
validate_repertoire
(filename, debug=False)¶ Validates an AIRR repertoire metadata file
- Parameters
filename (str) – path of the file to validate.
debug (bool) – debug flag. If True print debugging information to standard error.
- Returns
True if files passed validation, otherwise False.
- Return type
bool
-
airr.
repertoire_template
()¶ Return a blank repertoire object from the template. This object has the complete structure with all of the fields and all values set to None or empty string.
- Returns
empty repertoire object.
- Return type
object
Classes¶
-
class
airr.io.
RearrangementReader
(handle, base=1, validate=False, debug=False)¶ Iterator for reading Rearrangement objects in TSV format
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fields
¶ field names in the input Rearrangement file.
- Type
list
-
external_fields
¶ list of fields in the input file that are not part of the Rearrangement definition.
- Type
list
-
__init__
(handle, base=1, validate=False, debug=False)¶ Initialization
- Parameters
handle (file) – file handle of the open Rearrangement file.
base (int) – one of 0 or 1 specifying the coordinate schema in the input file. If 1, then the file is assumed to contain 1-based closed intervals that will be converted to python style 0-based half-open intervals for known fields. If 0, then values will be unchanged.
validate (bool) – perform validation. If True then basic validation will be performed will reading the data. A ValidationError exception will be raised if an error is found.
debug (bool) – debug state. If True prints debug information.
- Returns
reader object.
- Return type
-
__iter__
()¶ Iterator initializer
- Returns
airr.io.RearrangementReader
-
__next__
()¶ Next method
- Returns
parsed Rearrangement data.
- Return type
dict
-
close
()¶ Closes the Rearrangement file
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next
()¶ Next method
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-
class
airr.io.
RearrangementWriter
(handle, fields=None, base=1, debug=False)¶ Writer class for Rearrangement objects in TSV format
-
fields
¶ field names in the output Rearrangement file.
- Type
list
-
external_fields
¶ list of fields in the output file that are not part of the Rearrangement definition.
- Type
list
-
__init__
(handle, fields=None, base=1, debug=False)¶ Initialization
- Parameters
handle (file) – file handle of the open Rearrangements file.
fields (list) – list of non-required fields to add. May include fields undefined by the schema.
base (int) – one of 0 or 1 specifying the coordinate schema in the output file. Data provided to the write is assumed to be in python style 0-based half-open intervals. If 1, then data will be converted to 1-based closed intervals for known fields before writing. If 0, then values will be unchanged.
debug (bool) – debug state. If True prints debug information.
- Returns
writer object.
- Return type
-
close
()¶ Closes the Rearrangement file
-
write
(row)¶ Write a row to the Rearrangement file
- Parameters
row (dict) – row to write.
-
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class
airr.schema.
Schema
(definition)¶ AIRR schema definitions
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properties
¶ field definitions.
- Type
collections.OrderedDict
-
info
¶ schema info.
- Type
collections.OrderedDict
-
required
¶ list of mandatory fields.
- Type
list
-
optional
¶ list of non-required fields.
- Type
list
-
false_values
¶ accepted string values for False.
- Type
list
-
true_values
¶ accepted values for True.
- Type
list
-
from_bool
(value, validate=False)¶ Converts a boolean to a string
- Parameters
value (bool) – logical value.
validate (bool) – when True raise a ValidationError for an invalid value. Otherwise, set invalid values to None.
- Returns
conversion of True or False or ‘T’ or ‘F’.
- Return type
str
- Raises
airr.ValidationError
– raised if value is invalid when validate is set True.
-
spec
(field)¶ Get the properties for a field
- Parameters
name (str) – field name.
- Returns
definition for the field.
- Return type
collections.OrderedDict
-
to_bool
(value, validate=False)¶ Convert a string to a boolean
- Parameters
value (str) – logical value as a string.
validate (bool) – when True raise a ValidationError for an invalid value. Otherwise, set invalid values to None.
- Returns
conversion of the string to True or False.
- Return type
bool
- Raises
airr.ValidationError
– raised if value is invalid when validate is set True.
-
to_float
(value, validate=False)¶ Converts a string to a float
- Parameters
value (str) – float value as a string.
validate (bool) – when True raise a ValidationError for an invalid value. Otherwise, set invalid values to None.
- Returns
conversion of the string to a float.
- Return type
float
- Raises
airr.ValidationError
– raised if value is invalid when validate is set True.
-
to_int
(value, validate=False)¶ Converts a string to an integer
- Parameters
value (str) – integer value as a string.
validate (bool) – when True raise a ValidationError for an invalid value. Otherwise, set invalid values to None.
- Returns
conversion of the string to an integer.
- Return type
int
- Raises
airr.ValidationError
– raised if value is invalid when validate is set True.
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type
(field)¶ Get the type for a field
- Parameters
name (str) – field name.
- Returns
the type definition for the field
- Return type
str
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validate_header
(header)¶ Validate header against the schema
- Parameters
header (list) – list of header fields.
- Returns
True if a ValidationError exception is not raised.
- Return type
bool
- Raises
airr.ValidationError
– raised if header fails validation.
-
validate_object
(obj, missing=True, nonairr=True, context=None)¶ Validate Repertoire object data against schema
- Parameters
obj (dict) – dictionary containing a single repertoire object.
missing (bool) – provides warnings for missing optional fields.
(bool (nonairr) – provides warning for non-AIRR fields that cannot be validated.
context (string) – used by recursion to indicate place in object hierarchy
- Returns
True if a ValidationError exception is not raised.
- Return type
bool
- Raises
airr.ValidationError
– raised if object fails validation.
-
validate_row
(row)¶ Validate Rearrangements row data against schema
- Parameters
row (dict) – dictionary containing a single record.
- Returns
True if a ValidationError exception is not raised.
- Return type
bool
- Raises
airr.ValidationError
– raised if row fails validation.
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Schema¶
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airr.schema.
AlignmentSchema
Schema object for the Alignment definition¶ AIRR schema definitions
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airr.schema.
properties
¶ field definitions.
- Type
collections.OrderedDict
-
airr.schema.
info
¶ schema info.
- Type
collections.OrderedDict
-
airr.schema.
required
¶ list of mandatory fields.
- Type
list
-
airr.schema.
optional
¶ list of non-required fields.
- Type
list
-
airr.schema.
false_values
¶ accepted string values for False.
- Type
list
-
airr.schema.
true_values
¶ accepted values for True.
- Type
list
-
-
airr.schema.
RearrangementSchema
Schema object for the Rearrangement definition¶ AIRR schema definitions
-
airr.schema.
properties
field definitions.
- Type
collections.OrderedDict
-
airr.schema.
info
schema info.
- Type
collections.OrderedDict
-
airr.schema.
required
list of mandatory fields.
- Type
list
-
airr.schema.
optional
list of non-required fields.
- Type
list
-
airr.schema.
false_values
accepted string values for False.
- Type
list
-
airr.schema.
true_values
accepted values for True.
- Type
list
-
-
airr.schema.
RepertoireSchema
Schema object for the Repertoire definition¶ AIRR schema definitions
-
airr.schema.
properties
field definitions.
- Type
collections.OrderedDict
-
airr.schema.
info
schema info.
- Type
collections.OrderedDict
-
airr.schema.
required
list of mandatory fields.
- Type
list
-
airr.schema.
optional
list of non-required fields.
- Type
list
-
airr.schema.
false_values
accepted string values for False.
- Type
list
-
airr.schema.
true_values
accepted values for True.
- Type
list
-