diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index d702999ae21ca0c7ec3796541416f5365e8ba641..675783578ab91d7c1f107531cd96fd116c43a42f 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -25,10 +25,11 @@ def make_fs_tables(table_id):
a different reading frame. Do this for both alternative reading frames (+1
and +2).
- @arg table_id: Coding table ID.
- @type table_id: int
- @returns: Two dictionaries for the two alternative reading frames.
- @rtype: tuple(dict, dict)
+ :arg table_id: Coding table ID.
+ :type table_id: int
+
+ :returns: Two dictionaries for the two alternative reading frames.
+ :rtype: tuple(dict, dict)
"""
# Make the forward translation table.
table = dict(CodonTable.unambiguous_dna_by_id[table_id].forward_table)
@@ -57,10 +58,11 @@ def _peptide_overlaps(peptide):
"""
Make a list of overlapping 2-mers of {peptide} in order of appearance.
- @arg peptide: A peptide sequence.
- @type peptide: unicode
- @returns: All 2-mers of {peptide} in order of appearance.
- @rtype: list(unicode)
+ :arg peptide: A peptide sequence.
+ :type peptide: unicode
+
+ :returns: All 2-mers of {peptide} in order of appearance.
+ :rtype: list(unicode)
"""
return map(lambda x: peptide[x:x+2], range(len(peptide) - 1))
#_peptide_overlaps
@@ -69,14 +71,14 @@ def _options(peptide_overlaps, peptide_prefix, fs, output):
"""
Enumerate all peptides that could result from a frame shift.
- @arg peptide_overlaps: List of overlapping 2-mers of a peptide.
- @type peptide_overlaps: list(unicode)
- @arg peptide_prefix: Prefix of a peptide in the alternative reading frame.
- @type peptide_prefix: unicode
- @arg fs: Frame shift table.
- @type fs: dict
- @arg output: List of peptides, should be empty initially.
- @type output: list(unicode)
+ :arg peptide_overlaps: List of overlapping 2-mers of a peptide.
+ :type peptide_overlaps: list(unicode)
+ :arg peptide_prefix: Prefix of a peptide in the alternative reading frame.
+ :type peptide_prefix: unicode
+ :arg fs: Frame shift table.
+ :type fs: dict
+ :arg output: List of peptides, should be empty initially.
+ :type output: list(unicode)
"""
if not peptide_overlaps:
output.append(peptide_prefix)
@@ -90,10 +92,13 @@ def enum_fs(peptide, fs):
"""
Enumerate all peptides that could result from a frame shift.
- @arg peptide: Original peptide sequence.
- @type peptide: unicode
- @arg fs: Frame shift table.
- @type fs: dict
+ :arg peptide: Original peptide sequence.
+ :type peptide: unicode
+ :arg fs: Frame shift table.
+ :type fs: dict
+
+ :returns: List of peptides that could result from a frame shift.
+ :rtype: list(unicode)
"""
output = []
@@ -106,12 +111,15 @@ def fit_fs(peptide, alternative_peptide, fs):
Check whether peptide {alternative_peptide} is a possible frame shift of
peptide {peptide}.
- @arg peptide: Original peptide sequence.
- @type peptide: unicode
- @arg alternative_peptide: Observed peptide sequence.
- @type alternative_peptide: unicode
- @arg fs: Frame shift table.
- @type fs: dict
+ :arg peptide: Original peptide sequence.
+ :type peptide: unicode
+ :arg alternative_peptide: Observed peptide sequence.
+ :type alternative_peptide: unicode
+ :arg fs: Frame shift table.
+ :type fs: dict
+
+ :returns: Whether {alternative_peptide} is a frameshift of {peptide}.
+ :rtype: bool
"""
# Todo: This is a temporary fix to prevent crashing on frameshift
# detection (I think bug #124).
@@ -133,15 +141,15 @@ def find_fs(peptide, alternative_peptide, fs):
Find the longest part of {alternative_peptide} that fits in {peptide} in a
certain frame given by {fs}.
- @arg peptide: Original peptide sequence.
- @type peptide: unicode
- @arg alternative_peptide: Observed peptide sequence.
- @type alternative_peptide: unicode
- @arg fs: Frame shift table.
- @type fs: dict
+ :arg peptide: Original peptide sequence.
+ :type peptide: unicode
+ :arg alternative_peptide: Observed peptide sequence.
+ :type alternative_peptide: unicode
+ :arg fs: Frame shift table.
+ :type fs: dict
- @returns: The length and the offset in {peptide} of the largest frameshift.
- @rtype: tuple(int, int)
+ :returns: The length and the offset in {peptide} of the largest frameshift.
+ :rtype: tuple(int, int)
"""
peptide_overlaps = _peptide_overlaps(peptide)
max_fs = 0
@@ -226,30 +234,30 @@ class RawVar(models.RawVar):
"""
Initialise the class with the appropriate values.
- @arg start: Start position.
- @type start: int
- @arg start_offset:
- @type start_offset: int
- @arg end: End position.
- @type end: int
- @arg end_offset:
- @type end_offset: int
- @arg sample_start: Start position.
- @type sample_start: int
- @arg sample_start_offset:
- @type sample_start_offset: int
- @arg sample_end: End position.
- @type sample_end: int
- @arg sample_end_offset:
- @type sample_end_offset: int
- @arg type: Variant type.
- @type type: unicode
- @arg deleted: Deleted part of the reference sequence.
- @type deleted: unicode
- @arg inserted: Inserted part.
- @type inserted: object
- @arg shift: Amount of freedom.
- @type shift: int
+ :arg start: Start position.
+ :type start: int
+ :arg start_offset:
+ :type start_offset: int
+ :arg end: End position.
+ :type end: int
+ :arg end_offset:
+ :type end_offset: int
+ :arg sample_start: Start position.
+ :type sample_start: int
+ :arg sample_start_offset:
+ :type sample_start_offset: int
+ :arg sample_end: End position.
+ :type sample_end: int
+ :arg sample_end_offset:
+ :type sample_end_offset: int
+ :arg type: Variant type.
+ :type type: unicode
+ :arg deleted: Deleted part of the reference sequence.
+ :type deleted: unicode
+ :arg inserted: Inserted part.
+ :type inserted: object
+ :arg shift: Amount of freedom.
+ :type shift: int
"""
# TODO: Will this container be used for all variants, or only genomic?
# start_offset and end_offset may be never used.
@@ -276,8 +284,8 @@ class RawVar(models.RawVar):
"""
Give the HGVS description of the raw variant stored in this class.
- @returns: The HGVS description of the raw variant stored in this class.
- @rtype: unicode
+ :returns: The HGVS description of the raw variant stored in this class.
+ :rtype: unicode
"""
if not self.start:
return "="
@@ -305,8 +313,8 @@ class RawVar(models.RawVar):
Note that this function relies on the absence of values to make the
correct description. Also see the comment in the class definition.
- @returns: The HGVS description of the raw variant stored in this class.
- @rtype: unicode
+ :returns: The HGVS description of the raw variant stored in this class.
+ :rtype: unicode
"""
if self.type == "unknown":
return "?"
@@ -345,9 +353,9 @@ class RawVar(models.RawVar):
Note that this function relies on the absence of values to make the
correct description. Also see the comment in the class definition.
- @returns: The standardised length of the HGVS description of the raw
+ :returns: The standardised length of the HGVS description of the raw
variant stored in this class.
- @rtype: int
+ :rtype: int
"""
if not self.start: # `=' or `?'
return 1
@@ -376,9 +384,9 @@ class RawVar(models.RawVar):
Note that this function relies on the absence of values to make the
correct description. Also see the comment in the class definition.
- @returns: The standardised length of the HGVS description of the raw
+ :returns: The standardised length of the HGVS description of the raw
variant stored in this class.
- @rtype: int
+ :rtype: int
"""
if not self.start: # =
return 1
@@ -421,9 +429,9 @@ class RawVar(models.RawVar):
Give the standardised length of the HGVS description of the raw variant
stored in this class.
- @returns: The standardised length of the HGVS description of the raw
+ :returns: The standardised length of the HGVS description of the raw
variant stored in this class.
- @rtype: int
+ :rtype: int
"""
if self.dna:
return self._dna_description_length()
@@ -435,11 +443,11 @@ def allele_description(allele):
"""
Convert a list of raw variants to an HGVS allele description.
- @arg allele: A list of raw variants representing an allele description.
- @type allele: list(DescribeRawVar)
+ :arg allele: A list of raw variants representing an allele description.
+ :type allele: list(RawVar)
- @returns: The HGVS description of {allele}.
- @rval: unicode
+ :returns: The HGVS description of {allele}.
+ :rtype: unicode
"""
if len(allele) > 1:
return "[{}]".format(';'.join(map(lambda x: x.hgvs, allele)))
@@ -450,11 +458,11 @@ def allele_description_length(allele):
"""
Calculate the standardised length of an HGVS allele description.
- @arg allele: A list of raw variants representing an allele description.
- @type allele: list(DescribeRawVar)
+ :arg allele: A list of raw variants representing an allele description.
+ :type allele: list(RawVar)
- @returns: The standardised length of the HGVS description of {allele}.
- @rval: int
+ :returns: The standardised length of the HGVS description of {allele}.
+ :rtype: int
"""
# NOTE: Do we need to count the ; and [] ?
return sum(map(lambda x: x.hgvs_length, allele))
@@ -565,13 +573,13 @@ def describe(s1, s2, dna=True):
"""
Give an allele description of the change from {s1} to {s2}.
- arg s1: Sequence 1.
- type s1: unicode
- arg s2: Sequence 2.
- type s2: unicode
+ :arg s1: Sequence 1.
+ :type s1: unicode
+ :arg s2: Sequence 2.
+ :type s2: unicode
- @returns: A list of DescribeRawVar objects, representing the allele.
- @rval: list(DescribeRawVar)
+ :returns: A list of RawVar objects, representing the allele.
+ :rtype: list(RawVar)
"""
description = []