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Commit 6e16157e authored by Laros's avatar Laros Committed by Vermaat
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Sphinx documentation strings.

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with 90 additions and 82 deletions
mutalyzer/describe.py
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− 82
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......@@ -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 = []
......
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