From 647949305355505da9a157da2b5970627c296a82 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Sun, 27 Sep 2015 21:33:05 +0200
Subject: [PATCH] Fix return type docstring annotations
---
mutalyzer/Retriever.py | 53 +++++++++++++++++++++++++++---------------
mutalyzer/util.py | 6 +++--
2 files changed, 38 insertions(+), 21 deletions(-)
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index 85780b59..192716c4 100644
--- a/mutalyzer/Retriever.py
+++ b/mutalyzer/Retriever.py
@@ -61,7 +61,8 @@ class Retriever(object):
:arg unicode name: The accession number.
- :returns unicode: A filename.
+ :returns: A filename.
+ :rtype: unicode
"""
return os.path.join(
settings.CACHE_DIR, '{}.{}.bz2'.format(name, self.file_type))
@@ -73,7 +74,8 @@ class Retriever(object):
:arg str raw_data: The raw_data to be compressed and written.
:arg unicode filename: The intended name of the output filename.
- :returns unicode: The full path and name of the file written.
+ :returns: The full path and name of the file written.
+ :rtype: unicode
"""
result = chardet.detect(raw_data)
if result['confidence'] > 0.5:
@@ -108,7 +110,8 @@ class Retriever(object):
:arg unicode content: Arbitrary text.
- :returns unicode: The md5sum of 'content'.
+ :returns: The md5sum of 'content'.
+ :rtype: unicode
"""
hash_func = hashlib.md5()
hash_func.update(content)
@@ -120,7 +123,8 @@ class Retriever(object):
"""
Make a new UD number based on the current time (seconds since 1970).
- :returns unicode: A new UD number.
+ :returns: A new UD number.
+ :rtype: unicode
"""
ud = util.generate_id()
return 'UD_' + unicode(ud)
@@ -131,7 +135,8 @@ class Retriever(object):
:arg unicode name:
:arg unicode gi:
- :returns unicode : filename
+ :returns: filename
+ :rtype: unicode
"""
# TODO: Documentation.
try:
@@ -164,7 +169,8 @@ class Retriever(object):
:arg unicode rsId: The rsId of the SNP (example: 'rs9919552').
- :returns list(unicode): A list of HGVS notations.
+ :returns: A list of HGVS notations.
+ :rtype: list(unicode)
"""
# A simple input check.
id = rs_id[2:]
@@ -275,9 +281,10 @@ class GenBankRetriever(Retriever):
- 0 ; Do not extract, use 'filename'
- 1 ; Extract
- :returns tuple(unicode, unicode): Depending on the value of 'extract':
+ :returns: Depending on the value of 'extract':
- 0 ; ('filename', None)
- 1 ; (id, gi)
+ :rtype: tuple(unicode, unicode)
"""
if raw_data.strip() == b'Nothing has been found':
self._output.addMessage(
@@ -428,7 +435,8 @@ class GenBankRetriever(Retriever):
- 1 ; Forward.
- 2 ; Reverse complement.
- :returns unicode: An UD number.
+ :returns: An UD number.
+ :rtype: unicode
"""
# Not a valid slice.
if start > stop:
@@ -515,7 +523,8 @@ class GenBankRetriever(Retriever):
:arg int upstream: Number of upstream nucleotides for the slice.
:arg int downstream: Number of downstream nucleotides for the slice.
- :returns object: GenBank record.
+ :returns: GenBank record.
+ :rtype: object
"""
# Search the NCBI for a specific gene in an organism.
query = '{}[Gene] AND {}[Orgn]'.format(gene, organism)
@@ -647,7 +656,8 @@ class GenBankRetriever(Retriever):
:arg unicode url: Location of a GenBank record.
- :returns unicode: UD or None.
+ :returns: UD or None.
+ :rtype: unicode
"""
if not (url.startswith('http://') or url.startswith('https://') or
url.startswith('ftp://')):
@@ -703,7 +713,8 @@ class GenBankRetriever(Retriever):
:arg str raw_data: A GenBank record.
- :returns unicode: Accession number for the uploaded file.
+ :returns: Accession number for the uploaded file.
+ :rtype: unicode
"""
md5sum = self._calculate_hash(raw_data)
@@ -738,8 +749,9 @@ class GenBankRetriever(Retriever):
:arg unicode identifier: A RefSeq accession number or geninfo
identifier (GI).
- :returns object: A parsed RefSeq record or `None` if no record could be
- found for the given identifier.
+ :returns: A parsed RefSeq record or `None` if no record could be found
+ for the given identifier.
+ :rtype: object
"""
if identifier[0].isdigit():
# This is a GI number (geninfo identifier).
@@ -833,8 +845,8 @@ class LRGRetriever(Retriever):
:arg unicode identifier: The name of the LRG file to read.
- :returns object: GenRecord.Record of LRG file or None in case of
- failure.
+ :returns: GenRecord.Record of LRG file or None in case of failure.
+ :rtype: object
"""
# Make a filename based upon the identifier.
filename = self._name_to_file(identifier)
@@ -871,7 +883,8 @@ class LRGRetriever(Retriever):
:arg unicode name: The name of the LRG file to fetch.
- :returns unicode: the full path to the file; None in case of an error.
+ :returns: the full path to the file; None in case of an error.
+ :rtype: unicode
"""
prefix = settings.LRG_PREFIX_URL
url = prefix + '{}.xml'.format(name)
@@ -902,7 +915,8 @@ class LRGRetriever(Retriever):
:arg unicode url: Location of the LRG record.
- :returns unicode: The full path to the file or Nonein case of failure.
+ :returns: The full path to the file or Nonein case of failure.
+ :rtype: unicode
"""
lrg_id = name or os.path.splitext(os.path.split(url)[1])[0]
# if not lrg_id.startswith('LRG'):
@@ -973,8 +987,9 @@ class LRGRetriever(Retriever):
:arg str raw_data: The data.
:arg unicode filename: The intended name of the file.
- :returns unicode: The full path and name of the file written, None in
- case of an error.
+ :returns: The full path and name of the file written, None in case of
+ an error.
+ :rtype: unicode
"""
# Dirty way to test if a file is valid,
# Parse the file to see if it's a real LRG file.
diff --git a/mutalyzer/util.py b/mutalyzer/util.py
index 16667d58..a76ad361 100644
--- a/mutalyzer/util.py
+++ b/mutalyzer/util.py
@@ -359,7 +359,8 @@ def guess_file_type(handle):
:arg file handle: Open readable handle to an NGS data file.
- :returns unicode: Either 'fasta', 'fastq' or 'text'.
+ :returns: Either 'fasta', 'fastq' or 'text'.
+ :rtype: unicode
"""
try:
extension = getattr(handle, 'name').split('.')[-1]
@@ -397,7 +398,8 @@ def read_dna(handle):
:arg stream handle: Open readable handle to an NGS data file.
- :returns unicode: Content of the first record in the file.
+ :returns: Content of the first record in the file.
+ :rtype: unicode
"""
file_format = guess_file_type(handle)
--
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