Add Ter as a valid AA in the HGVS grammar

mutalyzer/Retriever.py

@@ -61,7 +61,8 @@ def _name_to_file(self, name):
 
         :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 @@ def _write(self, raw_data, filename):
         :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 @@ def _calculate_hash(self, content):
 
         :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 @@ def _new_ud(self):
         """
         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 @@ def _update_db_md5(self, raw_data, name, gi):
         :arg unicode name:
         :arg unicode gi:
 
-        :returns unicode : filename
+        :returns: filename
+        :rtype: unicode
         """
         # TODO: Documentation.
         try:
@@ -164,7 +169,8 @@ def snpConvert(self, rs_id):
 
         :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 @@ def write(self, raw_data, filename, extract):
             - 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 @@ def retrieveslice(self, accno, start, stop, orientation):
             - 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 @@ def retrievegene(self, gene, organism, upstream=0, downstream=0):
         :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 @@ def downloadrecord(self, url):
 
         :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 @@ def uploadrecord(self, raw_data):
 
         :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 @@ def loadrecord(self, identifier):
         :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 @@ def loadrecord(self, identifier):
 
         :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 @@ def fetch(self, name):
 
         :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 @@ def downloadrecord(self, url, name=None):
 
         :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 @@ def write(self, raw_data, filename):
         :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.

mutalyzer/db/queries.py

@@ -62,7 +62,8 @@ def get_transcript_protein_link(accession, reverse=False):
     according to the configuration settings `PROTEIN_LINK_EXPIRATION` and
     `NEGATIVE_PROTEIN_LINK_EXPIRATION`.
 
-    :arg str accession: Accession number to lookup link for.
+    :arg str accession: Accession number (without version number) to lookup
+      link for.
     :arg bool reverse: If `True`, `accession` is assumed to be a protein
       accession number, otherwise `accession` is assumed to be a transcript
       accession number.
@@ -101,6 +102,14 @@ def update_transcript_protein_link(transcript_accession=None,
     """
     Update cached link between a transcript and a protein, or create it if it
     doesn't exist yet.
+
+    :arg str transcript_accession: Transcript accession number (without
+      version number).
+    :arg str protein_accession: Protein accession number (without version
+      number).
+
+    At least one of `transcript_accession` or `protein_accession` must be not
+    `None`.
     """
     if transcript_accession is None and protein_accession is None:
         raise ValueError('Link must have a transcript or protein')

mutalyzer/grammar.py

@@ -342,12 +342,13 @@ class Grammar():
 
     # BNF: AA3 -> `Ala' | `Arg' | `Asn' | `Asp' | `Cys' | `Gln' | `Glu' |
     #             `Gly' | `His' | `Ile' | `Leu' | `Lys' | `Met' | `Phe' |
-    #             `Pro' | `Ser' | `Thr' | `Trp' | `Tyr' | `Val'
+    #             `Pro' | `Ser' | `Thr' | `Trp' | `Tyr' | `Val' | `Ter'
     AA3 = Literal('Ala') ^ Literal('Arg') ^ Literal('Asn') ^ Literal('Asp') ^ \
           Literal('Cys') ^ Literal('Gln') ^ Literal('Glu') ^ Literal('Gly') ^ \
           Literal('His') ^ Literal('Ile') ^ Literal('Leu') ^ Literal('Lys') ^ \
           Literal('Met') ^ Literal('Phe') ^ Literal('Pro') ^ Literal('Ser') ^ \
-          Literal('Thr') ^ Literal('Trp') ^ Literal('Tyr') ^ Literal('Val')
+          Literal('Thr') ^ Literal('Trp') ^ Literal('Tyr') ^ Literal('Val') ^ \
+          Literal('Ter')
 
     # BNF: AA1 -> `A' | `R' | `N' | `D' | `C' | `Q' | `E' | `G' | `H' | `I' |
     #             `L' | `K' | `M' | `F' | `P' | `S' | `T' | `W' | `Y' | `V'
@@ -377,8 +378,9 @@ class Grammar():
     # BNF: Subst -> AAPtLoc AA (`extX' `*'? Number)? | (`Met1' | `M1') (`?' | `ext' `-' Number)
     # Todo: 'extX' -> 'ext*' (and loose the optional '*'?)
     # Todo: Optional AA before 'ext' and 'fMet' after 'ext'?
-    PSubst = (AAPtLoc + AA.setResultsName('Args') + Optional(Literal('extX') + Optional('*') + Number)) ^ \
-             ((Literal('Met1') ^ Literal('M1')) + (Literal('?') ^ (Literal('ext') + Literal('-') + Number)))
+    PSubst = ((AAPtLoc + AA.setResultsName('Args') + Optional(Literal('extX') + Optional('*') + Number)) ^
+              ((Literal('Met1') ^ Literal('M1')) + (Literal('?') ^ (Literal('ext') + Literal('-') + Number)))) \
+             + Empty().setParseAction(replaceWith('subst'))('MutationType')
 
     # BNF: Del -> AALoc `del'
     PDel = AALoc + Literal('del')('MutationType')

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)