🚦v0.2.7a1

NatureGeorge · Feb 24, 2021 · 7f6e095 · 7f6e095
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diff --git a/pdb_profiling/__init__.py b/pdb_profiling/__init__.py
@@ -4,7 +4,7 @@
 # @Author: ZeFeng Zhu
 # @Last Modified: 2020-05-13 08:54:09 pm
 # @Copyright (c) 2020 MinghuiGroup, Soochow University
-__version__ = '0.2.6'
+__version__ = '0.2.7'
 
 
 def default_config(folder='./'):

diff --git a/pdb_profiling/commands/__init__.py b/pdb_profiling/commands/__init__.py
@@ -28,7 +28,26 @@ class IDMapping(orm.Model):
             Entry = orm.String(max_length=50, primary_key=True)
             isoform = orm.String(max_length=50, primary_key=True)
             is_canonical = orm.Boolean()
+
+        class ResidueMapping(orm.Model):
+            __tablename__ = 'ResidueMapping'
+            __metadata__ = self.metadata
+            __database__ = self.database
+            UniProt = orm.String(max_length=50, primary_key=True)
+            author_insertion_code = orm.String(max_length=50, allow_null=True, allow_blank=True, default='')
+            author_residue_number = orm.Integer()
+            chain_id = orm.String(max_length=10)
+            struct_asym_id = orm.String(max_length=10, primary_key=True)
+            entity_id = orm.Integer(primary_key=True)
+            pdb_id = orm.String(max_length=4, primary_key=True)
+            residue_number = orm.Integer(primary_key=True)
+            unp_residue_number = orm.Integer(primary_key=True)
+            residue_name = orm.String(max_length=10)
+            observed_ratio = orm.Float()
+            multiple_conformers = orm.JSON(allow_null=True)
+            conflict_code = orm.String(max_length=3, allow_null=True)
 
 
         self.Mutation = Mutation
         self.IDMapping = IDMapping
+        self.ResidueMapping = ResidueMapping
diff --git a/pdb_profiling/commands/command.py b/pdb_profiling/commands/command.py
@@ -129,7 +129,7 @@ def id_mapping(ctx, input, column, sep, chunksize):
 @click.option('--func', type=str, default='pipe_select_mo')
 @click.option('--kwargs', type=str, default='{}')
 @click.option('--chunksize', type=int, help="the chunksize parameter", default=200)
-@click.option('--entry_filter', type=str, default='(release_date < "20201020") and ((experimental_method in ["X-ray diffraction", "Electron Microscopy"] and resolution <= 3) or experimental_method == "Solution NMR")')
+@click.option('--entry_filter', type=str, default='(release_date < "20210101") and ((experimental_method in ["X-ray diffraction", "Electron Microscopy"] and resolution <= 3) or experimental_method == "Solution NMR")')
 @click.option('--chain_filter', type=str, default="UNK_COUNT < SEQRES_COUNT and ca_p_only == False and identity >=0.9 and repeated == False and reversed == False and OBS_COUNT > 20")
 @click.option('--skip_pdbs', type=str, default='1fc2,6wrg,5jm5,6vnn,2i6l,4zai,5jn1,6bj0,6yth,4fc3,7acu,6lsd,6llc,6xoz,6xp0,6xp1,6xp2,6xp3,6xp4,6xp5,6xp6,6xp7,6xp8,6xpa,6zqz,6t5h,6xwd,6xxc')
 @click.option('--omit', type=int, default=0)
@@ -204,9 +204,9 @@ def get_unp_id(args):
 @Interface.command("residue-mapping")
 @click.option('--input', type=click.Path())
 @click.option('--chunksize', type=int, help="the chunksize parameter", default=10000)
-@click.option('--output', type=str)
-def residue_mapping(input, chunksize, output):
-    output = Path(output)
+@click.option('--output', type=str, default=None)
+@click.pass_context
+def residue_mapping(ctx, input, chunksize, output):
     dfs = read_csv(input, sep='\t', keep_default_na=False,
                    na_values=['NULL', 'null'], chunksize=chunksize)
     for df in dfs:
@@ -222,7 +222,12 @@ def residue_mapping(input, chunksize, output):
         with Progress(*progress_bar_args) as p:
             res = ob.run(p.track).result()
         res_mapping_df = concat(res, sort=False, ignore_index=True)
-        res_mapping_df[sorted(res_mapping_df.columns)].to_csv(output, sep='\t', mode='a+', index=False, header=not output.exists())
+        if output is not None:
+            output = Path(output)
+            res_mapping_df[sorted(res_mapping_df.columns)].to_csv(output, sep='\t', mode='a+', index=False, header=not output.exists())
+        else:
+            sqlite_api = ctx.obj['custom_db']
+            sqlite_api.sync_insert(sqlite_api.ResidueMapping, res_mapping_df.to_dict('records'))
         sleep(uniform(0, 1))
 
 

diff --git a/pdb_profiling/data.py b/pdb_profiling/data.py
@@ -4,12 +4,37 @@
 # @Author: ZeFeng Zhu
 # @Last Modified: 2020-10-10 04:06:06 pm
 # @Copyright (c) 2020 MinghuiGroup, Soochow University
+# from copy import deepcopy
+
+'''
+class SwapKeyDict(dict):
+
+    def __missing__(self, key):
+        swap = key[::-1]
+        if swap not in self:
+            if hasattr(self, 'gap') and None in key:
+                return self.gap
+            raise KeyError(key)
+        else:
+            return self[swap]
+
+    def set_gap(self, gap):
+        cur = deepcopy(self)
+        cur.gap = gap
+        return cur
+'''
+
+def store_swap_key(data_from, data_to):
+    for key, value in data_from.items():
+        data_to[key] = value
+        data_to[key[::-1]] = value
+    return data_to
 
 '''
 Matrix Data From: https://github.com/biopython/biopython/blob/master/Bio/SubsMat/MatrixInfo.py
 '''
 
-blosum62 = {
+blosum62 = store_swap_key({
     ('W', 'F'): 1, ('L', 'R'): -2, ('S', 'P'): -1, ('V', 'T'): 0,
     ('Q', 'Q'): 5, ('N', 'A'): -2, ('Z', 'Y'): -2, ('W', 'R'): -3,
     ('Q', 'A'): -1, ('S', 'D'): 0, ('H', 'H'): 8, ('S', 'H'): -1,
@@ -79,7 +104,79 @@
     ('Z', 'N'): 0, ('X', 'A'): 0, ('B', 'R'): -1, ('B', 'N'): 3,
     ('F', 'D'): -3, ('X', 'Y'): -1, ('Z', 'R'): 0, ('F', 'H'): -1,
     ('B', 'F'): -3, ('F', 'L'): 0, ('X', 'Q'): -1, ('B', 'B'): 4
-}
+}, dict())
+
+blosum95 = store_swap_key({
+    ("W", "F"): 0, ("L", "R"): -3, ("S", "P"): -2, ("V", "T"): -1,
+    ("Q", "Q"): 7, ("N", "A"): -2, ("Z", "Y"): -4, ("W", "R"): -4,
+    ("Q", "A"): -1, ("S", "D"): -1, ("H", "H"): 9, ("S", "H"): -2,
+    ("H", "D"): -2, ("L", "N"): -5, ("W", "A"): -4, ("Y", "M"): -3,
+    ("G", "R"): -4, ("Y", "I"): -2, ("Y", "E"): -4, ("B", "Y"): -4,
+    ("Y", "A"): -3, ("V", "D"): -5, ("B", "S"): -1, ("Y", "Y"): 8,
+    ("G", "N"): -1, ("E", "C"): -6, ("Y", "Q"): -3, ("Z", "Z"): 4,
+    ("V", "A"): -1, ("C", "C"): 9, ("M", "R"): -2, ("V", "E"): -3,
+    ("T", "N"): -1, ("P", "P"): 8, ("V", "I"): 3, ("V", "S"): -3,
+    ("Z", "P"): -2, ("V", "M"): 0, ("T", "F"): -3, ("V", "Q"): -3,
+    ("K", "K"): 6, ("P", "D"): -3, ("I", "H"): -4, ("I", "D"): -5,
+    ("T", "R"): -2, ("P", "L"): -4, ("K", "G"): -3, ("M", "N"): -3,
+    ("P", "H"): -3, ("F", "Q"): -4, ("Z", "G"): -3, ("X", "L"): -2,
+    ("T", "M"): -1, ("Z", "C"): -5, ("X", "H"): -2, ("D", "R"): -3,
+    ("B", "W"): -6, ("X", "D"): -2, ("Z", "K"): 0, ("F", "A"): -3,
+    ("Z", "W"): -4, ("F", "E"): -5, ("D", "N"): 1, ("B", "K"): -1,
+    ("X", "X"): -2, ("F", "I"): -1, ("B", "G"): -2, ("X", "T"): -1,
+    ("F", "M"): -1, ("B", "C"): -4, ("Z", "I"): -4, ("Z", "V"): -3,
+    ("S", "S"): 5, ("L", "Q"): -3, ("W", "E"): -5, ("Q", "R"): 0,
+    ("N", "N"): 7, ("W", "M"): -2, ("Q", "C"): -4, ("W", "I"): -4,
+    ("S", "C"): -2, ("L", "A"): -2, ("S", "G"): -1, ("L", "E"): -4,
+    ("W", "Q"): -3, ("H", "G"): -3, ("S", "K"): -1, ("Q", "N"): 0,
+    ("N", "R"): -1, ("H", "C"): -5, ("Y", "N"): -3, ("G", "Q"): -3,
+    ("Y", "F"): 3, ("C", "A"): -1, ("V", "L"): 0, ("G", "E"): -3,
+    ("G", "A"): -1, ("K", "R"): 2, ("E", "D"): 1, ("Y", "R"): -3,
+    ("M", "Q"): -1, ("T", "I"): -2, ("C", "D"): -5, ("V", "F"): -2,
+    ("T", "A"): 0, ("T", "P"): -2, ("B", "P"): -3, ("T", "E"): -2,
+    ("V", "N"): -4, ("P", "G"): -4, ("M", "A"): -2, ("K", "H"): -1,
+    ("V", "R"): -4, ("P", "C"): -5, ("M", "E"): -3, ("K", "L"): -3,
+    ("V", "V"): 5, ("M", "I"): 1, ("T", "Q"): -1, ("I", "G"): -6,
+    ("P", "K"): -2, ("M", "M"): 7, ("K", "D"): -2, ("I", "C"): -2,
+    ("Z", "D"): 0, ("F", "R"): -4, ("X", "K"): -1, ("Q", "D"): -1,
+    ("X", "G"): -3, ("Z", "L"): -4, ("X", "C"): -3, ("Z", "H"): 0,
+    ("B", "L"): -5, ("B", "H"): -1, ("F", "F"): 7, ("X", "W"): -4,
+    ("B", "D"): 4, ("D", "A"): -3, ("S", "L"): -3, ("X", "S"): -1,
+    ("F", "N"): -4, ("S", "R"): -2, ("W", "D"): -6, ("V", "Y"): -3,
+    ("W", "L"): -3, ("H", "R"): -1, ("W", "H"): -3, ("H", "N"): 0,
+    ("W", "T"): -4, ("T", "T"): 6, ("S", "F"): -3, ("W", "P"): -5,
+    ("L", "D"): -5, ("B", "I"): -5, ("L", "H"): -4, ("S", "N"): 0,
+    ("B", "T"): -1, ("L", "L"): 5, ("Y", "K"): -3, ("E", "Q"): 2,
+    ("Y", "G"): -5, ("Z", "S"): -1, ("Y", "C"): -4, ("G", "D"): -2,
+    ("B", "V"): -5, ("E", "A"): -1, ("Y", "W"): 2, ("E", "E"): 6,
+    ("Y", "S"): -3, ("C", "N"): -4, ("V", "C"): -2, ("T", "H"): -2,
+    ("P", "R"): -3, ("V", "G"): -5, ("T", "L"): -2, ("V", "K"): -3,
+    ("K", "Q"): 1, ("R", "A"): -2, ("I", "R"): -4, ("T", "D"): -2,
+    ("P", "F"): -5, ("I", "N"): -4, ("K", "I"): -4, ("M", "D"): -5,
+    ("V", "W"): -3, ("W", "W"): 11, ("M", "H"): -3, ("P", "N"): -3,
+    ("K", "A"): -1, ("M", "L"): 2, ("K", "E"): 0, ("Z", "E"): 4,
+    ("X", "N"): -2, ("Z", "A"): -1, ("Z", "M"): -2, ("X", "F"): -2,
+    ("K", "C"): -5, ("B", "Q"): -1, ("X", "B"): -2, ("B", "M"): -4,
+    ("F", "C"): -3, ("Z", "Q"): 4, ("X", "Z"): -1, ("F", "G"): -5,
+    ("B", "E"): 0, ("X", "V"): -2, ("F", "K"): -4, ("B", "A"): -3,
+    ("X", "R"): -2, ("D", "D"): 7, ("W", "G"): -5, ("Z", "F"): -4,
+    ("S", "Q"): -1, ("W", "C"): -4, ("W", "K"): -5, ("H", "Q"): 1,
+    ("L", "C"): -3, ("W", "N"): -5, ("S", "A"): 1, ("L", "G"): -5,
+    ("W", "S"): -4, ("S", "E"): -1, ("H", "E"): -1, ("S", "I"): -3,
+    ("H", "A"): -3, ("S", "M"): -3, ("Y", "L"): -2, ("Y", "H"): 1,
+    ("Y", "D"): -5, ("E", "R"): -1, ("X", "P"): -3, ("G", "G"): 6,
+    ("G", "C"): -5, ("E", "N"): -1, ("Y", "T"): -3, ("Y", "P"): -5,
+    ("T", "K"): -1, ("A", "A"): 5, ("P", "Q"): -2, ("T", "C"): -2,
+    ("V", "H"): -4, ("T", "G"): -3, ("I", "Q"): -4, ("Z", "T"): -2,
+    ("C", "R"): -5, ("V", "P"): -4, ("P", "E"): -2, ("M", "C"): -3,
+    ("K", "N"): 0, ("I", "I"): 5, ("P", "A"): -1, ("M", "G"): -4,
+    ("T", "S"): 1, ("I", "E"): -4, ("P", "M"): -3, ("M", "K"): -2,
+    ("I", "A"): -2, ("P", "I"): -4, ("R", "R"): 7, ("X", "M"): -2,
+    ("L", "I"): 1, ("X", "I"): -2, ("Z", "B"): 0, ("X", "E"): -2,
+    ("Z", "N"): -1, ("X", "A"): -1, ("B", "R"): -2, ("B", "N"): 4,
+    ("F", "D"): -5, ("X", "Y"): -2, ("Z", "R"): -1, ("F", "H"): -2,
+    ("B", "F"): -5, ("F", "L"): 0, ("X", "Q"): -1, ("B", "B"): 4
+}, dict())
 
 
 '''
@@ -95,7 +192,8 @@
 After transform the distance matrix into a similarity matrix, normalize each value by the highest_similarity.
     NOTE: now the maximum similarity is 1
 '''
-miyata_similarity_matrix = {
+
+miyata_similarity_matrix = store_swap_key({
  ('A', 'A'): 1.0,
  ('A', 'C'): -0.112,
  ('A', 'P'): 0.952,
@@ -305,4 +403,4 @@
  ('Y', 'S'): -1.664,
  ('Y', 'T'): -0.96,
  ('Y', 'V'): -0.216,
- ('Y', 'Y'): 1.0}
+ ('Y', 'Y'): 1.0}, dict())