reflexive 1.2.3__py3-none-any.whl → 1.2.5__py3-none-any.whl

reflexive/analyse.py

@@ -8,7 +8,7 @@ from reflexive import cfg
 from reflexive import session
 
 import logging
-logging.basicConfig(level=logging.DEBUG)
+#logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 

reflexive/res.py

@@ -117,10 +117,94 @@ class Res_display:
             html_out = displacy.render(disp_data,manual=True,style="ent", options=self.res_analyse.config.display_options,page=True,jupyter=False)
         return html_out
     
-    def show_graph(self,reflexive_expressions) ->list:
+    def get_interactions(self,df:DataFrame) -> DataFrame:
         #Get RE sequence
-        reseq = [label for re,label in reflexive_expressions]
-        return reseq
+        df = self._add_res_sequence(df)
+        df = self._add_res_interactions(df)
+        df = self._add_res_adj_matrix(df)
+        return df
+    
+    def show_graph(self,df:DataFrame,inline=True) -> str:
+        for am in df.res_adj_matrix:
+            g = RES_graph(am)
+            g.show()
+        return("nothing yet")
+    
+    def _add_res_sequence(self,df):
+        temp_df = df.copy()
+        temp_df['res_sequence'] = temp_df.reflexive_expressions.apply(self._get_res_sequence)
+        return temp_df
+    
+    def _add_res_interactions(self,df):
+        temp_df = df.copy()
+        temp_df['res_interactions'] = temp_df.res_sequence.apply(self._count_res_interactions)
+        return temp_df
+    
+    def _add_res_weights(self,df):
+        temp_df = df.copy()
+        temp_df['res_weights'] = temp_df.res_interactions.apply(self._calc_res_weights)
+        return temp_df
+    
+    def _add_res_adj_matrix(self,df):
+        temp_df = df.copy()
+        temp_df['res_adj_matrix'] = temp_df.res_weights.apply(self._create_adj_matrix)
+        return temp_df
+    
+    def _get_res_sequence(self,reflexive_expressions):
+        re_seq = [label for re,label in reflexive_expressions]
+        res_seq = []
+        # Need to substitute new RES labels for old RE labels
+        for re in re_seq:
+            if re=='ER' or re=='VR':
+                res_seq.append('NR')
+            elif re=='EV':
+                res_seq.append('EP')
+            elif re=='CN':
+                res_seq.append('AF')
+            else:
+                res_seq.append(re)
+        return res_seq
+    
+    def _empty_res_interactions(self) -> dict[tuple,int]:
+        RE_types = ['RR','NR','AR','AF','EP']
+        RE_interactions:dict[tuple,int] = dict()
+        for t1 in RE_types:
+            for t2 in RE_types:
+                entry = tuple(sorted((t1,t2)))
+                if entry not in RE_interactions.keys():
+                    RE_interactions[entry] = 0
+        return RE_interactions
+    
+    def _count_res_interactions(self,re_sequence:list[str]) -> dict[tuple,int]:
+        re_ints = self._empty_res_interactions()
+        limit = len(re_sequence)-1
+        for i,s in enumerate(re_sequence):
+            if i < limit:
+                rei = tuple(sorted((s,re_sequence[i+1])))
+                #print(i,rei)
+                re_ints[rei] += 1 
+        return re_ints
+    
+    def _calc_res_weights(self,interactions:dict[tuple,int])->dict[tuple,float]:
+        max = max(interactions.values())
+        weights = dict()
+        for edge,count in interactions.items():
+            weights[edge] = round(count/(15*max),3)
+        return weights
+            
+    
+    def _create_adj_matrix(self,weights:dict[tuple,float])->list[list[float]]:
+        re_types = ["RR","NR","AR","AF","EP"]
+        matrix = []
+        for r in re_types:
+            row = []
+            for c in re_types:
+                key = tuple(sorted((r,c)))
+                #print(key)
+                weight = weights.get(key,0)
+                row.append(weight)
+            matrix.append(row)
+        return matrix
         
         
         

reflexive/res_functions.py

@@ -0,0 +1,62 @@
+# import text into dataframe
+# accepts either an iterable of strings, or an iterable over text files
+# returns a pandas series iterable of type string
+
+# clean text and calculate length
+# accepts an iterable of strings in form of pandas series of type string
+# returns a pandas series iterable of type int
+
+
+# chunk text and keep original index ref
+# accepts an iterable of dataframe rows
+# returns an iterable of dataframe rows with added column 'text_chunks' - list of strings
+
+# upload docs to s3 and save local copy - side effects
+# accepts an iterable of iterable of chunks (with ids)
+# returns an an iterable of s3 responses? URLs to S3 file?
+
+# initiate custom entity job on comprehend
+# no parameters
+# returns job id for checking status, and downloading
+
+# check status
+# accepts job id
+# returns status
+
+# download results
+# accepts job id
+# returns iterable of results
+
+# unpack results and load into dataframe
+
+
+# extract reflexive expressions into dataframe
+
+
+# get reflexive sequences
+
+
+# get interactions
+
+
+# create count adj matrix
+
+
+# create weighted adj matrix
+
+
+# save dataframe to file
+
+
+# visualise expressions in text
+
+
+# visualise reflexive sequence
+
+
+# visualise res graph
+
+
+#
+# Network analysis functions
+#

reflexive/session.py

@@ -7,7 +7,7 @@ import json
 from reflexive import cfg
 
 import logging
-logging.basicConfig(level=logging.DEBUG)
+#logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 class AWS:

reflexive/util.py

@@ -3,7 +3,7 @@ import json
 import pandas as pd
 from sklearn.preprocessing import MinMaxScaler
 import logging
-logging.basicConfig(level=logging.DEBUG)
+#logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 

{reflexive-1.2.3.dist-info → reflexive-1.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: reflexive
-Version: 1.2.3
+Version: 1.2.5
 Summary: Supports AWS Reflexive Expressions Systems (RES) Analysis
 Project-URL: Repository, https://github.com/nlytx/reflexive.git
 Author-email: Andrew Gibson <andrew@nlytx.io>

reflexive-1.2.5.dist-info/RECORD

@@ -0,0 +1,12 @@
+reflexive/__init__.py,sha256=x5l8GV_9yC8yJyjTLqiM_WkfuPMLuNgQxF6PIz5MfFU,422
+reflexive/analyse.py,sha256=CU6mQ8PxQrkOvuSe4mmnuI18jGMkuxql3zLZ1vEeMEY,17466
+reflexive/cfg.py,sha256=tDPiC9NwpEVoT05_831sMsMfHhJt8pVrSOsgbtzTNDM,4267
+reflexive/res.py,sha256=ekpjo-dA4QT3swE-HDsWrgHp2oYy8SD2qVAeUL4v1OM,7393
+reflexive/res_functions.py,sha256=YF45yUF8NYMSC19DFpE0lmV4xyNxv3QqbbzZmdwmFzg,1231
+reflexive/session.py,sha256=8STWo8sqmWn-1PHcloFbgmLEvd7lsiFTU4t7ESRTsvw,10046
+reflexive/util.py,sha256=uU7-lqUmiCiCaR85AdNFKXrdrBspjb1Rmd-yThA3fRU,3699
+reflexive/visualise.py,sha256=pVnsPJOnHiLAIvDDm9P0u6-sGQINC4GVOY9b0GrzTK4,11725
+reflexive-1.2.5.dist-info/METADATA,sha256=NLXNj7RjrhdIBaIezMJFtTXfayBQ7QAMiCCk6Y1LEYc,574
+reflexive-1.2.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+reflexive-1.2.5.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+reflexive-1.2.5.dist-info/RECORD,,

reflexive-1.2.3.dist-info/RECORD

@@ -1,11 +0,0 @@
-reflexive/__init__.py,sha256=x5l8GV_9yC8yJyjTLqiM_WkfuPMLuNgQxF6PIz5MfFU,422
-reflexive/analyse.py,sha256=LsDgFI_UUlK88ecQc19iPdcweAvT11CZCqtWtCsevC8,17465
-reflexive/cfg.py,sha256=tDPiC9NwpEVoT05_831sMsMfHhJt8pVrSOsgbtzTNDM,4267
-reflexive/res.py,sha256=D4LfMG20BikFHdLts3v6dbYZG6UubCNlGUBUJbpJfwg,4398
-reflexive/session.py,sha256=ttyUAowaKgkwAgejRb_af5nZruKeH_kn3NB1NtitYUk,10045
-reflexive/util.py,sha256=zwlFncsWrRSuK8rsQaZKFNVLTkRySb1WPeY6Hz6qHhc,3698
-reflexive/visualise.py,sha256=pVnsPJOnHiLAIvDDm9P0u6-sGQINC4GVOY9b0GrzTK4,11725
-reflexive-1.2.3.dist-info/METADATA,sha256=NlCGUhf0OJWmRImBng_9YQGTsWbDFf-roOwVT_xVl88,574
-reflexive-1.2.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-reflexive-1.2.3.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-reflexive-1.2.3.dist-info/RECORD,,