Plugins adaptation to the new gff3 converter plugin

Plugins/__init__.py

@@ -1,4 +1,4 @@
-#__init.py__
+#Plugins/__init.py__
 
 from Plugins.__caller__ import Caller, UnknownCallerModeError, CallerFailedVerification
 

Plugins/read_gff_maker_3UTR.py

@@ -1,4 +1,4 @@
-#read_gff_maker_3UTR.py
+#Plugin/sread_gff_maker_3UTR.py
 
 import pandas as pd
 from Plugins.__read_gff_maker__ import __ReadGFFMaker__
@@ -10,7 +10,9 @@ class Plugin(__ReadGFFMaker__):
     """
     def feature_initialize(self, pre_feature, metadata):
         return SeqFeature(
-            FeatureLocation(int(pre_feature["start"]), int(pre_feature["stop"]), (1,-1)[pre_feature["strand"] == "-"]),
+            FeatureLocation(int(pre_feature["start"]), 
+                            int(pre_feature["end"]), 
+                            (1,-1)[pre_feature["strand"] == "-"]),
             type="3'UTR",
             qualifiers={
                 "gene":None,
@@ -20,16 +22,18 @@ def feature_initialize(self, pre_feature, metadata):
     """
     def process(self, app, caller_mode, key_handle, calls:list=[], target=None):
         try:
-            feature = self.feature_initialize(
-                app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1", "three_prime_UTR"),:].reset_index().iloc[0,:],
-                app.metadata)
+            pre_feature = app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1:three_prime_utr", "three_prime_UTR"),:].iloc[0,:]
+            feature = self.feature_initialize(pre_feature, app.metadata)
+            feature.qualifiers["gene"] = target[1]
         except KeyError:
             return None
 
-        feature.qualifiers["gene"] = target[1]
-        receiver = self.callbacks(
-            app,
-            calls,
-            (target[0], f"{target[1]}-mRNA-1", "3'UTR"))
-
-        return self.merge(feature, receiver)
+        try:
+            receiver = self.callbacks(
+                    app,
+                    calls,
+                    (target[0], f"{target[1]}-mRNA-1", "3'UTR"))
+        except KeyError:
+            receiver = []
+
+        return self.merge(feature, receiver)

Plugins/read_gff_maker_5UTR.py

@@ -1,4 +1,4 @@
-#read_gff_maker_5UTR.py
+#Plugins/read_gff_maker_5UTR.py
 
 import pandas as pd
 from Plugins.__read_gff_maker__ import __ReadGFFMaker__
@@ -10,26 +10,29 @@ class Plugin(__ReadGFFMaker__):
     """
     def feature_initialize(self, pre_feature, metadata):
         return SeqFeature(
-            FeatureLocation(int(pre_feature["start"]), int(pre_feature["stop"]), (1,-1)[pre_feature["strand"] == "-"]),
+            FeatureLocation(int(pre_feature["start"]), 
+                            int(pre_feature["end"]), 
+                            (1,-1)[pre_feature["strand"] == "-"]),
             type="5'UTR",
-            qualifiers={
-                "gene":None,
-                "note":list()})
+            qualifiers={"gene":None,
+                        "note":list()})
 
     """
     """
     def process(self, app, caller_mode, key_handle, calls:list=[], target=None):
         try:
-            feature = self.feature_initialize(
-                app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1", "five_prime_UTR"),:].reset_index().iloc[0,:],
-                app.metadata)
+            pre_feature = app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1:five_prime_utr", "five_prime_UTR"),:].iloc[0,:]
+            feature = self.feature_initialize(pre_feature, app.metadata)
+            feature.qualifiers["gene"] = target[1]
         except KeyError:
             return None
-
-        feature.qualifiers["gene"] = target[1]
-        receiver = self.callbacks(
-            app,
-            calls,
-            (target[0], f"{target[1]}-mRNA-1", "5'UTR"))
-
-        return self.merge(feature, receiver)
+
+        try:
+            receiver = self.callbacks(
+                    app,
+                    calls,
+                    (target[0], f"{target[1]}-mRNA-1", "5'UTR"))
+        except KeyError:
+            receiver = []
+
+        return self.merge(feature, receiver)

Plugins/read_gff_maker_CDS.py

@@ -1,4 +1,4 @@
-#read_gff_maker_CDS.py
+#Plugins/read_gff_maker_CDS.py
 
 import pandas as pd
 import itertools
@@ -11,9 +11,9 @@ class Plugin(__ReadGFFMaker__):
     """
     def feature_initialize(self, pre_feature, metadata):
         refactor_pre_feature = lambda element: FeatureLocation(
-            int(element[0]),
-            int(element[1]),
-            (1,-1)[element[2] == "-"])
+            int(element["start"]),
+            int(element["end"]),
+            (1,-1)[element["strand"] == "-"])
         merge_pre_feature = lambda  array: array[0] if len(array) == 1 else CompoundLocation(array)
 
         return SeqFeature(
@@ -40,21 +40,23 @@ def merge(self, feature, receiver):
     """
     def process(self, app, caller_mode, key_handle, calls:list=[], target=None):
         try:
-            feature = self.feature_initialize(
-                app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1", "CDS"),:].reset_index(),
-                app.metadata)
+            pre_feature = app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1:cds", "CDS"),:]
+            feature = self.feature_initialize(pre_feature, app.metadata)
+            feature.qualifiers["gene"] = target[1]
         except KeyError:
             return None
-
-        feature.qualifiers["gene"] = target[1]
-        receiver = self.callbacks(
-            app,
-            calls,
-            (target[0], f"{target[1]}-mRNA-1", "CDS"))
-
+
+        try:
+            receiver = self.callbacks(
+                    app,
+                    calls,
+                    (target[0], f"{target[1]}-mRNA-1", "CDS"))
+        except KeyError:
+            receiver = []
+
         return self.merge(feature, receiver)
 
     """
     """
     def required_metadata_check(self, app, keys:list=[]):
-        return super().required_metadata_check(app, ["transl_table"])
+        return super().required_metadata_check(app, ["transl_table"])

Plugins/read_gff_maker_exon.py

@@ -1,7 +1,6 @@
-#read_gff_maker_exon.py
+#Plugins/read_gff_maker_exon.py
 
 import pandas as pd
-import re
 
 from Plugins.__read_gff_maker__ import __ReadGFFMaker__
 from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
@@ -13,29 +12,29 @@ class Plugin(__ReadGFFMaker__):
     """
     def feature_initialize(self, pre_feature, metadata):
         return SeqFeature(
-            FeatureLocation(int(pre_feature["start"]), int(pre_feature["stop"]), (1,-1)[pre_feature["strand"] == "-"]),
+            FeatureLocation(int(pre_feature["start"]), 
+                            int(pre_feature["end"]), 
+                            (1,-1)[pre_feature["strand"] == "-"]),
             type="exon",
             qualifiers={})
 
-    """
-    """
-    def multi_feature_initialize(self, pre_multi_feature, metadata):
-        for _, element in pre_multi_feature:
-            yield self.feature_initialize(element, metadata)
-
-
     """
     """
     def process(self, app, caller_mode, key_handle, calls:list=[], target=None):
         try:
-            feature = self.multi_feature_initialize(
-                app.handles[key_handle].loc[(target, slice(None), "exon"),:].reset_index().iterrows(),
-                app.metadata)
+            multi_pre_feature = app.handles[key_handle].loc[(target, slice(None), "exon"),:].iterrows()
         except KeyError:
-            return None
-
-        receiver = self.callbacks(
-            app,
-            calls,
-            target)
-        return self.merge(feature, receiver)
+            multi_pre_feature = []
+
+        for _, pre_feature in multi_pre_feature:
+            feature = self.feature_initialize(pre_feature, app.metadata)
+
+            try:
+                receiver = self.callbacks(
+                        app,
+                        calls,
+                        target)
+            except KeyError:
+                receiver = []
+
+            yield self.merge(feature, receiver)

Plugins/read_gff_maker_gene.py

@@ -1,7 +1,6 @@
-#read_gff_maker_gene.py
+#Plugins/read_gff_maker_gene.py
 
 import pandas as pd
-import itertools
 from Plugins.__read_gff_maker__ import __ReadGFFMaker__
 from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
 
@@ -10,7 +9,9 @@ class Plugin(__ReadGFFMaker__):
     """
     def feature_initialize(self, pre_feature, metadata):
         return SeqFeature(
-            FeatureLocation(int(pre_feature["start"]), int(pre_feature["stop"]), (1,-1)[pre_feature["strand"] == "-"]),
+            FeatureLocation(int(pre_feature["start"]), 
+                            int(pre_feature["end"]), 
+                            (1,-1)[pre_feature["strand"] == "-"]),
             type="gene",
             qualifiers={
                 "gene":None,
@@ -27,13 +28,21 @@ def merge(self, feature, receiver):
     """
     """
     def process(self, app, caller_mode, key_handle, calls:list=[], target=None):
-        feature = self.feature_initialize(
-            app.handles[key_handle].loc[(target[0], target[1], "gene"),:].reset_index().iloc[0,:],
-            app.metadata)
-        feature.qualifiers["gene"]=target[1]
-        receiver = self.callbacks(
-            app,
-            calls,
-            (target[0], f"{target[1]}-mRNA-1", "gene"))
-
-        return self.merge(feature, receiver)
+        try:
+            pre_feature = app.handles[key_handle].loc[(target[0], target[1], "gene"),:].iloc[0,:]
+            feature = self.feature_initialize(
+                    pre_feature,
+                    app.metadata)
+            feature.qualifiers["gene"] = target[1]
+        except KeyError:
+            return None
+
+        try:
+            receiver = self.callbacks(
+                    app,
+                    calls,
+                    (target[0], f"{target[1]}-mRNA-1", "gene"))
+        except KeyError:
+            receiver = []
+
+        return self.merge(feature, receiver)

Plugins/read_gff_maker_mRNA.py

@@ -1,4 +1,4 @@
-#read_gff_maker_mRNA.py
+#Plugins/read_gff_maker_mRNA.py
 
 import pandas as pd
 from Plugins.__read_gff_maker__ import __ReadGFFMaker__
@@ -10,38 +10,35 @@ class Plugin(__ReadGFFMaker__):
     """
     def feature_initialize(self, pre_feature, metadata):
         refactor_pre_feature = lambda element: FeatureLocation(
-            int(element[0]),
-            int(element[1]),
-            (1,-1)[element[2] == "-"]
-        )
+            int(element["start"]),
+            int(element["end"]),
+            (1,-1)[element["strand"] == "-"])
         merge_pre_feature = lambda  array: array[0] if len(array) == 1 else CompoundLocation(array)
 
         return SeqFeature(
-            merge_pre_feature(
-                pre_feature.apply(refactor_pre_feature, axis=1)
-            ),
+            merge_pre_feature(pre_feature.apply(refactor_pre_feature, axis=1)),
             type="mRNA",
             qualifiers={
-                "gene":None
-            }
-        )
+                "gene":None})
 
     """
     """
     def process(self, app, caller_mode, key_handle, calls:list=[], target=None):
         try:
+            pre_feature = app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1:cds", "CDS"),:]
             feature = self.feature_initialize(
-                app.handles[key_handle].loc[(target[0], f"{target[1]}-mRNA-1", "CDS"),:].reset_index(),
-                app.metadata
-            )
+                    pre_feature,
+                    app.metadata)
+            feature.qualifiers["gene"] = target[1]
         except KeyError:
             return None
-
-        feature.qualifiers["gene"]=target[1]
-        receiver = self.callbacks(
-            app,
-            calls,
-            (target[0], f"{target[1]}-mRNA-1", "mRNA")
-        )
-
-        return self.merge(feature, receiver)
+
+        try:
+            receiver = self.callbacks(
+                    app,
+                    calls,
+                    (target[0], f"{target[1]}-mRNA-1", "mRNA"))
+        except KeyError:
+            receiver = []
+
+        return self.merge(feature, receiver)

Plugins/read_gff_maker_misc_feature.py

@@ -1,7 +1,6 @@
-#read_gff_maker_misc_feature.py
+#Plugins/read_gff_maker_misc_feature.py
 
 import pandas as pd
-import itertools
 from Plugins.__read_gff_maker__ import __ReadGFFMaker__
 from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
 
@@ -10,23 +9,29 @@ class Plugin(__ReadGFFMaker__):
     """
     def feature_initialize(self, pre_feature, metadata):
         return SeqFeature(
-            FeatureLocation(int(pre_feature["start"]), int(pre_feature["stop"]), (1,-1)[pre_feature["strand"] == "-"]),
+            FeatureLocation(int(pre_feature["start"]), 
+                            int(pre_feature["end"]), 
+                            (1,-1)[pre_feature["strand"] == "-"]),
             type="misc_feature",
             qualifiers={
-                #"gene":None,
                 "note":list()})
 
     """
     """
     def process(self, app, caller_mode, key_handle, calls:list=[], target=None):
-        feature = self.feature_initialize(
-            app.handles[key_handle].loc[(target[0], target[1], "gene"),:].reset_index().iloc[0,:],
-            app.metadata)
-        feature.qualifiers["note"].append(target[1])
-        #feature.qualifiers["gene"]=target[1]
-        receiver = self.callbacks(
-            app,
-            calls,
-            (target[0], f"{target[1]}-mRNA-1", "misc_feature"))
-
-        return self.merge(feature, receiver)
+        try:
+            pre_feature = app.handles[key_handle].loc[(target[0], target[1], "gene"),:].iloc[0,:]
+            feature = self.feature_initialize(pre_feature, app.metadata)
+            feature.qualifiers["note"].append(target[1])
+        except KeyError:
+            return None
+
+        try:
+            receiver = self.callbacks(
+                    app,
+                    calls,
+                    (target[0], f"{target[1]}-mRNA-1", "misc_feature"))
+        except KeyError:
+            receiver = []
+
+        return self.merge(feature, receiver)