Merge pull request #62 from Luxxii/master

Release of ProtGraph 0.3.9

.github/workflows/functional_tests.yaml

@@ -7,7 +7,6 @@ jobs:
     strategy:
       matrix:
         python-version:
-        - '3.6' 
         - '3.7' 
         - '3.8' 
         - '3.9' 
@@ -22,16 +21,19 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install pipenv
-        run: |
-          python -m pip install --upgrade pipenv wheel
-
       - name: Install dependencies
         run: |
-          pipenv install
-          pipenv install -d
-          pipenv run pip install -e .
+          pip install -e . 
+          pip install pylint
+          pip install pytest
+          pip install redis
+          pip install redisgraph
+          pip install psycopg
+          pip install gremlinpython
+          pip install mysql-connector-python
+          pip install cassandra-driver
+          pip install apsw
 
       - name: Run Complete tests
         run: |
-          pipenv run pytest
+          python -m pytest

.github/workflows/pypi.yaml

@@ -3,16 +3,16 @@ on: [push, pull_request]
 
 jobs:
   build-publish:
-    runs-on: ubuntu-latest 
+    runs-on: ubuntu-latest
 
     steps:
       - name: Check out Repository
         uses: actions/checkout@v2
 
-      - name: Setup Python 3.6
+      - name: Setup Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: 3.6
+          python-version: 3.9
 
       - name: Install Python build
         run: |

MANIFEST.in

@@ -1 +1 @@
-include Pipfile LICENSE
+include requirements.txt LICENSE

protgraph/annotate_ptms.py

@@ -1,4 +1,5 @@
-from Bio.SwissProt import FeatureLocation, FeatureTable, UnknownPosition
+from Bio.SeqFeature import FeatureLocation, UnknownPosition
+from Bio.SwissProt import FeatureTable
 
 
 def annotate_ptms(graph_entry, var_mods: list, fix_mods: list, mass_factor: int):

protgraph/export/cassandra.py

@@ -1,7 +1,8 @@
 import json
 
 # import cassandra
-from Bio.SwissProt import FeatureLocation, FeatureTable
+from Bio.SeqFeature import FeatureLocation
+from Bio.SwissProt import FeatureTable
 # from cassandra.query import BatchStatement
 from cassandra import InvalidRequest
 from cassandra.cluster import Cluster

protgraph/export/mysql.py

@@ -1,7 +1,8 @@
 import json
 
 import mysql.connector
-from Bio.SwissProt import FeatureLocation, FeatureTable
+from Bio.SeqFeature import FeatureLocation
+from Bio.SwissProt import FeatureTable
 
 from protgraph.export.abstract_exporter import AExporter
 from protgraph.graph_collapse_edges import Or

protgraph/export/peptides/abstract_peptide_exporter.py

@@ -75,12 +75,12 @@ def export(self, prot_graph, queue):
         # Iterate over all peptides
         for path in self._get_peps(prot_graph, __start_node__, __stop_node__):
 
-
             # Get the actual peptide (concatenated aminoacids)
             aas = "".join(prot_graph.vs[path[1:-1]]["aminoacid"])
 
             # Get the edge ids from a path
-            edge_ids = prot_graph.get_eids(path=path)
+            pairs = [(a, b) for a, b in zip(path, path[1:])]
+            edge_ids = prot_graph.get_eids(pairs=pairs)
 
             # Skip Peptides, which contain an X
             if self.skip_x and "X" in aas:

protgraph/export/peptides/pep_fasta.py

@@ -1,4 +1,4 @@
-from Bio.SwissProt import UnknownPosition
+from Bio.SeqFeature import UnknownPosition
 
 from protgraph.export.peptides.abstract_peptide_exporter import \
     APeptideExporter

protgraph/export/peptides/pep_sqlite.py

@@ -123,7 +123,7 @@ def _create_tables(self, **kwargs):
                     peptide {B},
                     meta {B});""".format(B="BLOB" if self.use_blob else "TEXT"))
         except Exception as e:
-            print("Warning: Failed creating table 'peptides_meta' (Reason: {})".format(str(e)))
+            print("Warning: Failed creating table 'peptide_meta' (Reason: {})".format(str(e)))
         finally:
             # self.conn.commit()
             cur.close()
@@ -195,7 +195,7 @@ def export_peptides(self, prot_graph, l_path_nodes, l_path_edges, l_peptide, l_m
             self._retry_query_many(
                 cur,
                 """
-                INSERT INTO peptides_meta (peptide, meta)
+                INSERT INTO peptide_meta (peptide, meta)
                 VALUES (?, ?);
                 """,
                 zip(compressed_peptides, compressed_metas)

protgraph/export/postgres.py

@@ -1,7 +1,8 @@
 import json
 
 import psycopg
-from Bio.SwissProt import FeatureLocation, FeatureTable
+from Bio.SeqFeature import FeatureLocation
+from Bio.SwissProt import FeatureTable
 
 from protgraph.export.abstract_exporter import AExporter
 from protgraph.graph_collapse_edges import Or

protgraph/export/redisgraph.py

@@ -1,5 +1,6 @@
 import redis
-from Bio.SwissProt import FeatureLocation, FeatureTable
+from Bio.SeqFeature import FeatureLocation
+from Bio.SwissProt import FeatureTable
 from redisgraph import Edge, Graph, Node
 
 from protgraph.export.abstract_exporter import AExporter