a few minor code changes

ppanggolin/RGP/genomicIsland.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/RGP/rgp_cluster.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging
@@ -101,8 +100,7 @@ def genes(self):
         Return iterable of genes from all RGPs that are identical in families
         """
         for rgp in self.rgps:
-            for gene in rgp.genes:
-                yield gene
+            yield from rgp.genes
     @property
     def spots(self) -> Set[Spot]:
         """
@@ -283,7 +281,7 @@ def add_info_to_identical_rgps(rgp_graph: nx.Graph, identical_rgps_objects: List
                            name=identical_rgp_obj.name,
                            families_count=len(identical_rgp_obj.families),
                            identical_rgp_count=len(identical_rgp_obj.rgps),
-                           identical_rgp_names=';'.join([i_rgp.name for i_rgp in identical_rgp_obj.rgps]),
+                           identical_rgp_names=';'.join(i_rgp.name for i_rgp in identical_rgp_obj.rgps),
                            identical_rgp_genomes=';'.join({i_rgp.organism.name for i_rgp in identical_rgp_obj.rgps}),
                            identical_rgp_contig_border_count=len(
                                [True for i_rgp in identical_rgp_obj.rgps if i_rgp.is_contig_border]),

ppanggolin/align/alignOnPang.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import time

ppanggolin/annotate/annotate.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/annotate/synta.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/cluster/cluster.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/context/searchGeneContext.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/edge.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding: utf8
 
 # default libraries
 from collections import defaultdict
@@ -50,8 +49,7 @@ def organisms(self) -> Generator[Organism, None, None]:
 
         :return: Generator with organisms as the key and an iterable of the gene pairs as value
         """
-        for organism in self._organisms.keys():
-            yield organism
+        yield from self._organisms.keys()
 
     @property
     def number_of_organisms(self) -> int:

ppanggolin/figures/draw_spot.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 
 # default libraries

ppanggolin/figures/drawing.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/figures/tile_plot.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/formats/readBinaries.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging
@@ -152,8 +151,7 @@ def read_chunks(table: tables.Table, column: str = None, chunk: int = 10000):
     :param chunk:
     """
     for i in range(0, table.nrows, chunk):
-        for row in table.read(start=i, stop=i + chunk, field=column):
-            yield row
+        yield from table.read(start=i, stop=i + chunk, field=column)
 
 
 def read_genedata(h5f: tables.File) -> Dict[int, Genedata]:

ppanggolin/formats/writeAnnotations.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/formats/writeBinaries.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/formats/writeFlatGenomes.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/formats/writeFlatMetadata.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/formats/writeFlatPangenome.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/formats/writeMSA.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse
@@ -123,7 +122,7 @@ def write_fasta_families(family: GeneFamily, tmpdir: tempfile.TemporaryDirectory
 
     # get genes that are present in only one copy for our family in each organism.
     single_copy_genes = []
-    for _, genes in family.get_org_dict().items():
+    for genes in family.get_org_dict().values():
         if len(genes) == 1:
             single_copy_genes.extend(genes)
 

ppanggolin/formats/writeMetadata.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging
@@ -58,7 +57,7 @@ def write_metadata_status(pangenome: Pangenome, h5f: tables.File, status_group:
         metadata_group._v_attrs.modules = True
         metasources_group._v_attrs.modules = metasources["modules"]
 
-    return True if any(metadata_group._v_attrs._f_list()) else False
+    return any(metadata_group._v_attrs._f_list())
 
 
 def write_metadata_group(h5f: tables.File, metatype: str) -> tables.Group:

ppanggolin/formats/writeSequences.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/formats/write_proksee.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import json

ppanggolin/geneFamily.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding: utf8
 
 # default libraries
 from __future__ import annotations
@@ -259,26 +258,23 @@ def edges(self) -> Generator[Edge, None, None]:
 
         :return: Edges of the gene family
         """
-        for edge in self._edges_getter.values():
-            yield edge
+        yield from self._edges_getter.values()
 
     @property
     def neighbors(self) -> Generator[GeneFamily, None, None]:
         """Returns all the GeneFamilies that are linked with an edge
 
         :return: Neighbors
         """
-        for neighbor in self._edges_getter.keys():
-            yield neighbor
+        yield from self._edges_getter.keys()
 
     @property
     def genes(self):
         """Return all the genes belonging to the family
 
         :return: Generator of genes
         """
-        for gene in self._genes_getter.values():
-            yield gene
+        yield from self._genes_getter.values()
 
     @property
     def organisms(self) -> Generator[Organism, None, None]:
@@ -288,17 +284,15 @@ def organisms(self) -> Generator[Organism, None, None]:
         """
         if len(self._genePerOrg) == 0:
             _ = self.get_org_dict()
-        for org in self._genePerOrg.keys():
-            yield org
+        yield from self._genePerOrg.keys()
 
     @property
     def spots(self) -> Generator[Spot, None, None]:
         """Return all the spots belonging to the family
 
         :return: Generator of spots
         """
-        for spot in self._spots:
-            yield spot
+        yield from self._spots
 
     @property
     def module(self) -> Module:
@@ -446,8 +440,7 @@ def get_genes_per_org(self, org: Organism) -> Generator[Gene, None, None]:
             _ = self.get_org_dict()
         if org not in self._genePerOrg:
             raise KeyError(f"Genome does not have the gene family: {self.name}")
-        for gene in self._genePerOrg[org]:
-            yield gene
+        yield from self._genePerOrg[org]
 
 
     def is_single_copy(self, dup_margin: float, exclude_fragment: bool) -> bool:
@@ -459,10 +452,7 @@ def is_single_copy(self, dup_margin: float, exclude_fragment: bool) -> bool:
         :return: A boolean indicating whether the gene family is single copy.
         """
 
-        if self.duplication_ratio(exclude_fragment) < dup_margin:
-            return True
-        else:
-            return False
+        return self.duplication_ratio(exclude_fragment) < dup_margin
 
     def duplication_ratio(self, exclude_fragment: bool) -> bool:
         """

ppanggolin/genome.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding: utf8
 
 from __future__ import annotations
 import logging
@@ -230,7 +229,7 @@ def string_coordinates(self) -> str:
         """
         Return a string representation of the coordinates
         """
-        return ','.join([f'{start}..{stop}' for start, stop in self.coordinates])
+        return ','.join(f'{start}..{stop}' for start, stop in self.coordinates)
 
     def start_relative_to(self, gene):
         """

ppanggolin/graph/makeGraph.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/info/info.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/main.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import sys

ppanggolin/meta/meta.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/metadata.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding: utf8
 
 # default libraries
 import logging
@@ -119,8 +118,7 @@ def metadata(self) -> Generator[Metadata, None, None]:
         """
 
         for meta_dict in self._metadata_getter.values():
-            for metadata in meta_dict.values():
-                yield metadata
+            yield from meta_dict.values()
 
     @property
     def sources(self) -> Generator[str, None, None]:
@@ -260,7 +258,7 @@ def has_metadata(self) -> bool:
         :return: True if it has metadata else False
         """
 
-        return True if self.number_of_metadata > 0 else False
+        return self.number_of_metadata > 0
 
     def has_source(self, source: str) -> bool:
         """Check if the source is in the metadata feature
@@ -269,4 +267,4 @@ def has_source(self, source: str) -> bool:
 
         :return: True if the source is in the metadata feature else False
         """
-        return True if source in self._metadata_getter else False
+        return source in self._metadata_getter

ppanggolin/metrics/fluidity.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/metrics/metrics.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse

ppanggolin/mod/module.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging

ppanggolin/nem/partition.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import logging
@@ -166,7 +165,7 @@ def run_partitioning(nem_dir_path: Path, nb_org: int, beta: float = 2.5, free_di
                         partitions_list[i] = "S_"  # SHELL in case of doubt gene families is attributed to shell
                     else:
                         partitions_list[i] = parti[positions_max_prob.pop()]
-    except IOError:
+    except OSError:
         logging.getLogger("PPanGGOLiN").debug(
             "partitioning did not work (the number of genomes used is probably too low), "
             "see logs here to obtain more details " + nem_dir_path.as_posix() + "/nem_file_" +

ppanggolin/nem/rarefaction.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# coding:utf-8
 
 # default libraries
 import argparse