Correctiong imports for module pgGraphs

pgGraphs/__init__.py

@@ -2,5 +2,4 @@
 from .abstractions import GFALine, GFAFormat, Orientation
 from .gfaparser import GFAParser
 from .graph import Graph
-from .io import GFAIO
 from .networkx import GFANetwork

pgGraphs/abstractions.py

@@ -1,12 +1,12 @@
 "Abstractions over GFA formats"
-from enum import Enum, auto
+from enum import Enum
 
 
 class Orientation(Enum):
     "Describes the way a node is read"
     FORWARD = '+'
     REVERSE = '-'
-    ANY = '?' | auto()
+    ANY = '?'
 
 
 class GFAFormat(Enum):
@@ -16,7 +16,7 @@ class GFAFormat(Enum):
     GFA1_1 = 'GFA1.1'
     GFA1_2 = 'GFA1.2'
     GFA2 = 'GFA2'
-    ANY = 'unknown' | auto()
+    ANY = 'unknown'
 
 
 class GFALine(Enum):
@@ -26,4 +26,4 @@ class GFALine(Enum):
     WALK = 'W'
     PATH = 'P'
     HEADER = 'H'
-    ANY = auto()
+    ANY = '?'

pgGraphs/gfaparser.py

@@ -3,7 +3,8 @@
 from typing import Callable
 from json import loads, dumps
 from os import path, stat
-from abstractions import Orientation, GFALine
+from tharospytools.path_tools import path_allocator
+from pgGraphs.abstractions import Orientation, GFALine, GFAFormat
 
 
 class GFAParser:
@@ -208,3 +209,41 @@ def read_gfa_line(datas: list[str], load_sequence_in_memory: bool = True) -> tup
                 return (datas[1], line_type, {**line_datas, **GFAParser.supplementary_datas(datas, 7)})
             case GFALine.HEADER | GFALine.ANY:
                 return (None, line_type, GFAParser.supplementary_datas(datas, 1))
+
+    @staticmethod
+    def save_graph(graph, output_path: str) -> None:
+        """Given a gfa Graph object, saves to a valid gfa file the Graph.
+
+        Args:
+            output_path (str): a path on disk where to save
+            output_format (GfaStyle): a format to choose for output.
+                if None, default graph format will be used.
+        """
+        line_number: int = 0
+        with open(path_allocator(output_path), 'w', encoding='utf-8') as gfa_writer:
+            if graph.headers:
+                for header in graph.headers:
+                    gfa_writer.write(
+                        "H\t"+'\t'.join([f"{key}:{GFAParser.get_python_type(value)}:{value}" if not key.startswith('ARG') else str(value) for key, value in header.items()])+"\n")
+            if graph.segments:
+                for segment_name, segment_datas in graph.segments.items():
+                    gfa_writer.write("S\t"+f"{segment_name}\t{segment_datas['seq'] if 'seq' in segment_datas else 'N'*segment_datas['length']}\t" + '\t'.join(
+                        [f"{key}:{GFAParser.get_python_type(value)}:{value}" if not key.startswith('ARG') else str(value) for key, value in segment_datas.items() if key not in ['length', 'seq']])+"\n")
+            if graph.lines:
+                for line in graph.lines:
+                    ori1, ori2 = line['orientation'].split('/')
+                    gfa_writer.write(f"L\t"+f"{line['start']}\t{ori1}\t{line['end']}\t{ori2}\t" + '\t'.join(
+                        [f"{key}:{GFAParser.get_python_type(value)}:{value}" if not key.startswith('ARG') else str(value) for key, value in line.items() if key not in ['orientation', 'start', 'end']])+"\n")
+            if graph.paths:
+                for path_name, path_datas in graph.paths.items():
+                    if graph.metadata['version'] == GFAFormat.GFA1:  # P-line
+                        gfa_writer.write(
+                            f"P\t{path_name}\t{','.join([node_name+'+' if orient == Orientation.FORWARD else node_name+'-' for node_name, orient in path_datas['path']])}\t*")
+                    else:
+                        # W-line
+                        offset_start: int | str = path_datas['start_offset'] if 'start_offset' in path_datas else '?'
+                        offset_stop: int | str = path_datas['stop_offset'] if 'stop_offset' in path_datas else '?'
+                        strpath: str = ''.join(
+                            [f"{'>' if orient == Orientation.FORWARD else '<'}{node_name}" for node_name, orient in path_datas['path']])
+                        return f"W\t{path_name}\t{path_datas['origin'] if 'origin' in path_datas else line_number}\t{path_datas['name']}\t{offset_start}\t{offset_stop}\t{strpath}\t*\n"
+                    line_number += 1

pgGraphs/graph.py

@@ -1,7 +1,6 @@
 "Modelizes a graph object"
 from pgGraphs.abstractions import GFALine, Orientation
 from pgGraphs.gfaparser import GFAParser
-from pgGraphs.io import GFAIO
 
 
 class Graph():
@@ -72,7 +71,7 @@ def save_graph(self, output_file: str) -> None:
         Args:
             output_file (str): path where to output the graph
         """
-        GFAIO.save_graph(self, output_path=output_file)
+        GFAParser.save_graph(self, output_path=output_file)
 
 ################################################# ADD ELEMNTS TO GRAPH #################################################
 

requirements.txt

@@ -0,0 +1,2 @@
+networkx
+tharos-pytools

test_pggraphs.py

@@ -0,0 +1,5 @@
+from pgGraphs import Graph
+
+
+def test_init_empty_graph() -> None:
+    graph: Graph = Graph()