GFAvc v0.4.2

Sorting paths by name

GFAvc.py

@@ -5,14 +5,14 @@ GFAvc: GFA version converter.
 Convert GFA from v1.1 to v1.0 (Convert walk to paths) and vice versa.
 
 @author: alexis.mergez@inrae.fr
-@version: 0.4.1
+@version: 0.4.2
 """
 import re
 import argparse
 import os
 import gzip
 
-version = "0.4.1"
+version = "0.4.2"
 
 ## Argument parser
 arg_parser = argparse.ArgumentParser(description='GFAvc: GFA version converter')
@@ -92,6 +92,9 @@ def gfa11_to_gfa10(gfa1_file = args.GFA1):
     _[1] = "VN:Z:1.0"
     gfa[0] = "\t".join(_)
 
+    # Used to store paths are order them at the end
+    paths_dict = {}
+
     #% Iterating in reverse to put paths at the end.
     for lineID in sorted(range(len(gfa)), reverse = True):
         if gfa[lineID][0] == "S" :
@@ -115,13 +118,19 @@ def gfa11_to_gfa10(gfa1_file = args.GFA1):
 
             newLine = ['P', name, ','.join(path), '*']
 
-            gfa.append('\t'.join(newLine))
+            paths_dict[name] = '\t'.join(newLine)
+            #gfa.append('\t'.join(newLine))
 
         #% Moving path lines to the end
         if gfa[lineID][0] == "P" :
 
             curLine = gfa.pop(lineID)
-            gfa.append(curLine)
+            name = curLine.split('\t')[1]
+            paths_dict[name] = '\t'.join(curLine)
+            #gfa.append(curLine)
+
+    for name in sorted(paths_dict.keys()):
+        gfa.append(paths_dict[name])
 
     return gfa
 
@@ -141,6 +150,9 @@ def gfa10_to_gfa11(gfa_file = args.GFA, index = index):
     sign = {"+": ">", "-": "<"}
     samples = []
 
+    # Used to store paths are order them at the end
+    paths_dict = {}
+
     #% Iterating in reverse to put walks at the end.
     for lineID in sorted(range(len(gfa)), reverse = True):
 
@@ -169,15 +181,22 @@ def gfa10_to_gfa11(gfa_file = args.GFA, index = index):
             newLine = ['W'] + ID + RANGE + [f"{''.join(walk)}"]
             samples.append(ID[0])
 
-            gfa.append('\t'.join(newLine))
+            paths_dict[splittedID[0]] = '\t'.join(newLine)
+            #gfa.append('\t'.join(newLine))
 
         #% Moving walk lines to the end
         if gfa[lineID][0] == "W" :
 
             curLine = gfa.pop(lineID)
-            gfa.append(curLine)
+            name = '#'.join(curLine.split('\t')[1:4])
+            paths_dict[name] = '\t'.join(curLine)
+            #gfa.append(curLine)
+
+    for name in sorted(paths_dict.keys()):
+        gfa.append(paths_dict[name])
 
     samples = list(set(samples))
+
     #% Changing version number in header
     assert gfa[0].split('\t')[1] == "VN:Z:1.0"
     _ = gfa[0].split('\t')