1.7.3.2

Kinggerm · Feb 3, 2021 · d43673f · d43673f
1 parent 107a8f1
commit d43673f
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Showing 2 changed files with 24 additions and 5 deletions.
diff --git a/GetOrganelleLib/assembly_parser.py b/GetOrganelleLib/assembly_parser.py
@@ -289,7 +289,7 @@ def parse_gfa(self, gfa_file, default_cov=1., min_cov=0., max_cov=inf):
                 for line in gfa_open:
                     if line.startswith("S\t"):
                         elements = line.strip().split("\t")
-                        record_type = elements.pop(0)  # not used
+                        elements.pop(0)  # record_type
                         vertex_name = elements.pop(0)  # segment name
                         sequence = elements.pop(0)
                         seq_len_tag = None
@@ -341,7 +341,13 @@ def parse_gfa(self, gfa_file, default_cov=1., min_cov=0., max_cov=inf):
                 gfa_open.seek(0)
                 for line in gfa_open:
                     if line.startswith("L\t"):
-                        flag, vertex_1, end_1, vertex_2, end_2, alignment_cigar = line.strip().split("\t")
+                        elements = line.strip().split("\t")
+                        elements.pop(0)  # flag
+                        vertex_1 = elements.pop(0)
+                        end_1 = elements.pop(0)
+                        vertex_2 = elements.pop(0)
+                        end_2 = elements.pop(0)
+                        alignment_cigar = elements.pop(0)
                         # "head"~False, "tail"~True
                         if vertex_1 in self.vertex_info and vertex_2 in self.vertex_info:
                             # different notation as to our Assembly system
@@ -354,9 +360,9 @@ def parse_gfa(self, gfa_file, default_cov=1., min_cov=0., max_cov=inf):
                 for line in gfa_open:
                     if line.startswith("S\t"):
                         elements = line.strip().split("\t")
-                        record_type = elements.pop(0)  # not used
+                        elements.pop(0)  # record_type
                         vertex_name = elements.pop(0)  # segment name
-                        seq_len_tag = int(elements.pop(0))
+                        int(elements.pop(0))  # seq_len_tag
                         sequence = elements.pop(0)
                         seq_len_tag = None
                         kmer_count = None
@@ -405,7 +411,13 @@ def parse_gfa(self, gfa_file, default_cov=1., min_cov=0., max_cov=inf):
                 gfa_open.seek(0)
                 for line in gfa_open:
                     if line.startswith("E\t"):  # gfa2 uses E
-                        flag, vertex_1, end_1, vertex_2, end_2, alignment_cigar = line.strip().split("\t")
+                        elements = line.strip().split("\t")
+                        elements.pop(0)  # flag
+                        vertex_1 = elements.pop(0)
+                        end_1 = elements.pop(0)
+                        vertex_2 = elements.pop(0)
+                        end_2 = elements.pop(0)
+                        alignment_cigar = elements.pop(0)
                         # "head"~False, "tail"~True
                         if vertex_1 in self.vertex_info and vertex_2 in self.vertex_info:
                             end_1 = {"+": True, "-": False}[end_1]

diff --git a/GetOrganelleLib/versions.py b/GetOrganelleLib/versions.py
@@ -5,6 +5,13 @@ def get_versions():
 
 
 versions = [
+    {
+        "number": "1.7.3.2",
+        "features": [
+            "1. improve support for standard gfa format: E/L with optional fields",
+        ],
+        "time": "2021-02-03 13:30 UTC+8"
+    },
     {
         "number": "1.7.3.1",
         "features": [