further cross-validations and errmsg

gfapy/gfa.py

@@ -101,7 +101,8 @@ def validate(self):
     """
     self.__validate_segment_references()
     self.__validate_path_links()
-    self.__validate_group_references()
+    self.__validate_group_items()
+    self.__validate_gfa2_positions()
 
   def __str__(self):
     return "\n".join([str(line) for line in self.lines])
@@ -262,7 +263,7 @@ def __validate_path_links(self):
               "does not exist, but is required by the following paths:\n"+
               l.refstr())
 
-  def __validate_group_references(self):
+  def __validate_group_items(self):
     if self.version == "gfa1":
       return
     for group in self.sets + self.paths:
@@ -275,6 +276,12 @@ def __validate_group_references(self):
               "does not exist, but is required by the following groups:\n"+
               item.refstr())
 
+  def __validate_gfa2_positions(self):
+    if self.version == "gfa1":
+      return
+    for line in self.edges + self.fragments:
+      line.validate_positions()
+
   def _validate_version(self):
     if (self._version != None) and (self._version not in gfapy.VERSIONS):
       raise gfapy.VersionError("GFA specification version {} not supported".

gfapy/line/edge/gfa2/gfa2.py

@@ -4,10 +4,11 @@
 from ..gfa2.alignment_type import AlignmentType as GFA2_AlignmentType
 from ..gfa2.references import References
 from ..gfa2.other import Other
+from ..gfa2.validation import Validation
 from ..edge import Edge
 
 class GFA2(Other, References, GFA2_AlignmentType, AlignmentType, FromTo,
-           ToGFA1, Edge):
+           ToGFA1, Validation, Edge):
   """An edge line of a GFA2 file."""
 
   RECORD_TYPE = "E"

gfapy/line/edge/gfa2/validation.py

@@ -0,0 +1,22 @@
+import gfapy
+
+class Validation:
+
+  def validate_positions(self):
+    "Checks that positions suffixed by $ are the last position of segments"
+    if self.is_connected():
+      for n in ["1","2"]:
+        seg = self.get("sid"+n).line
+        seq = seg.sequence
+        if not gfapy.is_placeholder(seq):
+          seqlen = len(seq)
+          for pfx in ["beg", "end"]:
+            fn = pfx+n
+            pos = self.get(fn)
+            if gfapy.islastpos(pos):
+              if pos != seqlen:
+                raise gfapy.InconsistencyError(
+                    "Edge: {}\n".format(str(self))+
+                    "Field {}: $ after ".format(fn)+
+                    "non-last position\n".format(str(pos))+
+                    "Segment: {}".format(str(seg)))

gfapy/line/fragment/fragment.py

@@ -1,7 +1,8 @@
 from .references import References
+from .validation import Validation
 from ..line import Line
 
-class Fragment(References, Line):
+class Fragment(References, Validation, Line):
   """
   A fragment line of a GFA2 file
   """

gfapy/line/fragment/validation.py

@@ -0,0 +1,21 @@
+import gfapy
+
+class Validation:
+
+  def validate_positions(self):
+    "Checks that positions suffixed by $ are the last position of segments"
+    if self.is_connected():
+      seg = self.get("sid")
+      seq = seg.sequence
+      if not gfapy.is_placeholder(seq):
+        seqlen = len(seq)
+        for sfx in ["beg", "end"]:
+          fn = "s_"+sfx
+          pos = self.get(fn)
+          if gfapy.islastpos(pos):
+            if pos != seqlen:
+              raise gfapy.InconsistencyError(
+                  "Edge: {}\n".format(str(self))+
+                  "Field {}: $ after ".format(str(fn))+
+                  "non-last position ({})\n".format(str(pos))+
+                  "Segment: {}".format(str(seg)))

gfapy/line/segment/length_gfa1.py

@@ -51,6 +51,7 @@ def validate_length(self):
     if not gfapy.is_placeholder(self.sequence) and "LN" in self.tagnames:
       if self.LN != len(self.sequence):
         raise gfapy.InconsistencyError(
+          "Segment: {}\n".format(str(self))+
           "Length in LN tag ({}) ".format(self.LN)+
           "is different from length of sequence field ({})"
           .format(len(self.sequence)))

tests/testdata/invalid/edge_wrong_lastpos.gfa2

@@ -0,0 +1,12 @@
+H	VN:Z:2.0
+H	ul:Z:https://github.com/sjackman/assembly-graph/blob/master/sample.gfa
+S	1	8	CGATGCAA
+S	2	10	TGCAAAGTAC
+S	3	21	TGCAACGTATAGACTTGTCAC	RC:i:4
+S	4	7	GCATATA
+S	5	8	CGATGATA
+S	6	4	ATGA
+E	*	1+	2+	3	9$	0	5	5M
+E	*	3+	2+	21$	21$	0	0	0M
+E	*	3+	4-	17	21$	3	7$	1M1D2M
+E	*	4-	5+	0	0	0	0	0M

tests/testdata/invalid/fragment_wrong_lastpos.gfa2

@@ -0,0 +1,33 @@
+# File used for the collections test
+# similar but NOT equivalent to the gfa1 file!
+S	1	122	*
+S	3	29	TGCTAGCTGACTGTCGATGCTGTGTG
+E	1_to_2	1+	2+	110	122$	0	12	12M
+S	5	130	*
+S	13	150	*
+E	2_to_6	2+	6+	0	122$	10	132	122M
+O	14	11+ 12+
+S	11	140	*	xx:i:11
+F	3	read1+	0	42$	12	55	*	id:Z:read1_in_3
+F	2	read2+	45	62	0	18	*	id:Z:read2_in_2
+U	16	1 3 15 2_to_6 16sub
+H	ac:Z:test2
+# another comment
+S	12	150	*
+S	4	120	*
+H	VN:Z:2.0
+E	1_to_3	1+	3+	112	122$	0	12	10M
+G	1_to_11	1+	11-	120	*
+E	11_to_12	11+	12+	18	140$	0	122	122M
+S	6	150	*
+X	custom_record	xx:Z:testtag
+X	custom_record	X2
+E	11_to_13	11+	13+	20	140$	0	120	120M
+G	2_to_12	2-	12+	500	50
+O	15	11+ 11_to_13+ 13+	xx:i:-1
+Y	another_custom_record
+U	16sub	2 3
+S	2	120	*	xx:Z:sometag
+H	aa:i:12	ab:Z:test1
+H	aa:i:15
+E	1_to_5	1+	5+	0	122$	2	124	*	zz:Z:tag

tests/testdata/invalid/inconsistent_length.gfa1

@@ -0,0 +1,12 @@
+H	VN:Z:1.0
+H	ul:Z:https://github.com/sjackman/assembly-graph/blob/master/sample.gfa
+S	1	CGATGCAA	LN:i:12
+S	2	TGCAAAGTAC
+S	3	TGCAACGTATAGACTTGTCAC	RC:i:4
+S	4	GCATATA
+S	5	CGATGATA
+S	6	ATGA
+L	1	+	2	+	5M
+L	3	+	2	+	0M
+L	3	+	4	-	1M1D2M1S
+L	4	-	5	+	0M