gfapy.error.NotFoundError: A link equivalent to ... does not exist

[MrTomRod]

Dear Giorgio

Thanks for your nice library!

I get this exception:

gfapy.error.NotFoundError: A link equivalent to:
L	edge_2	-	edge_1	+	*
does not exist, but is required by the following paths:
P	contig_4	edge_4+,edge_2-,edge_1+,edge_2+	*

When trying this .gfa file produced by Flye:

H	VN:Z:1.0
S	edge_1	GCCAGCCTAAGAAAGACGCAT	dp:i:1384
S	edge_2	CACGAACTGCACCTTTCAATT	dp:i:1370
S	edge_3	TATAGTCATAAATTATTAGTT	dp:i:453
S	edge_4	ACTTAGTGGTTTTGTATATTT	dp:i:858
L	edge_1	+	edge_2	+	0M	RC:i:1288
L	edge_2	+	edge_4	+	0M	RC:i:604
L	edge_2	+	edge_4	-	0M	RC:i:602
L	edge_3	+	edge_3	+	0M	RC:i:0
L	edge_3	-	edge_3	-	0M	RC:i:0
P	contig_3	edge_3+	*
P	contig_4	edge_4+,edge_2-,edge_1+,edge_2+	*

Is this a Flye or a gfapy bug? (Made the plot using gfaviz which didn't complain.)

Could you perhaps change from an exception to printing a mere warning? This is my ugly monkey patch that allows me to continue working:

[ggonnella]

Dear Thomas, I think it's not a bug. Indeed the Path contains "edge_2-,edge_1+" thus requires a link from edge_2 to edge_1 with inverted orientation, which is not present in the gfa file.

…

________________________________________ From: Thomas Roder ***@***.***> Sent: Thursday, 4 July 2024 14:29 To: ggonnella/gfapy Cc: Subscribed Subject: [ggonnella/gfapy] gfapy.error.NotFoundError: A link equivalent to ... does not exist (Issue #31) Dear Giorgio Thanks for your nice library! I get this exception: gfapy.error.NotFoundError: A link equivalent to: L edge_2 - edge_1 + * does not exist, but is required by the following paths: P contig_4 edge_4+,edge_2-,edge_1+,edge_2+ * When trying this .gfa file produced by Flye: H VN:Z:1.0 S edge_1 GCCAGCCTAAGAAAGACGCAT dp:i:1384 S edge_2 CACGAACTGCACCTTTCAATT dp:i:1370 S edge_3 TATAGTCATAAATTATTAGTT dp:i:453 S edge_4 ACTTAGTGGTTTTGTATATTT dp:i:858 L edge_1 + edge_2 + 0M RC:i:1288 L edge_2 + edge_4 + 0M RC:i:604 L edge_2 + edge_4 - 0M RC:i:602 L edge_3 + edge_3 + 0M RC:i:0 L edge_3 - edge_3 - 0M RC:i:0 P contig_3 edge_3+ * P contig_4 edge_4+,edge_2-,edge_1+,edge_2+ * assembly_graph.gfa.svg (view on web)<https://github.com/ggonnella/gfapy/assets/40867365/67405328-9649-4590-9c4e-93d2de674495> Is this a Flye or a gfapy bug? — Reply to this email directly, view it on GitHub<#31>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAAFI5DXGGI62JVH2U34XXLZKU5YZAVCNFSM6AAAAABKLOPQ6CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4TANZVGY4TAMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>