exporting all possible closed circular path in fasta from a gfa file

[splaisan]

Hi

I am new to graph analysis and was sent here by Erik Garrison (GFA-spec/GFA-spec#123)

Could someone guide me on which odgi command(s) to use to achieve my goal of generating all possible closed circular paths (in fasta) format from a gfa graph obtained from Flye.

Manually I can create the four models from this gfa but I would like to automate the process for future pipelines

Here is the truncated gfa content (cut at 40 char-)

thanks in advance

H	VN:Z:1.0
S	1	CTATCTTGGTTCCACAAATCTCATTACACCAATATT
S	2	AAGTGGGAGTGGATTAACAGAAATGGCCCCGTACGG
S	3	AAGTGGGGGTGGAGTAAGAGAAATTGCCCCGTACTG
S	4	TAATTGAGTTCCGTGTTCCGGGCAGCACCACCACTG
S	5	GCACTCGAACGACGAAGTAAAGAACGCGAAAAAGCG
S	6	CACTCTGACAATTCGTTGATCAAGTCACGGTATTTA
L	1	+	6	-	0M	RC:i:37
L	1	-	5	+	0M	RC:i:43
L	2	+	6	+	0M	RC:i:96
L	2	-	5	-	0M	RC:i:91
L	3	+	6	+	0M	RC:i:60
L	3	-	5	-	0M	RC:i:58
L	4	-	5	+	0M	RC:i:108
L	4	+	6	-	0M	RC:i:115
P	contig_5	5+	*
P	contig_6	6+	*
P	contig_1	1+	*
P	contig_2	2+	*
P	contig_3	3+	*
P	contig_4	4+	*

[sivico26]

@splaisan, have you tried the get_organelle_from_assembly.py script from GetOrganelle? I think it does what you want.