can we convert the cDBG to GFA format with the current output files from spacegraphcats?

[taylorreiter]

I'm wondering if we can convert the current bcalm output by spacegraphcats to gfa. These are the current output files in *_k31:

bcalm.inputlist.txt  bcalm.unitigs.db      cdbg.gxt          contigs.mphf   reads.bgz.index
bcalm.log.txt        bcalm.unitigs.fa.sig  contigs.indices   contigs.sig
bcalm_to_gxt.log     bcalm.unitigs.pickle  contigs.info.csv  contigs.sizes

I used to do the conversion from the *unitigs.fa file but i think that became a temp() file that gets deleted.

[ctb]

yes, it's a temp file - https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/conf/Snakefile#L168

and the header information is neither preserved nor output-table per https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/cdbg/dump_contigs_db_to_fasta.py

so, we can't convert the current output, no :(.

might be something to consider doing as part of https://github.com/spacegraphcats/spacegraphcats/pull/430 tho.

[taylorreiter]

ok great, thanks. I'm increasingly thinking of ways to better integrate with other people interested in metagenome assembly graphs, and I think gfa is a pretty standard format that wouldn't be a bad idea to either output or have a simple conversion script for. #430 looks exciting!