Resuming falcon_unzip from specific step

[bostanict]

in another topic in falcon ( https://github.com/PacificBiosciences/FALCON/issues/472 ) I asked the way I can get the unassembled reads from falcon. As sugested I ran:

python -m falcon_kit.mains.get_read_ctg_map
python -m falcon_kit.mains.rr_ctg_track
python -m falcon_kit.mains.pr_ctg_track
mkdir -p 3-unzip/reads/
python -m falcon_kit.mains.fetch_reads

now that I am trying to run falcon_unzip,

I see that the first step is this tracker. Since I have already this files and did it before, is there anyway I can continue from this point and avoid reduing them?

Moreover, is there any folder we might need to remove after each re-run? like falcon that we needed to remove mywatcher..

Thanks

[pb-jchin]

if you are sure the results from the earlier step is done, you can just comment out the command and re-run the script. get_read_ctg_map generates 2-asm-falcon/read_maps/pread_ids, raw_read_ids, read_to_contig_map. rr_ctg_track generates 2-asm-falcon/read_maps/rawread_to_contigs and pr_ctg_track generates 2-asm-falcon/read_maps/pr_ctg_track. The fetch_reads generates all files inside 3-unzip/reads/.

You can delete the files and regenerate them.

[pb-cdunn]

Moreover, is there any folder we might need to remove after each re-run? like falcon that we needed to remove mywatcher?

Yes, for now you also need to remove mypwatcher/.

[bostanict]

ok. I got a little bit confused.

if you are sure the results from the earlier step is done, you can just comment out the command and re-run the script.

which earlier commands you mean? Falcon assembly? or there are other commands before these for the unzip.

so to be clear. I did the falcon assembly and I have the whole folder. I want now to run unzip to separate the haplotypes. before I ram only:

python -m falcon_kit.mains.get_read_ctg_map
python -m falcon_kit.mains.rr_ctg_track
python -m falcon_kit.mains.pr_ctg_track
mkdir -p 3-unzip/reads/
python -m falcon_kit.mains.fetch_reads

nothing more, nothing less and I have the result. So if I want to have the haploypes from the unzip, should I run the falcon_unzip or there is any way to use the results from these few lines mentioned.

you can just comment out the command and re-run the script.

where? in falcon unzip code? or there is any sh file for that so I comment out. Just to say, I am using slurm as the job scheduler.

You can delete the files and regenerate them.

the files you mentioned here right?

sorry if the questions are confusing. First time using unzip :)

Thanks alot~

[pb-jchin]

nothing more, nothing less and I have the result. So if I want to have the haploypes from the unzip, should I run the falcon_unzip or there is any way to use the results from these few lines mentioned.

yes

where? in falcon unzip code? or there is any sh file for that so I comment out. Just to say, I am using slurm as the job scheduler.

No , I meant something like:

#python -m falcon_kit.mains.get_read_ctg_map
#python -m falcon_kit.mains.rr_ctg_track
python -m falcon_kit.mains.pr_ctg_track
mkdir -p 3-unzip/reads/
python -m falcon_kit.mains.fetch_reads

if you already get pread_ids, raw_read_ids, read_to_contig_map, rr_ctg_track.

the files you mentioned here right?

yes

[bostanict]

ok.

I ran fc_unzip.py fc_unzip.cfg before and it created the file track_reads.sh

SO if I got it right, I will comment the commands:

#python -m falcon_kit.mains.get_read_ctg_map
#python -m falcon_kit.mains.rr_ctg_track
#python -m falcon_kit.mains.pr_ctg_track
#mkdir -p 3-unzip/reads/
#python -m falcon_kit.mains.fetch_reads

in the track_reads.sh file since I already have them run before. Then I run only:

fc_quiver.py fc_unzip.cfg

to get the results.

right? thanks