ChaoXianSen
commented
11 months ago Dear @joacjo you can use the following two files for testing: contigs file : https://drive.google.com/file/d/1s9zOQnPp9yEygeJcWNcCM2VUJJla66Ln/view?usp=sharing BAM file : https://drive.google.com/file/d/17E8LbtzF6MJVmq5IlR8OFq3PAsGrB2k6/view?usp=sharing
Any idea about this problem?
Looking forward to you reply ! thanks a lot !
Dear @joacjo
Question: Which part of the source code can I change, to fit my contigs file and Run the 'run_RF.py ' to get the final result ??
R63.contigs.fa.gz header format : >k141_84347 flag=1 multi=9.0000 len=118435
CCATAAATCTGATTTTAGTCAAAAAAATATGCAGTTTTTCAAAAAGGGTGTATAATTCTTTCGTTAC
'vae_clusters.tsv' format : ‘vae_1 k141_84347 vae_2 k141_92682 vae_2 k141_551576 vae_2 k141_358295’
run mode: python run_RF.py \ R63.contigs.fa.gz \ vae_clusters.tsv \ annotations \ resultdir
err report : Traceback (most recent call last): File "/public/home/bioinfo_wang/00_software/phamb-v.1.0.1/phamb/run_RF.py", line 223, in
reference = run_RF_modules.Reference.from_clusters(clusters = clusters, fastadict=fastadict, minimum_contig_len=2000)
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/phamb/lib/python3.9/site-packages/phamb/run_RF_modules.py", line 272, in from_clust
genomes = cls._parse_clusters(clusters,fastadict,minimum_contig_len=minimum_contig_len)
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/phamb/lib/python3.9/site-packages/phamb/run_RF_modules.py", line 286, in _parse_clu
contig_len = fastadict[contig].len()
KeyError: 'k141_84347'
Thanks !