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Using FOAM with BATH
- Bathconvert FOAM HMMs to BHMMs
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/xdisk/twheeler/nsontakke/GapFilling/FOAM_BATH_Jul24/Scripts/bathconvert_foam.sh - Concatenate the files
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for file in FOAM_BATH_HMMs_Jul24/*.bhmm; do cat "$file" >> ALL_FOAM_BHMMs_1Aug24.bhmm done
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Running MetaPathPredict with kofamscan
- config.yml specifications for ko_list and profiles db
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sbatch /xdisk/twheeler/nsontakke/GapFilling/MPP_Jul24/Scripts/run_kofamscan_metapath.sh - (Convert .fna file to MPP format, also uses kofam_to_mpp_format_conversion.py script, run MPP on file to generate .tsv)
- kofamscan/ kofamkoala uses HMMs made from KEGG modules to find modules in amino acid sequences.
- Where do I get amino acids from?
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- BATH using TIGRFAM or something on bin82 data
- Prokka .faa file which I already have available?
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Preliminary Output Analysis
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Comparing pathways
- MPP
- kofamscan
- Bathsearch
- FOAM
ECOLI EXPTS SEPERATE: Follow these steps to run your analysis:
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Download E. coli data from NCBI
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Run it through kofamscan
Clone the kofamscan repository Download ko list and hmm profiles from ftp://ftp.genome.jp/pub/db/kofam/ Specify these paths in config.yml config.yml is stored in the same spot exec_annotation is stored in (the bin)
conda activate kofamscan-env /home/u13/nsontakke/miniconda3/envs/kofamscan_env/bin/exec_annotation --cpu=8 -k /xdisk/twheeler/nsontakke/GapFilling/kofamscan_input/ko_list -o /xdisk/twheeler/nsontakke/GapFilling/Ecoli_Data/KO_GCF_000005845.2_ASM584v2.txt /xdisk/twheeler/nsontakke/GapFilling/Ecoli_Data/GCF_000005845.2_ASM584v2_cds_from_genomic.fna
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Run kofamscan output through MetaPathPredict
Clone the MetaPathPredict repository and set it up.
conda activate MetaPathPredict MetaPathPredict --input /xdisk/twheeler/nsontakke/GapFilling/kofamscan_output/Ecoli_kofamscan_output.tsv --annotation-format kofamscan --output Ecoli_Metapath.tsv