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HOWTO
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#Download Protopterus annections protein complement
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/279/795/GCF_019279795.1_PAN1.0/GCF_019279795.1_PAN1.0_protein.faa.gz
#run setup
./phylociraptor setup -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#reduce busco set to only 20 busco genes
./modify_busco.sh
#orthology
./phylociraptor orthology -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#cleanup
rm -rf $(find ./results/orthology/busco/busco_runs/ -name "softw*")
rm ./results/orthology/busco/busco_runs/Latimeria_chalumnae/run_busco/hmmer_output.tar.gz
rm results/orthology/busco/busco_runs/Latimeria_chalumnae/run_busco/augustus_output.tar.gz
rm results/orthology/busco/busco_runs/Latimeria_chalumnae/run_busco/blast_output.tar.gz
#filter-orthology
./phylociraptor filter-orthology -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#align
./phylociraptor align -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#filter align
./phylociraptor filter-align -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#modeltest
./phylociraptor modeltest -t serial=2 --config-file data/config.vertebrata_minimal.yaml
#ml tree
./phylociraptor mltree -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#speciestree
./phylociraptor speciestree -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#figure
./phylociraptor report --config-file data/config.vertebrata_minimal.yaml
./phylociraptor report --figure --config-file data/config.vertebrata_minimal.yaml
#manual
#summarize busco results
singularity exec docker://reslp/biopython_plus:1.77 bin/extract_busco_table.py --hmm results/orthology/busco/busco_set/vertebrata_odb10/hmms --busco_results results/orthology/busco/busco_runs/ -o busco_table.tsv
mkdir -p by_gene/raw
singularity exec docker://reslp/biopython_plus:1.77 bin/create_sequence_files.py --busco_table busco_table.tsv --busco_results results/orthology/busco/busco_runs --cutoff 0.5 --outdir by_gene/raw --minsp 20 --type aa --gene_statistics gene_stats.txt --genome_statistics genome_statistics.txt
#do 409625at7742
mkdir by_gene/aligned
singularity exec docker://reslp/clustalo:1.2.4 clustalo -i by_gene/raw/409625at7742_all.fas -o by_gene/aligned/409625at7742.clustalo.fasta --threads=2
mkdir by_gene/trimmed
singularity exec docker://reslp/trimal:1.4.1 trimal -in by_gene/aligned/409625at7742.clustalo.fasta -out by_gene/trimmed/409625at7742.clustalo.trimal.fasta -gappyout
#now let's do for some genes
for gene in $(echo "359032at7742 413149at7742 409719at7742 406935at7742")
do
echo -e "\n$(date)\t$gene"
echo -e "$(date)\taligning"
singularity exec docker://reslp/clustalo:1.2.4 clustalo -i by_gene/raw/${gene}_all.fas -o by_gene/aligned/${gene}.clustalo.fasta --threads=2
echo -e "$(date)\ttrimming"
singularity exec docker://reslp/trimal:1.4.1 trimal -in by_gene/aligned/${gene}.clustalo.fasta -out by_gene/trimmed/${gene}.clustalo.trimal.fasta -gappyout
echo -e "$(date)\tDone"
done
#run iqtree
singularity exec docker://reslp/iqtree:2.0.7 iqtree -s by_gene/trimmed/ --prefix five_genes -m MFP --seqtype AA -T 2 -bb 1000
### this has been run for you
#run setup
./phylociraptor setup -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#reduce busco set to only 20 busco genes
./modify_busco.sh
#orthology
./phylociraptor orthology -t serial=2 --snakemake="--until busco" --config-file data/config.vertebrata_minimal.yaml --verbose --dry
#cleanup
rm -rf $(find ./results/orthology/busco/busco_runs/ -name "softw*")
rm ./results/orthology/busco/busco_runs/Latimeria_chalumnae/run_busco/hmmer_output.tar.gz
rm results/orthology/busco/busco_runs/Latimeria_chalumnae/run_busco/augustus_output.tar.gz
rm results/orthology/busco/busco_runs/Latimeria_chalumnae/run_busco/blast_output.tar.gz
#########
## in course
#get table
./phylociraptor orthology -t serial=2 --config-file data/config.vertebrata_minimal.yaml
#filter-orthology
./phylociraptor filter-orthology -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#align
./phylociraptor align -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#filter align
./phylociraptor filter-align -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#modeltest
./phylociraptor modeltest -t serial=2 --config-file data/config.vertebrata_minimal.yaml
#ml tree
./phylociraptor mltree -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#speciestree
./phylociraptor speciestree -t serial=2 --config-file data/config.vertebrata_minimal.yaml --verbose
#figure
./phylociraptor report --config-file data/config.vertebrata_minimal.yaml
./phylociraptor report --figure --config-file data/config.vertebrata_minimal.yaml