Mercurial > repos > menegidio > mitos
comparison mitos/gen.sh @ 2:de4408d88c67 draft default tip
Uploaded
| author | menegidio |
|---|---|
| date | Thu, 17 Jun 2021 15:27:29 +0000 |
| parents | 1f945d382bc7 |
| children |
comparison
equal
deleted
inserted
replaced
| 1:d472d16b99c5 | 2:de4408d88c67 |
|---|---|
| 1 ## Activate MITOS(1) conda env | |
| 2 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=1.0.5 zip | |
| 3 | |
| 4 conda activate mitos1 | |
| 5 | |
| 6 tmp=$(mktemp -d) | |
| 7 runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir '/home/maze/workspace/tools-iuc/tools/mitos/test-data/mitos1-refdata/' && zip -9 -y -r $tmp/result.zip $tmp | |
| 8 | |
| 9 for i in bed faa fas geneorder gff seq | |
| 10 do | |
| 11 cp $tmp/result.$i test-data/NC_012920.$i | |
| 12 done | |
| 13 cp $tmp/result test-data/NC_012920.mito | |
| 14 cp $tmp/plots/trnA-*.svg test-data/NC_012920_trnA.svg | |
| 15 cp $tmp/plots/prot.pdf test-data/NC_012920_prot.pdf | |
| 16 cp $tmp/plots/rna.pdf test-data/NC_012920_ncrna.pdf | |
| 17 rm -rf $tmp | |
| 18 | |
| 19 conda deactivate | |
| 20 | |
| 21 ## Activate MITOS2 conda env | |
| 22 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=2.0.6 zip | |
| 23 | |
| 24 conda activate mitos2 | |
| 25 | |
| 26 # data for 1st test | |
| 27 tmp=$(mktemp -d) | |
| 28 runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --finovl 50 --fragovl 0.2 --fragfac 10.0 --evalue 2.0 --cutoff 0.50 --clipfac 10.0 --ncev 0.01 --maxtrnaovl 50 --maxrrnaovl 50 --noplots | |
| 29 cp $tmp/result.bed test-data/mitos2_NC_012920.bed | |
| 30 rm -rf $tmp | |
| 31 | |
| 32 # data for 3rd test | |
| 33 tmp=$(mktemp -d) | |
| 34 runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --evalue 3.0 --cutoff 0.49 --clipfac 9.0 --ncbicode --alarab --oldstst --ncev 0.1 --sensitive --maxtrnaovl 51 --maxrrnaovl 49 && zip -9 -y -r $tmp/result.zip $tmp | |
| 35 for i in faa fas geneorder gff mitos seq | |
| 36 do | |
| 37 cp $tmp/result.$i test-data/mitos2_NC_012920.$i | |
| 38 done | |
| 39 cp $tmp/plots/prot.pdf test-data/mitos2_NC_012920_prot.pdf | |
| 40 cp $tmp/plots/rna.pdf test-data/mitos2_NC_012920_ncrna.pdf | |
| 41 rm -rf $tmp | |
| 42 | |
| 43 conda deactivate |