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1 #!/bin/bash
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2
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3 export DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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4 export TEXT_DATA="$DIR/test-data"
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5 export classification_tbl=${DIR}/tool-data/protein_domains/Viridiplantae_v3.0_class
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6 export pdb=${DIR}/tool-data/protein_domains/Viridiplantae_v3.0_pdb
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7
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8 # make sure dir for testing exists
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9 mkdir -p $DIR/tmp
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10
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11 ######## DANTE
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12 ## single_seq, for/rev strand of mapping
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13 $DIR/dante.py -q ${TEXT_DATA}/GEPY_test_long_1 -pdb $pdb -cs $classification_tbl \
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14 --domain_gff $PWD/tmp/single_fasta.gff3
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15 ## multifasta
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16 $DIR/dante.py -q ${TEXT_DATA}/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl \
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17 --domain_gff $PWD/tmp/multifasta.gff3
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18 ## multifasta_win
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19 $DIR/dante.py -q ${TEXT_DATA}/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl \
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20 -wd 3100 -od 1500 --domain_gff $PWD/tmp/multifasta_win.gff3
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21
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22 # test filtering
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23 $DIR/dante_gff_output_filtering.py --dom_gff $PWD/tmp/single_fasta.gff3 \
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24 --domains_filtered $PWD/tmp/single_fasta_filtered.gff3 \
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