Mercurial > repos > petr-novak > dante

comparison tests.sh @ 9:ed4d9ede9cb4 draft

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author petr-novak
date Wed, 03 Jul 2019 09:21:52 -0400
parents 77d9f2ecb28a
children
comparison
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8:cc10173bd0c5 9:ed4d9ede9cb4
1 #!/bin/bash 1 #!/bin/bash
2 2
3 export DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" 3 export DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
4 export test_data="$DIR/test_data" 4 export TEXT_DATA="$DIR/test-data"
5 export classification_tbl=${DIR}/tool-data/protein_domains/Viridiplantae_v3.0_class 5 export classification_tbl=${DIR}/tool-data/protein_domains/Viridiplantae_v3.0_class
6 export pdb=${DIR}/tool-data/protein_domains/Viridiplantae_v3.0_pdb 6 export pdb=${DIR}/tool-data/protein_domains/Viridiplantae_v3.0_pdb
7 7
8 # make sure dir for testing exists 8 # make sure dir for testing exists
9 mkdir -p $DIR/tmp 9 mkdir -p $DIR/tmp
10 10
11 ######## DANTE 11 ######## DANTE
12 ## single_seq, for/rev strand of mapping 12 ## single_seq, for/rev strand of mapping
13 $DIR/dante.py -q $test_data/GEPY_test_long_1 -pdb $pdb -cs $classification_tbl \ 13 $DIR/dante.py -q ${TEXT_DATA}/GEPY_test_long_1 -pdb $pdb -cs $classification_tbl \
14 --domain_gff $PWD/tmp/single_fasta.gff3 14 --domain_gff $PWD/tmp/single_fasta.gff3
15 ## multifasta 15 ## multifasta
16 $DIR/dante.py -q $test_data/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl \ 16 $DIR/dante.py -q ${TEXT_DATA}/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl \
17 --domain_gff $PWD/tmp/multifasta.gff3 17 --domain_gff $PWD/tmp/multifasta.gff3
18 ## multifasta_win 18 ## multifasta_win
19 $DIR/dante.py -q $test_data/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl \ 19 $DIR/dante.py -q ${TEXT_DATA}/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl \
20 -wd 3100 -od 1500 --domain_gff $PWD/tmp/multifasta_win.gff3 20 -wd 3100 -od 1500 --domain_gff $PWD/tmp/multifasta_win.gff3
21 21
22 # test filtering 22 # test filtering
23 $DIR/dante_gff_output_filtering.py --dom_gff $PWD/tmp/single_fasta.gff3 \ 23 $DIR/dante_gff_output_filtering.py --dom_gff $PWD/tmp/single_fasta.gff3 \
24 --domains_filtered $PWD/tmp/single_fasta_filtered.gff3 \ 24 --domains_filtered $PWD/tmp/single_fasta_filtered.gff3 \