diff testing.sh @ 0:a5f1638b73be draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testing.sh	Wed Jun 26 08:01:42 2019 -0400
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+test_data="$DIR/test_data"
+classification_tbl='!!!! set up the path !!!!!'
+pdb='!!! set up the path'
+
+######## Protein Domais Finder
+## single_seq, for/rev strand of mapping
+$DIR/protein_domains_pd.py -q $test_data/GEPY_test_long_1 -pdb $pdb -cs $classification_tbl -dir $PWD/tmp/single_fasta/
+## multifasta
+$DIR/protein_domains_pd.py -q $test_data/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl -dir $PWD/tmp/multifasta/
+## multifasta_win
+$DIR/protein_domains_pd.py -q $test_data/vyber-Ty1_01.fasta -pdb $pdb -cs $classification_tbl -wd 3100 -od 1500 -dir $PWD/tmp/multifasta_win
+
+## testing if outputs are the same in case of using sliding window and not
+if [[ $(diff $PWD/tmp/multifasta/output_domains.gff $PWD/tmp/multifasta_win/output_domains.gff) -eq 0 ]];then
+	echo "Testing output of sliding window comparing to no window accomplished sucessfuly"
+else
+	echo "WARNING! There is difference between outputs of sliding window and no window used"
+fi
+######## Protein Domains Filter
+## default params
+$DIR/domains_filtering.py -dom_gff $PWD/tmp/single_fasta/output_domains.gff 
+if [[ -e $PWD/tmp/single_fasta/domains_filtered.gff ]] && [[ -e $PWD/tmp/single_fasta/dom_prot_seq.txt ]] ; then
+	echo -e "Filtered file and protein seqs file for default parameters exists"
+else
+	echo -e "Filtered outputs for default parameters are missing"
+fi
+if [[ $(cat $PWD/tmp/single_fasta/domains_filtered.gff | wc -l) -gt 1 ]];then
+	echo "File was correctly filtered using default parameters"
+fi
+## Ty1-RT filtering
+$DIR/domains_filtering.py -dom_gff $PWD/tmp/multifasta/output_domains.gff -sd Ty1-RT
+if [[ -e $PWD/tmp/multifasta/domains_filtered.gff ]] && [[ -e $PWD/tmp/multifasta/dom_prot_seq.txt ]]; then
+	echo -e "Filtered file and protein seqs file of Ty1-RT domains exist"
+else
+	echo -e "Filtered outputs of Ty1-RT domains are missing"
+fi
+if [[ $(cat $PWD/tmp/multifasta/domains_filtered.gff | wc -l) -gt 1 ]];then
+	echo "File was correctly filtered for Ty1-RT domains"
+fi