/
run_test.sh
39 lines (39 loc) · 3.27 KB
/
run_test.sh
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#/bin/bash
set -eox pipefail
wget -c https://www.dropbox.com/s/xr0xsdluuni2b95/ribotricer_test_data_tair10.zip
unzip ribotricer_test_data_tair10.zip
ribotricer detect-orfs --bam ribotricer_test_data_tair10/bams_unique/SRX219170.bam --ribotricer_index ribotricer_test_data_tair10/index/ribotricer_v44_annotation_longest_candidate_orfs.tsv --prefix ribotricer_test_data_tair10/SRX219170_generated
#MD5_expected=$(md5sum ribotricer_test_data_tair10/translating_ORFs/SRX219170_translating_ORFs.tsv | awk '{ print $1 }')
#MD5_observed=$(md5sum ribotricer_test_data_tair10/SRX219170_generated_translating_ORFs.tsv | awk '{ print $1 }')
#if [ $MD5_expected != $MD5_observed ]; then
#echo "detect-orfs MD5 mismatch";
#exit 1;
#fi
ribotricer count-orfs --detected_orfs ribotricer_test_data_tair10/SRX219170_generated_translating_ORFs.tsv --ribotricer_index ribotricer_test_data_tair10/index/ribotricer_v44_annotation_longest_candidate_orfs.tsv --features annotated --out ribotricer_test_data_tair10/SRX219170_generated_annotated_counts.tsv
#MD5_expected=$(md5sum ribotricer_test_data_tair10/orfs_count/SRX219170_annotated_counts_cnt.txt | awk '{ print $1 }')
#MD5_observed=$(md5sum ribotricer_test_data_tair10/SRX219170_generated_annotated_counts.tsv | awk '{ print $1 }')
#if [ $MD5_expected != $MD5_observed ]; then
#echo "count-orfs MD5 mismatch";
#exit 1;
#fi
#ribotricer detect-orfs --bam ribotricer_test_data_tair10/bams_unique/SRX219170.bam --ribotricer_index ribotricer_test_data_tair10/index/ribotricer_v44_annotation_longest_candidate_orfs.tsv --prefix ribotricer_test_data_tair10/SRX219170_generated_readdensity_10 --min_read_density 10
#MD5_expected=$(md5sum ribotricer_test_data_tair10/translating_ORFs/SRX219170_translating_ORFs_readdensity_10.tsv | awk '{ print $1 }')
#MD5_observed=$(md5sum ribotricer_test_data_tair10/SRX219170_generated_readdensity_10_translating_ORFs.tsv | awk '{ print $1 }')
#if [ $MD5_expected != $MD5_observed ]; then
#echo "detect-orfs readdensity=10 MD5 mismatch";
#exit 1;
#fi
#ribotricer detect-orfs --bam ribotricer_test_data_tair10/bams_unique/SRX219170.bam --ribotricer_index ribotricer_test_data_tair10/index/ribotricer_v44_annotation_longest_candidate_orfs.tsv --prefix ribotricer_test_data_tair10/SRX219170_generated_validcodons_75 --min_valid_codons_ratio 0.75
#MD5_expected=$(md5sum ribotricer_test_data_tair10/translating_ORFs/SRX219170_translating_ORFs_minvalidcodons_075.tsv | awk '{ print $1 }')
#MD5_observed=$(md5sum ribotricer_test_data_tair10/SRX219170_generated_validcodons_75_translating_ORFs.tsv | awk '{ print $1 }')
#if [ $MD5_expected != $MD5_observed ]; then
#echo "detect-orfs validcodons=0.75 MD5 mismatch";
#exit 1;
#fi
#ribotricer detect-orfs --bam ribotricer_test_data_tair10/bams_unique/SRX219170.bam --ribotricer_index ribotricer_test_data_tair10/index/ribotricer_v44_annotation_longest_candidate_orfs.tsv --prefix ribotricer_test_data_tair10/SRX219170_generated_readspercodon_10 --min_reads_per_codon 10
#MD5_expected=$(md5sum ribotricer_test_data_tair10/translating_ORFs/SRX219170_translating_ORFs_readspercodon_10.tsv | awk '{ print $1 }')
#MD5_observed=$(md5sum ribotricer_test_data_tair10/SRX219170_generated_readspercodon_10_translating_ORFs.tsv | awk '{ print $1 }')
#if [ $MD5_expected != $MD5_observed ]; then
#echo "detect-orfs readspercodon=10 MD5 mismatch";
#exit 1;
#fi