-
Notifications
You must be signed in to change notification settings - Fork 9
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
create script to generate estimate and ground truth outputs #14
- Loading branch information
Showing
1 changed file
with
73 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| #!/bin/bash | ||
|
|
||
| # This is to compare the results of CMash against a brute force calculated containment indicies. | ||
| # WARNING: this uses a LOT of memory and is CPU intensive as well, so use with caution (and use on a server) | ||
|
|
||
| # In case you have multiple versions installed (eg. Metalign as well as CMash), make sure python is looking in the right place: | ||
| export PYTHONPATH="$(dirname $(dirname "`pwd`"))":$PYTHONPATH | ||
|
|
||
| #Make sure the correct CMash is being pulled from | ||
| testFile=$(python -c "from CMash import MinHash as MH; print(MH.__file__)") | ||
| parentDir=`dirname $PWD` | ||
| parentDir=`dirname ${parentDir}` | ||
| correctFile="${parentDir}/CMash/MinHash.py" | ||
| if [ "$testFile" == "$correctFile" ]; | ||
| then | ||
| echo "Files are correct" | ||
| else | ||
| echo "Files are not correct" | ||
| exit 1 | ||
| fi | ||
|
|
||
| testOrganism="../Organisms/taxid_1192839_4_genomic.fna.gz" | ||
| maxK=5 | ||
| kSizes="4-${maxK}-1" | ||
| numHashes=10 | ||
| containmentThresh=.01 | ||
| locationOfThresh=-1 | ||
|
|
||
| scriptsDir="${parentDir}/scripts" | ||
| modulesDir="${parentDir}/CMash" | ||
|
|
||
| # make the training database | ||
| echo "Training on data" | ||
| rm TrainingDatabase.h5 2> /dev/null | ||
| rm TrainingDatabase.tst 2> /dev/null | ||
| /usr/bin/time python ${scriptsDir}/MakeStreamingDNADatabase.py filenames.txt TrainingDatabase.h5 -n ${numHashes} -k ${maxK} | ||
| if test -f TrainingDatabase.h5; then | ||
| if test -f TrainingDatabase.tst; then | ||
| echo "Training file successfully created" | ||
| else | ||
| echo "SOMETHING WENT WRONG!!!!" | ||
| exit 1 | ||
| fi | ||
| else | ||
| echo "SOMETHING WENT WRONG!!!!" | ||
| exit 1 | ||
| fi | ||
|
|
||
| echo "Classifying sample with CMash" | ||
| outName="est_results.csv" | ||
| rm ${outName} 2> /dev/null | ||
| # make a streaming pre-filter | ||
| /usr/bin/time python ${scriptsDir}/StreamingQueryDNADatabase.py ${testOrganism} TrainingDatabase.h5 ${outName} $kSizes --sensitive -l $locationOfThresh -c $containmentThresh | ||
| if test -f ${outName}; then | ||
| echo "sensitive classify successful" | ||
| cat ${outName} | ||
| else | ||
| echo "SOMETHING WENT WRONG!!!!" | ||
| exit 1 | ||
| fi | ||
|
|
||
| echo "Computing ground truth containment indicies" | ||
| outName="true_results.csv" | ||
| rm ${outName} 2> /dev/null | ||
| # make a streaming pre-filter | ||
| /usr/bin/time python ${modulesDir}/GroundTruth.py ${testOrganism} TrainingDatabase.h5 ${outName} $kSizes -l $locationOfThresh -c $containmentThresh | ||
| if test -f ${outName}; then | ||
| echo "sensitive classify successful" | ||
| cat ${outName} | ||
| else | ||
| echo "SOMETHING WENT WRONG!!!!" | ||
| exit 1 | ||
| fi |