fix --test

Author: andrewprzh

README.md

@@ -93,10 +93,10 @@ You can leave your comments and bug reports at our [GitHub repository tracker](h
 
     For example, using the toy data provided within this repository,
 
-        ./isoquant.py --reference tests/toy_data/MAPT.Mouse.reference.fasta \
-        --genedb tests/toy_data/MAPT.Mouse.genedb.gtf \
-        --fastq tests/toy_data/MAPT.Mouse.ONT.simulated.fastq \
-        --data_type nanopore -o toy_data_out
+        ./isoquant.py --fastq /home/andreyp/ablab/IsoQuant/tests/simple_data/chr9.4M.ont.sim.fq.gz \
+        --reference /home/andreyp/ablab/IsoQuant/tests/simple_data/chr9.4M.fa.gz \
+        --genedb /home/andreyp/ablab/IsoQuant/tests/simple_data/chr9.4M.gtf.gz \
+        --data_type nanopore --complete_genedb -p TEST_DATA --output isoquant_test 
 
 
 * To run IsoQuant on aligned reads (make sure your BAM is sorted and indexed) use the following command:

docs/getting-started.md

@@ -19,10 +19,10 @@
 
     For example, using the toy data provided within this repository,
 
-        ./isoquant.py --reference tests/toy_data/MAPT.Mouse.reference.fasta \
-        --genedb tests/toy_data/MAPT.Mouse.genedb.gtf \
-        --fastq tests/toy_data/MAPT.Mouse.ONT.simulated.fastq \
-        --data_type nanopore -o toy_data_out
+        ./isoquant.py --fastq /home/andreyp/ablab/IsoQuant/tests/simple_data/chr9.4M.ont.sim.fq.gz \
+        --reference /home/andreyp/ablab/IsoQuant/tests/simple_data/chr9.4M.fa.gz \
+        --genedb /home/andreyp/ablab/IsoQuant/tests/simple_data/chr9.4M.gtf.gz \
+        --data_type nanopore --complete_genedb -p TEST_DATA --output isoquant_test 
 
 
 * To run IsoQuant on aligned reads (make sure your BAM is sorted and indexed) use the following command:

isoquant.py

@@ -1082,16 +1082,18 @@ def run_pipeline(args):
 # Test mode is triggered by --test option
 class TestMode(argparse.Action):
     def __call__(self, parser, namespace, values, option_string=None):
-        out_dir = 'isoquant_test'
-        if os.path.exists(out_dir):
-            shutil.rmtree(out_dir)
+        self.out_dir = 'isoquant_test'
+        if os.path.exists(self.out_dir):
+            shutil.rmtree(self.out_dir)
         source_dir = os.path.dirname(os.path.realpath(__file__))
-        options = ['--output', out_dir, '--threads', '2',
+        options = ['--output', self.out_dir, '--threads', '2',
                    '--fastq', os.path.join(source_dir, 'tests/simple_data/chr9.4M.ont.sim.fq.gz'),
                    '--reference', os.path.join(source_dir, 'tests/simple_data/chr9.4M.fa.gz'),
                    '--genedb', os.path.join(source_dir, 'tests/simple_data/chr9.4M.gtf.gz'),
                    '--clean_start', '--data_type', 'nanopore', '--complete_genedb', '--force', '-p', 'TEST_DATA']
         print('=== Running in test mode === ')
+        print("Running IsoQuant in test mode with the following options:")
+        print(' '.join(options))
         print('Any other option is ignored ')
         main(options)
         if self._check_log():
@@ -1101,9 +1103,9 @@ def __call__(self, parser, namespace, values, option_string=None):
             sys.exit(IsoQuantExitCode.TEST_FAILED)
         parser.exit()
 
-    @staticmethod
-    def _check_log():
-        with open('isoquant_test/isoquant.log', 'r') as f:
+
+    def _check_log(self):
+        with open(os.path.join(self.out_dir, 'isoquant.log'), 'r') as f:
             log = f.read()
 
         correct_results = ['total assignments 4', 'polyA tail detected in 2', 'unique: 1', 'known: 2', 'Processed 1 experiment']

make-targz.sh

@@ -25,6 +25,8 @@ cp -r ./tests $TARGET_DIR/
 cp -r ./docs $TARGET_DIR/
 
 
+rm -fr $TARGET_DIR/tests/short_reads_toy/
+
 cp isoquant.py $TARGET_DIR/
 cp visualize.py $TARGET_DIR/
 cp README.md $TARGET_DIR/