Move igquast test datasets

igquast.py

@@ -20,7 +20,7 @@ def parse_command_line():
     import argparse
 
     def ActionTestFactory(name):
-        initial_reads = igrec_dir + "/igquast_test_dataset/%s/input_reads.fa.gz" % name
+        initial_reads = igrec_dir + "/test_dataset/igquast/%s/input_reads.fa.gz" % name
         import os.path
         if not os.path.isfile(initial_reads):
             return None
@@ -33,10 +33,10 @@ def __init__(self, option_strings, dest, nargs=None, **kwargs):
             def __call__(self, parser, namespace, values, option_string=None):
                 setattr(namespace, "initial_reads", initial_reads)
                 setattr(namespace, "output_dir", "igquast_test_%s" % name)
-                setattr(namespace, "constructed_repertoire", igrec_dir + "/igquast_test_dataset/%s/igrec/final_repertoire.fa.gz" % name)
-                setattr(namespace, "constructed_rcm", igrec_dir + "/igquast_test_dataset/%s/igrec/final_repertoire.rcm" % name)
-                setattr(namespace, "reference_repertoire", igrec_dir + "/igquast_test_dataset/%s/repertoire.fa.gz" % name)
-                setattr(namespace, "reference_rcm", igrec_dir + "/igquast_test_dataset/%s/repertoire.rcm" % name)
+                setattr(namespace, "constructed_repertoire", igrec_dir + "/test_dataset/igquast/%s/igrec/final_repertoire.fa.gz" % name)
+                setattr(namespace, "constructed_rcm", igrec_dir + "/test_dataset/igquast/%s/igrec/final_repertoire.rcm" % name)
+                setattr(namespace, "reference_repertoire", igrec_dir + "/test_dataset/igquast/%s/repertoire.fa.gz" % name)
+                setattr(namespace, "reference_rcm", igrec_dir + "/test_dataset/igquast/%s/repertoire.rcm" % name)
 
         return ActionTest
 

igquast_manual.html

@@ -202,7 +202,7 @@ <h3 id="igquast_misc_options">3.4. Miscellaneous options</h3>
     <code>--test</code><br> Running on the toy test dataset. Command line corresponding to the test run is equivalent to the following:
     <pre class="code">
     <code>
-    ./igquast.py -s igquast_test_dataset/test/input_reads.fa.gz -c igquast_test_dataset/igrec/final_repertoire.fa.gz -C igquast_test_dataset/igrec/final_repertoire.rcm -r igquast_test_dataset/test/repertoire.fa.gz -R igquast_test_dataset/test/repertoire.rcm -o igquast_test_test
+    ./igquast.py -s test_dataset/igquast/test/input_reads.fa.gz -c test_dataset/igquast/igrec/final_repertoire.fa.gz -C test_dataset/igquast/igrec/final_repertoire.rcm -r test_dataset/igquast/test/repertoire.fa.gz -R test_dataset/igquast/test/repertoire.rcm -o igquast_test_test
     </code>
 </pre>
 
@@ -213,12 +213,12 @@ <h3 id="igquast_examples">3.5. Examples</h3>
     Perform reference-free analysis only:
     <pre class="code">
     <code>
-    ./igquast.py -s igquast_test_dataset/test/input_reads.fa.gz -c igquast_test_dataset/test/igrec_bad/final_repertoire.fa.gz -C igquast_test_dataset/test/igrec_bad/final_repertoire.rcm -o igquast_test --reference-free
+    ./igquast.py -s test_dataset/igquast/test/input_reads.fa.gz -c test_dataset/igquast/test/igrec_bad/final_repertoire.fa.gz -C test_dataset/igquast/test/igrec_bad/final_repertoire.rcm -o igquast_test --reference-free
     </code>
 </pre> Do not plot figures, make reports only:
     <pre class="code">
     <code>
-    ./igquast.py -s igquast_test_dataset/test/input_reads.fa.gz -c igquast_test_dataset/test/igrec/final_repertoire.fa.gz -C igquast_test_dataset/test/igrec/final_repertoire.rcm -r igquast_test_dataset/test/repertoire.fa.gz -R igquast_test_dataset/test/repertoire.rcm --figure-format= -o igquast_test
+    ./igquast.py -s test_dataset/igquast/test/input_reads.fa.gz -c test_dataset/igquast/test/igrec/final_repertoire.fa.gz -C test_dataset/igquast/test/igrec/final_repertoire.rcm -r test_dataset/igquast/test/repertoire.fa.gz -R test_dataset/igquast/test/repertoire.rcm --figure-format= -o igquast_test
     </code>
 </pre>
 

py/hgc.py

@@ -51,15 +51,15 @@ def hgc_estimator_all(input_file, output_dir):
     #
     # datas += ["/Nancy/data/input/ImmunoSeq/roche_datasets/%d_SAM133069%d/merged_reads/%d_SAM133069%d.cleaned.fastq" % (n + 1, n + 69, n + 1, n + 69) for n in xrange(8)]
     # names += ["ROCHE_%d" % (n + 1) for n in xrange(8)]
-    # datas += ["/home/ashlemov/Git/ig_repertoire_constructor/igquast_test_dataset/age3/input_reads.fa.gz"]
+    # datas += ["/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/age3/input_reads.fa.gz"]
     # names += ["REAL"]
-    # datas += ["/home/ashlemov/Git/ig_repertoire_constructor/igquast_test_dataset/SIMULATED_1/input_reads.fa.gz"]
+    # datas += ["/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/SIMULATED_1/input_reads.fa.gz"]
     # names += ["SIMULATED_1"]
-    # datas += ["/home/ashlemov/Git/ig_repertoire_constructor/igquast_test_dataset/SYNTHETIC_1/input_reads.fa.gz"]
+    # datas += ["/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/SYNTHETIC_1/input_reads.fa.gz"]
     # names += ["SYNTHETIC_1"]
-    datas += ["/home/ashlemov/Git/ig_repertoire_constructor/igquast_test_dataset/SIMULATED_0.5/input_reads.fa.gz"]
+    datas += ["/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/SIMULATED_0.5/input_reads.fa.gz"]
     names += ["SIMULATED_0.5"]
-    datas += ["/home/ashlemov/Git/ig_repertoire_constructor/igquast_test_dataset/SYNTHETIC_0.5/input_reads.fa.gz"]
+    datas += ["/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/SYNTHETIC_0.5/input_reads.fa.gz"]
     names += ["SYNTHETIC_0.5"]
     queue = zip(datas, names)
 
@@ -69,6 +69,6 @@ def JOB(a):
 
     n_jobs = 1 if multiprocessing.cpu_count() <= 16 else 3
     Parallel(n_jobs=n_jobs)(delayed(JOB)(q) for q in queue)
-    data = "/home/ashlemov/Git/ig_repertoire_constructor/igquast_test_dataset/age3/input_reads.fa.gz"
+    data = "/home/ashlemov/Git/ig_repertoire_constructor/test_dataset/igquast/age3/input_reads.fa.gz"
     name = "REAL_ALL"
     # hgc_estimator_all(data, name)

py/simulate.py

@@ -665,7 +665,7 @@ def run_presto(input_file, output_dir,
 
 if __name__ == "__main__":
     ig_simulator_output_dir = "/tmp/ig_simulator"
-    output_dir = igrec_dir + "/igquast_test_dataset"
+    output_dir = igrec_dir + "/test_dataset/igquast"
     run_ig_simulator(ig_simulator_output_dir)
     simulate_data(ig_simulator_output_dir + "/final_repertoire.fasta", output_dir)
 

py/test_on_paper_data.py

@@ -6,9 +6,9 @@
 
 
 def test_on_aq_data(name, out_dir, threads=16, do_not_run=False):
-    run_and_quast_all(igrec_dir + "/igquast_test_dataset/%s/input_reads.fa.gz" % name,
-                      igrec_dir + "/igquast_test_dataset/%s/repertoire.fa.gz" % name,
-                      # igrec_dir + "/igquast_test_dataset/%s/repertoire.rcm" % name,
+    run_and_quast_all(igrec_dir + "/test_dataset/igquast/%s/input_reads.fa.gz" % name,
+                      igrec_dir + "/test_dataset/igquast/%s/repertoire.fa.gz" % name,
+                      # igrec_dir + "/test_dataset/igquast/%s/repertoire.rcm" % name,
                       "None",
                       out_dir=out_dir,
                       threads=threads,