Update example.py

Author: RJMW

examples/examples.py

@@ -5,6 +5,7 @@
 from dimspy.tools import replicate_filter
 from dimspy.tools import create_sample_list
 from dimspy.tools import align_samples
+from dimspy.tools import hdf5_peak_matrix_to_txt
 from dimspy.tools import blank_filter
 from dimspy.tools import sample_filter
 from dimspy.portals.hdf5_portal import save_peaklists_as_hdf5, save_peak_matrix_as_hdf5
@@ -13,68 +14,48 @@
 
 def main():
 
-    # Example 1 - mzML files (zip file)
-    source = os.path.join("Y:\users\zhangcy\polar_positive_data")
-    fn_filelist = os.path.join("Y:\users\zhangcy\polar_positive_data\pos_filelist.txt")
-    output = os.path.join("Y:\\users\\zhangcy\\polar_positive_data_results\\")
-
-    source = os.path.join("Y:\users\zhangcy\polar_positive_data")
-    fn_filelist = os.path.join("E:\\raw_109\pos_filelist.txt")
-    output = os.path.join("E:\\raw_109")
+    source = os.path.join("..", "tests", "data", "MTBLS79_subset", "MTBLS79_mzml_triplicates.zip")
+    fn_filelist = os.path.join("..", "tests", "data", "MTBLS79_subset", "filelist_mzml_triplicates.txt")
+    output = os.path.join("..", "tests", "test_results")
 
     print "Process Scans....."
-    pls = process_scans(source, min_scans=1, function_noise="noise_packets",
+    pls = process_scans(source, min_scans=1, function_noise="median",
                         snr_thres=3.0, ppm=2.0, min_fraction=None, rsd_thres=None,
-                        filelist=fn_filelist, remove_mz_range=[], filter_scan_events={"exclude":[[50.0, 620.0, "full"]]}, block_size=2000, ncpus=None)
+                        filelist=fn_filelist, remove_mz_range=[], block_size=5000, ncpus=None)
     print "Finished"
-
-    sample_list = os.path.join("E:\\raw_109\\sample_list.txt")
-    create_sample_list(pls, sample_list, delimiter="\t")
-
     print
-    print pls
-    for pl in pls:
-        print pl.ID, pl.shape
-        with open(os.path.join(output, pl.ID + ".txt"), "w") as out: out.write(pl.to_str("\t"))
 
-    """
-    save_peaklists_as_hdf5(pls, os.path.join(output, "pls.h5"))
-    pls = load_peaklists_from_hdf5(os.path.join(output, "pls.h5"))
-    """
-
-    print
     print "Replicate Filter....."
-    logfile = os.path.join("E:\\raw_109\\log_replicate_filter.txt")
-    pls_rf = replicate_filter(pls, ppm=2.0, replicates=3, min_peaks=2, rsd_thres=None, quality_logfile=logfile)
+    logfile = os.path.join(output, "log_replicate_filter.txt")
+    pls_rf = replicate_filter(pls, ppm=2.0, replicates=3, min_peaks=2, rsd_thres=None, report=logfile, block_size=5000)
     print "Finished"
     print
 
-    sample_list = os.path.join("E:\\raw_109\\sample_list.txt")
+    print "Create a new sample list"
+    sample_list = os.path.join(output, "sample_list.txt")
     create_sample_list(pls_rf, sample_list, delimiter="\t")
-    """
-    save_peaklists_as_hdf5(pls, os.path.join(output, "pls_rf.h5"))
+    print "Finished"
+    print
 
     print "Align Samples...."
-    pm = align_samples(pls_rf, ppm=3.0)
+    pm = align_samples(pls_rf, ppm=3.0, ncpus=1, block_size=5000)
     print "Finished", pm.shape
     print
 
     save_peak_matrix_as_hdf5(pm, os.path.join(output, "pm.h5"))
+    hdf5_peak_matrix_to_txt(os.path.join(output, "pm.h5"), path_out=os.path.join(output, "pm.txt"), attr_name="intensity", comprehensive=True)
+
+    pm = load_peak_matrix_from_hdf5(os.path.join(output, "pm.h5"))
 
     print "Blank Filter"
     pm_bf = blank_filter(pm, "blank", min_fraction=1.0, min_fold_change=10.0, function="mean", rm_samples=True)
     print "Finished", pm_bf.shape
     print
 
-    save_peak_matrix_as_hdf5(pm_bf, os.path.join(output, "pm_bf.h5"))
-
     print "Sample Filter"
     pm_bf_sf = sample_filter(pm, 0.8, within=False)
     print "Finished", pm_bf_sf.shape
     print
 
-    save_peak_matrix_as_hdf5(pm_bf_sf, os.path.join(output, "pm_bf_sf.h5"))
-    """
-
 if __name__ == '__main__':
     main()