Change barcode file add

workflows/pacbio_qc/components/rs_subreads.py

@@ -18,6 +18,7 @@
 
 import os
 import json
+import logging
 
 from workflows.pacbio_qc.lib.pacbiolib import h5file
 
@@ -29,10 +30,11 @@ def rs_subreads(inputfile, stdout, componentdir, smrtpipe, fofnToSmrtpipeInput,
     
     import subprocess
     import os
+    import logging
     
     from workflows.pacbio_qc.lib.pacbiolib import PacbioH5Reader
-    
-    # crate directory
+    logging.getLogger("jflow").debug("Begin rs_subreads!")
+    # create directory
     filebase = os.path.basename(os.path.splitext(os.path.splitext(inputfile)[0])[0])
     outputdir = os.path.join(componentdir, filebase)
     settings_xml = os.path.join(componentdir, filebase + "_settings.xml" )
@@ -52,9 +54,9 @@ def rs_subreads(inputfile, stdout, componentdir, smrtpipe, fofnToSmrtpipeInput,
         </param>
         <param name='score'><value>{1}</value></param>
     </module>""".format(barcode_file, barcode_score)
-    # write settings
-    with open( settings_xml, "w") as fh:
-        fh.write(("""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+        # write settings
+        with open( settings_xml, "w") as fh:
+            fh.write(("""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <smrtpipeSettings>
     <module id="P_Fetch" />
     <module id="P_Filter" >
@@ -73,6 +75,27 @@ def rs_subreads(inputfile, stdout, componentdir, smrtpipe, fofnToSmrtpipeInput,
 </smrtpipeSettings>
     """).format(min_subreads_length, polymerase_read_qual, polymerase_read_length))
 
+    if barcode_file == 'None' or barcode_file is None :
+        # write settings
+        with open( settings_xml, "w") as fh:
+            fh.write(("""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<smrtpipeSettings>
+    <module id="P_Fetch" />
+    <module id="P_Filter" >
+        <param name="minSubReadLength">
+            <value>{0}</value>
+        </param>
+        <param name="readScore">
+            <value>{1}</value>
+        </param>
+        <param name="minLength">
+            <value>{2}</value>
+        </param>
+    </module>
+    <module id="P_FilterReports"/>
+</smrtpipeSettings>
+    """).format(min_subreads_length, polymerase_read_qual, polymerase_read_length))
+
     # write fofn and xml
     reader = PacbioH5Reader(inputfile)
     with open( inputs_fofn, "w") as fh:
@@ -104,6 +127,7 @@ class RS_Subreads (Analysis):
     """
     
     def define_parameters(self, sample_names, input_files, min_subreads_length = 0, polymerase_read_qual = 0, polymerase_read_length = 0, barcode_file=None, barcode_score=22):
+        logging.getLogger("jflow").debug("Begin RS_Subreads.define_parameters!")
         self.add_parameter_list("sample_names", "sample names, each sample name must correspond to an input file", default=sample_names, required=True)
         self.add_input_file_list( "input_files", "Input pacbio bas.h5 files", default=input_files, file_format = h5file, required=True)
         self.add_parameter("min_subreads_length", "Subreads shorter than this value (in base pairs) are filtered out and excluded from analysis", default=min_subreads_length, type='int')
@@ -117,12 +141,25 @@ class RS_Subreads (Analysis):
         self.add_output_file_list( 'stdouts', "logs", pattern="{basename}.stdout", items=items)
 
     def process(self):
+        logging.getLogger("jflow").debug("Begin RS_Subreads.process!")
         subreads = PythonFunction(rs_subreads, cmd_format="{EXE} {IN} {OUT} {ARG}")
         for i,e in  enumerate(self.input_files) :
+            logging.getLogger("jflow").debug("Begin RS_Subreads.process! " + e)
+            print('START FOR ',i,'------>',e)
+            '''self.add_python_execution(rs_subreads, 
+                cmd_format="{EXE} {IN} {OUT} {ARG}",
+                map=False,
+                inputs = [self.input_files[i]],
+                outputs = [self.stdouts[i]],
+                arguments = [self.output_directory, self.get_exec_path("smrtpipe"), self.get_exec_path("fofnToSmrtpipeInput.py"), self.min_subreads_length, self.polymerase_read_qual, self.polymerase_read_length, self.barcode_file, self.barcode_score]
+                )'''
+
             subreads(inputs = self.input_files[i],
                      outputs = [self.stdouts[i]],
                      arguments = [self.output_directory, self.get_exec_path("smrtpipe"), self.get_exec_path("fofnToSmrtpipeInput.py"),
                                   self.min_subreads_length, self.polymerase_read_qual, self.polymerase_read_length, self.barcode_file, self.barcode_score ])
+        logging.getLogger("jflow").debug("End RS_Subreads.process! ")
+        print('END PROCESS')
         
     def get_version(self):
         return "1.0"
@@ -135,11 +172,15 @@ class RS_Subreads (Analysis):
     
     def post_process(self):
         metrics = []
+        metrics2 = []
         
         for i,samplefile in enumerate(self.input_files) :
             sample = self.sample_names[i]
             sdir = os.path.basename(os.path.splitext(os.path.splitext(samplefile)[0])[0])
             sample_outdir = os.path.join(self.output_directory, sdir)
+            '''print ('sample ------->  ',sample,'\n')
+            print ('self.sample_names ------->  ',self.sample_names,'\n')'''
+
             
             # loading 
             jsonfile = os.path.join(sample_outdir, 'results', 'filter_reports_loading.json')
@@ -213,6 +254,21 @@ class RS_Subreads (Analysis):
                 
                 image = os.path.join(sample_outdir, 'results', 'filtered_subread_report.png')
                 self._add_result_element(sample, "report", self._save_file(image, sample + ".filtered_subread_report.png"), group)
+                
+            # Barcode report
+            jsonfile = os.path.join(sample_outdir, 'results', 'barcode_report.json')
+            if os.path.isfile(jsonfile):
+                group = 'barcode_results'
+                
+                if group not in metrics2 : 
+                    metrics2.append(group)
+                    self._add_result_element("metrics2", "headers", ','.join(['Reads', 'Bases']), group)
+                stats = self.parse_barcode_report_json(jsonfile)
+
+                for i,barcode in enumerate(stats['Barcode Name']):
+                   self._add_result_element(barcode, 'Reads', stats['Reads'][i] , group)
+                   self._add_result_element(barcode, 'Bases', stats['Bases'][i] , group)
+                
             
     # ------ parsing of json files ------
     
@@ -292,6 +348,25 @@ class RS_Subreads (Analysis):
                 res["Number of Reads"] = e['value']
         return res
         
+    def parse_barcode_report_json(self,jsonfile):
+        obj = self.load_json(jsonfile)
+        '''print (obj)'''
+        res = {}
+        for e in obj['tables'] :
+            '''print ("ATTRIBUTE")
+            print ("e ----> ",e,'\n')'''
+            for c in e['columns']:
+                '''print ('c------> ', c,'\n')'''
+
+                if c['id'] == 'barcode.barcode_table.barcode' :
+                   res['Barcode Name'] = c['values']
+                elif c['id'] == 'barcode.barcode_table.number_of_reads' :
+                   res['Reads'] = c['values']
+                elif c['id'] == 'barcode.barcode_table.number_of_bases' :
+                   res['Bases'] = c['values']
+
+            '''print ("res ---> ",res,'\n')'''
+        return res