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workflows/components/sffExtract.py

@@ -27,50 +27,12 @@ from weaver.function import ShellFunction
 from weaver.abstraction import Map
 
 
-class SFFExtract (Analysis):
+class SFFextract (Component):
     
-    def define_parameters(self, input_files, archive_name=None):
+    def define_parameters(self, input_files):
         self.input_files = InputFileList(input_files, Formats.SFF)
-        self.archive_name = archive_name
         self.fastq_files = OutputFileList(self.get_outputs('{basename_woext}.fastq', self.input_files), Formats.FASTQ)
         self.stdouts = OutputFileList(self.get_outputs('{basename_woext}.stdout', self.input_files))
-        
-    def define_analysis(self):
-        self.name = "Convert"
-        self.description = "Convert sff file in fastq format."
-        self.software = "sff_extract.py"
-        self.options = "-c"
-        
-    def post_process(self):
-        import re
-        extract_regex = re.compile("Converted (.*) reads into (.*) sequences.")
-        clips_regexp = re.compile("After applying left clips, (.*) sequences \(=(.*)%\) start with these bases:")
-        for stdout in self.stdouts:
-            found = False
-            nb_reads, nb_seq, cliped, perc_cliped, seq_cliped = 0, 0, 0, 0, ""
-            for line in open(stdout).readlines():
-                mr = extract_regex.match(line)
-                cr = clips_regexp.match(line)
-                if found:
-                    seq_cliped = line.strip()
-                    found = False
-                if mr != None:
-                    nb_reads, nb_seq = mr.group(1), mr.group(2)
-                if cr != None:
-                    cliped, perc_cliped = cr.group(1), cr.group(2)
-                    found = True
-            self._add_result_element(os.path.basename(stdout), "nb_reads", nb_reads)
-            self._add_result_element(os.path.basename(stdout), "nb_seq", nb_seq)
-            self._add_result_element(os.path.basename(stdout), "cliped", cliped)
-            self._add_result_element(os.path.basename(stdout), "perc_cliped", perc_cliped)
-            self._add_result_element(os.path.basename(stdout), "seq_cliped", seq_cliped)
-        self._create_and_archive(self.fastq_files, self.archive_name)
-        
-    def get_version(self):
-        cmd = [self.get_exec_path("sff_extract.py"), "--version"]
-        p = Popen(cmd, stdout=PIPE, stderr=PIPE)
-        stdout, stderr = p.communicate()
-        return stdout.split()[1]
     
     def process(self):
         sff_extract = ShellFunction(self.get_exec_path("sff_extract.py") + " -c $1 -s $2 > $3", cmd_format='{EXE} {IN} {OUT}')

workflows/components/sffExtractA.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+from subprocess import Popen, PIPE
+
+from jflow.component import Component
+from jflow.iotypes import OutputFileList, InputFileList, Formats
+from jflow.abstraction import MultiMap
+from ng6.analysis import Analysis
+
+from weaver.function import ShellFunction
+from weaver.abstraction import Map
+
+
+class SFFExtract (Analysis):
+    
+    def define_parameters(self, input_files, archive_name=None):
+        self.input_files = InputFileList(input_files, Formats.SFF)
+        self.archive_name = archive_name
+        self.fastq_files = OutputFileList(self.get_outputs('{basename_woext}.fastq', self.input_files), Formats.FASTQ)
+        self.stdouts = OutputFileList(self.get_outputs('{basename_woext}.stdout', self.input_files))
+        
+    def define_analysis(self):
+        self.name = "Convert"
+        self.description = "Convert sff file in fastq format."
+        self.software = "sff_extract.py"
+        self.options = "-c"
+        
+    def post_process(self):
+        import re
+        extract_regex = re.compile("Converted (.*) reads into (.*) sequences.")
+        clips_regexp = re.compile("After applying left clips, (.*) sequences \(=(.*)%\) start with these bases:")
+        for stdout in self.stdouts:
+            found = False
+            nb_reads, nb_seq, cliped, perc_cliped, seq_cliped = 0, 0, 0, 0, ""
+            for line in open(stdout).readlines():
+                mr = extract_regex.match(line)
+                cr = clips_regexp.match(line)
+                if found:
+                    seq_cliped = line.strip()
+                    found = False
+                if mr != None:
+                    nb_reads, nb_seq = mr.group(1), mr.group(2)
+                if cr != None:
+                    cliped, perc_cliped = cr.group(1), cr.group(2)
+                    found = True
+            self._add_result_element(os.path.basename(stdout), "nb_reads", nb_reads)
+            self._add_result_element(os.path.basename(stdout), "nb_seq", nb_seq)
+            self._add_result_element(os.path.basename(stdout), "cliped", cliped)
+            self._add_result_element(os.path.basename(stdout), "perc_cliped", perc_cliped)
+            self._add_result_element(os.path.basename(stdout), "seq_cliped", seq_cliped)
+        self._create_and_archive(self.fastq_files, self.archive_name)
+        
+    def get_version(self):
+        cmd = [self.get_exec_path("sff_extract.py"), "--version"]
+        p = Popen(cmd, stdout=PIPE, stderr=PIPE)
+        stdout, stderr = p.communicate()
+        return stdout.split()[1]
+    
+    def process(self):
+        sff_extract = ShellFunction(self.get_exec_path("sff_extract.py") + " -c $1 -s $2 > $3", cmd_format='{EXE} {IN} {OUT}')
+        sff_extract = MultiMap(sff_extract, self.input_files, [self.fastq_files, self.stdouts])