add --from-project option and remove --paired-data

README.rst

@@ -73,6 +73,8 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.2.1     * add --from-project option to import existing config file
+          * remove --paired-data option
 0.2.0     add content from sequana.pipeline_common to handle all kind of 
           options in the argparse of all pipelines. This is independent of 
           sequana to speed up the --version and --help calls

sequana_pipetools/completion.py

@@ -15,16 +15,16 @@ def __init__(self, prog="sequana_completion"):
     sequana_completion --name all
     """
 
-        super(Options, self).__init__(usage=usage, prog=prog, 
+        super(Options, self).__init__(usage=usage, prog=prog,
             description="""This tool creates completion script for sequana
 pipelines. Each pipeline has its own in .config/sequana/pipelines that you can
 source at your convenience""",
             formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-        self.add_argument("--force", action="store_true", 
+        self.add_argument("--force", action="store_true",
             help="""overwrite files in sequana config pipeline directory""")
         self.add_argument("--name",  type=str,
-            help="""Name of a pipelines for which you wish to 
+            help="""Name of a pipelines for which you wish to
             create the completion file. Set to a valid name ror to create all
 scripts, use --name all """)
 
@@ -78,7 +78,7 @@ def save_completion_script(self):
         arguments = self.get_arguments()
 
         with open(output_filename, "w") as fout:
-            fout.write(self.setup.format(version=self.pipeline_version, 
+            fout.write(self.setup.format(version=self.pipeline_version,
                                          options=" ".join(arguments)))
             for action in self._actions:
                 option_name = action.option_strings[0]
@@ -87,6 +87,8 @@ def save_completion_script(self):
                     fout.write(self.set_option_with_choice(option_name, option_choices))
                 elif option_name.endswith("directory"):
                     fout.write(self.set_option_directory(option_name))
+                elif option_name in ["--databases"]:
+                    fout.write(self.set_option_directory(option_name))
             fout.write(self.teardown.format(pipeline_name=self.pipeline_name))
 
     def _init_config_file(self):
@@ -145,6 +147,7 @@ def set_option_directory(self, option_name):
         return data
 
 
+
 def main(args=None):
 
     if args is None:

sequana_pipetools/options.py

@@ -68,6 +68,13 @@ def add_options(self, parser):
         parser.add_argument("--level", dest="level", default="INFO",
             choices=['INFO', 'DEBUG', 'WARNING', 'ERROR', 'CRITICAL'],
             help="logging level in INFO, DEBUG, WARNING, ERROR, CRITICAL")
+        parser.add_argument("--from-project", dest="from_project", default=None,
+            help="""You can initiate a new analysis run from an existing project.
+                In theory, sequana project have a hidden .sequana directory, 
+                which can be used as input. The name of the run directory itself 
+                should suffice (if .sequana is found inside). From there, 
+                the config file and the pipeline files are copied in your new 
+                working directory""")
 
 
 def guess_scheduler():
@@ -125,8 +132,7 @@ def add_options(self, parser):
 
 class InputOptions():
     def __init__(self, group_name="data", input_directory=".",
-                 input_pattern="*fastq.gz", add_input_readtag=True,
-                 add_is_paired=True):
+                 input_pattern="*fastq.gz", add_input_readtag=True):
         """
 
         By default, single-end data sets. If paired, set is_paired to True
@@ -135,7 +141,6 @@ def __init__(self, group_name="data", input_directory=".",
         self.group_name = group_name
         self.input_directory = input_directory
         self.input_pattern = input_pattern
-        self.add_is_paired = add_is_paired
         self.add_input_readtag = add_input_readtag
 
     def add_options(self, parser):
@@ -166,14 +171,6 @@ def add_options(self, parser):
                 --paired-data is used""",
             )
 
-        if self.add_is_paired:
-            self.group.add_argument(
-                "--paired-data",
-                dest="paired_data",
-                action="store_true",
-                help="""NOT IMPLEMENTED YET"""
-            )
-
 
 class KrakenOptions():
     def __init__(self, group_name="section_kraken"):