From 64a745ce0bbae40df13079f1db52f293542c4409 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 11 Aug 2016 17:32:08 +0200
Subject: [PATCH] First very basic version of obi grep command

---
 python/obitools3/commands/grep.pyx | 93 ++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 python/obitools3/commands/grep.pyx

diff --git a/python/obitools3/commands/grep.pyx b/python/obitools3/commands/grep.pyx
new file mode 100644
index 0000000..ffcbe3e
--- /dev/null
+++ b/python/obitools3/commands/grep.pyx
@@ -0,0 +1,93 @@
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_NUC_SEQS    # TODO cimport doesn't work
+
+
+import time
+
+__title__="Grep view lines that match the given predicates"
+
+
+default_config = {   'inputview'    : None,
+                     'outputview'   : None
+                 }
+
+def addOptions(parser):
+
+    # TODO put this common group somewhere else but I don't know where
+    group=parser.add_argument_group('DMS and view options')
+
+    group.add_argument('--default-dms','-d', 
+                       action="store", dest="obi:defaultdms",
+                       metavar='<DMS NAME>',
+                       default=None,
+                       type=str,
+                       help="Name of the default DMS for reading and writing data.")
+
+    group.add_argument('--input-view','-i',
+                       action="store", dest="obi:inputview",
+                       metavar='<INPUT VIEW NAME>',
+                       default=None,
+                       type=str,
+                       help="Name of the input view, either raw if the view is in the default DMS,"
+                            " or in the form 'dms:view' if it is in another DMS.")
+
+    group.add_argument('--output-view','-o',
+                       action="store", dest="obi:outputview",
+                       metavar='<OUTPUT VIEW NAME>',
+                       default=None,
+                       type=str,
+                       help="Name of the output view, either raw if the view is in the default DMS,"
+                            " or in the form 'dms:view' if it is in another DMS.")
+
+
+    group=parser.add_argument_group('obi grep specific options')
+
+    group.add_argument('--predicate','-p',
+                       action="store", dest="grep:predicate",
+                       metavar='<PREDICATE>',
+                       default=None,
+                       type=str,
+                       help="Grep lines that match the given python expression on <line> or <sequence>.")
+
+    
+def run(config):
+    
+    # Open DMS
+    d = OBIDMS(config['obi']['defaultdms'])
+    
+    # Open input view 1
+    iview = d.open_view(config['obi']['inputview'])
+    
+    # Initialize the progress bar
+    #pb = ProgressBar(len(iview), config, seconde=5)
+        
+    # Apply filter
+    # TODO try both kinds of line selection functions to check efficiency
+    selection = []
+    for i in range(len(iview)) :
+        #pb(i)
+        line = iview[i]
+        if isinstance(iview, OBIView_NUC_SEQS) :    # put this somewhere else for efficiency
+            sequence = line
+        if eval(config['grep']['predicate']) :
+            selection.append(i)
+         
+    # Create output view with the line selection
+    if isinstance(iview, OBIView_NUC_SEQS) :    # TODO make view type automatic when cloning
+        oview = d.new_view(config['obi']['outputview'], view_type="NUC_SEQS_VIEW", view_to_clone=iview, line_selection=selection, comments="obi grep: "+config['grep']['predicate']+'\n')
+    else :
+        oview = d.new_view(config['obi']['outputview'], view_to_clone=iview, line_selection=selection, comments="obi grep: "+config['grep']['predicate'])
+
+    iview.save_and_close()
+    oview.save_and_close()
+    d.close()
+    
+    print("Done.")
+    
+    
+
+    
+    
+    
+    
+        
\ No newline at end of file