Basic obi export command exporting from view to fasta or fastq format,

for testing purposes

python/obitools3/commands/export.pyx

@@ -0,0 +1,93 @@
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.obidms._obidms import OBIDMS       # TODO cimport doesn't work
+from obitools3.utils cimport bytes2str
+
+import time
+import re
+
+__title__="Export a NUC_SEQS view to a fasta file"
+
+
+default_config = {   'inputview'    : 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=parser.add_argument_group('obi export specific options')
+
+    group.add_argument('--format','-f',
+                       action="store", dest="export:format",
+                       metavar='<FORMAT>',
+                       default="fasta",
+                       type=str,
+                       help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.")
+
+def run(config):
+    
+    # TODO import doesn't work
+    NUC_SEQUENCE_COLUMN = "NUC_SEQ"
+    ID_COLUMN = "ID"
+    DEFINITION_COLUMN = "DEFINITION"
+    QUALITY_COLUMN = "QUALITY"    
+    
+    # Open DMS
+    d = OBIDMS(config['obi']['defaultdms'])
+    
+    # Open input view
+    iview = d.open_view(config['obi']['inputview'])
+    
+    # Initialize the progress bar
+    #pb = ProgressBar(len(iview), config, seconde=5)
+    
+    i=0
+    for seq in iview :
+        #pb(i)
+        toprint = ">"+seq.get_id()+" "
+        for col_name in seq :
+            if col_name != NUC_SEQUENCE_COLUMN and col_name != ID_COLUMN and col_name != DEFINITION_COLUMN and col_name != QUALITY_COLUMN :
+                toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
+        if DEFINITION_COLUMN in seq :
+            toprint = toprint + seq.get_definition()
+        nucseq = bytes2str(seq.get_sequence())
+        
+        if config['export']['format'] == "fasta" :
+            nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)
+            toprint = toprint + "\n" + nucseq
+        elif config['export']['format'] == "fastq" :
+            toprint = toprint + "\n" + nucseq
+            toprint = toprint + "\n" + "+"
+            toprint = toprint + "\n" + seq.get_str_quality()
+            
+        print(toprint)
+        i+=1
+        
+    iview.save_and_close()
+    d.close()
+    
+    print("Done.")
+    
+    
+
+    
+    
+    
+    
+