Add a rank option allowing to add a rank attribute to sequences containing an integer value indicating the position of the sequence in the input file.

src/obitools/format/options.py

@@ -18,10 +18,16 @@ from obitools.format._format import printOutput
 
 from array import array
 from itertools import chain
+import sys
 
 
 
 def addInputFormatOption(optionManager):
+    optionManager.add_option('--rank',
+                             action="store_true", dest='addrank',
+                             default=False,
+                             help="add a rank attribute to the sequence "
+                                  "indicating the sequence position in the input data")
     optionManager.add_option('--genbank',
                              action="store_const", dest="seqinformat",
                              default=None,
@@ -127,6 +133,15 @@ def autoEntriesIterator(options):
 
         return iterator
 
+    def withRankIterator(formatIterator):
+        def iterator(lineiterator):
+            rank=0
+            for s in formatIterator(lineiterator):
+                rank+=1
+                s['rank']=rank
+                yield s
+
+        return iterator
     def withQualIterator(qualityfile):
         options.outputFormater=formatFastq
         options.outputFormat="fastq"
@@ -206,7 +221,9 @@ def autoEntriesIterator(options):
             reader=withQualIterator(qualfile)
             options.outputFormater=formatFastq
             options.outputFormat="fastq"
-        
+            
+    if options.addrank:
+        reader = withRankIterator(reader)
     return reader