From 067c5cdf74daf7257faa05a98d511b25d0114535 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 12 Oct 2009 15:25:26 +0000
Subject: [PATCH] add option to specify input format in fastaGrep

---
 src/fastaGrep.py | 50 +++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 41 insertions(+), 9 deletions(-)

diff --git a/src/fastaGrep.py b/src/fastaGrep.py
index 63b2fb6..4a1f2f6 100644
--- a/src/fastaGrep.py
+++ b/src/fastaGrep.py
@@ -1,24 +1,56 @@
 #!/usr/local/bin/python
 
-import re
-import sys
-
 from obitools.fasta import fastaIterator,formatFasta
+from obitools.format.sequence.embl import emblIterator
+from obitools.format.sequence.genbank import genbankIterator
+from obitools.format.sequence.fnaqual import fnaFastaIterator
 from obitools.options import getOptionManager
 from obitools.options.bioseqfilter import addSequenceFilteringOptions
 from obitools.options.bioseqfilter import sequenceFilterIteratorGenerator
 
-	
-	
+def addInputFormatOption(optionManager):
+    optionManager.add_option('--genbank',
+                             action="store_const", dest="seqinformat",
+                             type="string",
+                             default='fasta',
+                             const='genbank',
+                             help="input file is in genbank format")
+    optionManager.add_option('--embl',
+                             action="store_const", dest="seqinformat",
+                             type="string",
+                             default='fasta',
+                             const='embl',
+                             help="input file is in embl format")
+
+    optionManager.add_option('--fna',
+                             action="store_const", dest="seqinformat",
+                             type="string",
+                             default='fasta',
+                             const='fna',
+                             help="input file is in fasta nucleic format produced by 454 sequencer pipeline")
+
+
+
 if __name__=='__main__':
     
-    optionParser = getOptionManager([addSequenceFilteringOptions], 
-                                    entryIterator=fastaIterator)
+    optionParser = getOptionManager([addSequenceFilteringOptions])
     
     (options, entries) = optionParser()
-    goodFasta   = sequenceFilterIteratorGenerator(options)
     
-    for seq in goodFasta(entries):
+    if options.seqinformat=='fasta':
+        reader=fastaIterator
+    elif options.seqinformat=='genbank':
+        reader=genbankIterator
+    elif options.seqinformat=='embl':
+        reader=emblIterator
+    elif options.seqinformat=='fna':
+        reader=fnaFastaIterator
+        
+    entries=reader(entries)
+    
+    goodSeq   = sequenceFilterIteratorGenerator(options)
+    
+    for seq in goodSeq(entries):
         print formatFasta(seq)
             
             
\ No newline at end of file