From 573bd5bad7b125bd08f71e442e843294eab03b64 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Mon, 6 Feb 2017 11:24:32 +0100
Subject: [PATCH] Removed deprecated code in ecoPCRFormat

---
 tools/ecoPCRFormat.py | 73 +++++--------------------------------------
 1 file changed, 7 insertions(+), 66 deletions(-)

diff --git a/tools/ecoPCRFormat.py b/tools/ecoPCRFormat.py
index 3884001..c829ec8 100755
--- a/tools/ecoPCRFormat.py
+++ b/tools/ecoPCRFormat.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2.7
 
 import re
 import gzip
@@ -7,11 +7,8 @@ import sys
 import time
 import getopt
 
-try:
-    import psycopg2
-    _dbenable=True
-except ImportError:
-    _dbenable=False
+_dbenable=False
+
 
 #####
 #
@@ -221,56 +218,7 @@ def readTaxonomyDump(taxdir):
     
     return taxonomy,ranks,alternativeName,index
 
-def readTaxonomyDB(dbname):
-    connection = psycopg2.connect(database=dbname)
-    
-    cursor = connection.cursor()
-    cursor.execute("select numid,rank,parent from ncbi_taxonomy.taxon")
-    taxonomy=[list(x) for x in cursor]
 
-    cursor.execute("select rank_class from ncbi_taxonomy.taxon_rank_class order by rank_class")
-    ranks=cursor.fetchall()
-    ranks = dict(map(None,(x[0] for x in ranks),xrange(len(ranks))))
-    
-    print >>sys.stderr,"Sorting taxons..."
-    taxonomy.sort(taxonCmp)
-
-    print >>sys.stderr,"Indexing taxonomy..."
-    index = {}
-    for t in taxonomy:
-        index[t[0]]=bsearchTaxon(taxonomy, t[0])
-    
-    print >>sys.stderr,"Indexing parent and rank..."
-    for t in taxonomy:
-        t[1]=ranks[t[1]]
-        try:
-            t[2]=index[t[2]]
-        except KeyError,e:
-            if t[2] is None and t[0]==1:
-                t[2]=index[t[0]]
-            else:
-                raise e
-        
-    cursor.execute("select taxid,name,category from ncbi_taxonomy.name")
-    
-    alternativeName=[]
-    for taxid,name,classname in cursor:
-        alternativeName.append((name,classname,index[taxid]))
-        if classname == 'scientific name':
-            taxonomy[index[taxid]].append(name)
-    
-    cursor.execute("select old_numid,current_numid from ncbi_taxonomy.taxon_id_alias")
- 
-    print >>sys.stderr,"Adding taxid alias..."
-    for taxid,current in cursor:
-        if current is not None:
-            index[taxid]=index[current]
-        else:
-            index[taxid]=None
-            
-       
-    return taxonomy,ranks,alternativeName,index
-    
 #####
 #
 #
@@ -585,10 +533,9 @@ def ecoParseOptions(arguments):
            }
     
     o,filenames = getopt.getopt(arguments,
-                                'ht:T:n:gfe',
+                                'ht:n:gfe',
                                 ['help',
                                  'taxonomy=',
-                                 'taxonomy_db=',
                                  'name=',
                                  'genbank',
                                  'fasta',
@@ -601,9 +548,6 @@ def ecoParseOptions(arguments):
         elif name in ('-t','--taxonomy'):
             opt['taxmod']='dump'
             opt['taxdir']=value
-        elif name in ('-T','--taxonomy_db'):
-            opt['taxmod']='db'
-            opt['taxdb']=value
         elif name in ('-n','--name'):
             opt['prefix']=value
         elif name in ('-g','--genbank'):
@@ -622,6 +566,7 @@ def ecoParseOptions(arguments):
 
     return opt,filenames
 
+
 def printHelp():
     print "-----------------------------------"
     print " ecoPCRFormat.py"
@@ -641,11 +586,7 @@ if __name__ == '__main__':
     
     opt,filenames = ecoParseOptions(sys.argv[1:])
     
-    if opt['taxmod']=='dump':
-        taxonomy = readTaxonomyDump(opt['taxdir'])
-    elif opt['taxmod']=='db':
-        taxonomy = readTaxonomyDB(opt['taxdb'])
-        
-   
+    taxonomy = readTaxonomyDump(opt['taxdir'])
+    
     ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])