Commit 573bd5ba by Celine Mercier

Removed deprecated code in ecoPCRFormat

parent 17387dae
#!/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'])
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