diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py index 9fdc739cf56bf28bd902b9ddc63194c315def01b..73fe18754427d5461f25101f471c6f8468712eaf 100644 --- a/modules/bindings/pymod/blast.py +++ b/modules/bindings/pymod/blast.py @@ -144,12 +144,13 @@ def CreateDB(infasta, dbout, mkdb_cmd=None): """ if mkdb_cmd==None: try: - exe=settings.Locate('makeblastdb') - args=[exe, '-in', infasta, ' -max_file_sz 10GB -out', dbout,'-dbtype','prot'] + exe=settings.Locate('formatdb') + args=[exe, '-i', infasta, '-v',str(10000),'-n',dbout] except: try: - exe=settings.Locate('formatdb') - args=[exe, '-i', infasta, '-v',str(10000),'-n',dbout] + exe=settings.Locate('makeblastdb') + args=[exe, '-in', infasta, ' -max_file_sz 10GB -out', dbout,'-dbtype','prot'] + except: raise RuntimeError('could not find makeblastdb/formatdb executable') else: @@ -172,10 +173,10 @@ def BlastVersion(blast_location=None): """ try: - blast_exe=settings.Locate('blastp',explicit_file_name=blast_location) + blast_exe=settings.Locate('blastall',explicit_file_name=blast_location) except: try: - blast_exe=settings.Locate('blastall', explicit_file_name=blast_location) + blast_exe=settings.Locate('blastp', explicit_file_name=blast_location) except: raise RuntimeError('could not find blast executable') @@ -233,12 +234,12 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62', if blast_location==None: try: - blast_exe=settings.Locate('blastp') + blast_exe=settings.Locate('blastall') except: try: - blast_exe=settings.Locate('blastall') + blast_exe=settings.Locate('blastp') except: - raise BlastError('could not find blast executable') + raise RuntimeError('could not find blast executable') else: blast_exe=settings.Locate(os.path.basename(blast_location),explicit_file_name=blast_location)