Updated check for dependencies and fixed spelling error in arguments.

biobakery · Jan 15, 2016 · d5d0897 · d5d0897
1 parent cdf6075
commit d5d0897
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Showing 3 changed files with 16 additions and 10 deletions.
diff --git a/shortbred_identify.py b/shortbred_identify.py
@@ -57,7 +57,7 @@
 from Bio.Data import CodonTable
 from Bio import SeqIO
 
-VERSION="0.9.1"
+VERSION="0.9.2"
 
 ###############################################################################
 #COMMAND LINE ARGUMENTS
@@ -86,10 +86,10 @@
 grpInput.add_argument('--goi', type=str, dest='sGOIProts',default= "", help='Enter the path and name of the proteins of interest file.')
 grpInput.add_argument('--ref', type=str, dest='sRefProts',default= "", help='Enter the path and name of the file containing reference protein sequences.')
 grpInput.add_argument('--refdb', type=str, dest='dirRefDB', default= "",help='Can be specified in place of reference proteins [--ref]. Enter the path and name for a blastdb of reference proteins.')
-grpInput.add_argument('--goiblast', type=str, default = "", dest='sGOIBlast', help='Used when modifying existing ShortBRED-Identiy results. Enter the path and name of the blast results from the goi-to-goi search.')
-grpInput.add_argument('--refblast', type=str, dest='sRefBlast', default= "", help='Used when modifying existing ShortBRED-Identiy results. Enter the path and name of the blast results from the goi-to-ref search.')
-grpInput.add_argument('--goiclust', type=str, default ="", dest='sClust', help='Used when modifying existing ShortBRED-Identiy results. Enter the path and name of the clustered genes of interest file.')
-grpInput.add_argument('--map_in', type=str, dest='sMapIn',default="", help='Used when modifying existing ShortBRED-Identiy results. Enter the path and name of the two column file connecting proteins to families.')
+grpInput.add_argument('--goiblast', type=str, default = "", dest='sGOIBlast', help='Used when modifying existing ShortBRED-Identify results. Enter the path and name of the blast results from the goi-to-goi search.')
+grpInput.add_argument('--refblast', type=str, dest='sRefBlast', default= "", help='Used when modifying existing ShortBRED-Identify results. Enter the path and name of the blast results from the goi-to-ref search.')
+grpInput.add_argument('--goiclust', type=str, default ="", dest='sClust', help='Used when modifying existing ShortBRED-Identify results. Enter the path and name of the clustered genes of interest file.')
+grpInput.add_argument('--map_in', type=str, dest='sMapIn',default="", help='Used when modifying existing ShortBRED-Identify results. Enter the path and name of the two column file connecting proteins to families.')
 
 
 
@@ -153,7 +153,7 @@
     #return iReturnCode
 
 print "Checking dependencies..."
-src.CheckDependency(args.strUSEARCH,"","Usearch")    
+src.CheckDependency(args.strUSEARCH,"","usearch")    
 src.CheckDependency(args.strBLASTP,"-h","blastp")
 src.CheckDependency(args.strMUSCLE,"-h","muscle")
 src.CheckDependency(args.strCDHIT,"-h","cdhit")

diff --git a/shortbred_quantify.py b/shortbred_quantify.py
@@ -48,7 +48,7 @@
 from Bio.Seq import Seq
 from Bio import SeqIO
 
-VERSION="0.9.1"
+VERSION="0.9.2"
 
 
 ################################################################################

diff --git a/src/__init__.py b/src/__init__.py
@@ -25,9 +25,15 @@ def check_file(strPath):
 		return
 
 def CheckDependency(strCmd,strArg,strIntendedProgram):
-
-    if (os.path.isfile(distutils.spawn.find_executable(strCmd))==False):
-        raise IOError("\nShortBRED was unable to find " +  strIntendedProgram + " at the path *" + strCmd +  "*\nPlease check that the program is installed and the path is correct.")
+    #print strCmd
+    #print distutils.spawn.find_executable("usearch")
+    #print distutils.spawn.find_executable("ls")
+    #print os.access("usearch",os.F_OK)
+    #print distutils.spawn.find_executable("muscle")
+    #print distutils.spawn.find_executable("cd-hit")
+
+    if ((distutils.spawn.find_executable(strCmd))==None):
+        raise IOError("\nShortBRED was unable to find " +  strIntendedProgram + " at the path *" + strCmd +  "*\nPlease check that the program is installed and the path is correct. Please note that ShortBRED will not be able to use the unix alias for the program.")
         #print "\nShortBRED was unable to load " +  strIntendedProgram + "at the path " + strCmd +  "\nPlease check to make sure the program is installed and the path is correct."
         sys.exit(1)