v2.1.5

RELEASE_NOTES

@@ -92,5 +92,15 @@ V2.1.2 - Jun. 23rd, 2017
 1. [bs_seeker2-align.py] : Add option "--XSteve", alternative filtering method proposed by Prof. Steve Jacobson
 
 
+------------------------------------------
 V2.1.3 - Oct. 25th, 2017
 1. [bs_seeker2-call_methylation.py] : Add option "-d", allow user-defined highest coverage.
+
+
+------------------------------------------
+V2.1.4 - Nov. 13rd, 2017
+1. [bs_align/bs_align_util.py] : fix bug in function of getting methylation levels for one read
+
+------------------------------------------
+V2.1.4 - Nov. 21st, 2017
+1. [bs_seeker2-build.py] : fix bug in finding genome file

bs_seeker2-build.py

@@ -8,17 +8,17 @@
 
 
 if __name__ == '__main__':
-
+    #
     parser = OptionParser()
-
+    #
     parser.add_option("-f", "--file", dest="filename", help="Input your reference genome file (fasta)", metavar="FILE")
     parser.add_option("--aligner", dest="aligner", help="Aligner program to perform the analysis: " + ', '.join(supported_aligners) + " [Default: %default]", metavar="ALIGNER", default = BOWTIE)
     parser.add_option("-p", "--path", dest="aligner_path", help="Path to the aligner program. Detected: " +' '*70+ '\t'.join(('%s: %s '+' '*70) % (al, aligner_path[al]) for al in sorted(supported_aligners)),
                   metavar="PATH")
     parser.add_option("-d", "--db", type="string", dest="dbpath", help="Path to the reference genome library (generated in preprocessing genome) [Default: %default]", metavar="DBPATH", default = reference_genome_path)
 
     parser.add_option("-v", "--version", action="store_true", dest="version", help="show version of BS-Seeker2", default=False)
-
+    #
     # RRBS options
     rrbs_opts = OptionGroup(parser, "Reduced Representation Bisulfite Sequencing Options",
                                 "Use this options with conjuction of -r [--rrbs]")
@@ -27,74 +27,79 @@
     rrbs_opts.add_option("-u", "--up", type= "int", dest="up_bound", help="upper bound of fragment length (excluding recognition sequence such as C-CGG ends) [Default: %default]", default = 500)
     rrbs_opts.add_option("-c", "--cut-site", type= "string", dest="cut_format", help="Cut sites of restriction enzyme. Ex: MspI(C-CGG), Mael:(C-TAG), double-enzyme MspI&Mael:(C-CGG,C-TAG). [Default: %default]", default = "C-CGG")
     parser.add_option_group(rrbs_opts)
-
-
+    #
+    #
     (options, args) = parser.parse_args()
-
+    #
     # if no options were given by the user, print help and exit
     if len(sys.argv) == 1:
         parser.print_help()
         exit(0)
-
+    #
     if options.version :
         show_version()
         exit (-1)
     else :
         show_version()
-
+    #
     rrbs = options.rrbs
-
+    #
     if options.filename is not None :
         fasta_file=os.path.expanduser(options.filename)
     else :
         error("Please specify the genome file (Fasta) using \"-f\"")
-
+    #
     if fasta_file is None:
         error('Fasta file for the reference genome must be supported')
-
+    #
     if not os.path.isfile(fasta_file):
-        if os.path.isfile(os.path.join(os.dbpath, fasta_file)):
-            # Search for os.dbpath to check if the genome file is stored there.
-            fasta_file = os.path.join(os.dbpath, fasta_file)
+        if os.path.isfile(os.path.join(options.dbpath, fasta_file)):
+            # Search for options.dbpath to check if the genome file is stored there.
+            fasta_file = os.path.join(options.dbpath, fasta_file)
         else:
             error('%s cannot be found' % fasta_file)
-
+        #
+    #
+    #
     if options.aligner not in supported_aligners:
         error('-a option should be: %s' % ' ,'.join(supported_aligners)+'.')
-
+    #
     builder_exec = os.path.join(options.aligner_path or aligner_path[options.aligner],
                                 {BOWTIE   : 'bowtie-build',
                                  BOWTIE2  : 'bowtie2-build',
                                  SOAP     : '2bwt-builder',
                                  RMAP     : '' # do nothing
                                 }[options.aligner])
-
+    #
     build_command = builder_exec + { BOWTIE   : ' -f %(fname)s.fa %(fname)s',
                                      BOWTIE2  : ' -f %(fname)s.fa %(fname)s',
                                      SOAP     : ' %(fname)s.fa'
                                    }[options.aligner]
-
-
+    #
+    #
     print "Reference genome file: %s" % fasta_file
     print "Reduced Representation Bisulfite Sequencing: %s" % rrbs
     print "Short reads aligner you are using: %s" % options.aligner
     print "Builder path: %s" % builder_exec
-
+    #
     #---------------------------------------------------------------
-
+    #
     if not os.path.isfile( builder_exec ) :
         error("Cannot file program %s for execution." % builder_exec)
-
+    #
     ref_path = options.dbpath
-
+    #
     if os.path.exists(ref_path):
         if not os.path.isdir(ref_path):
             error("%s must be a directory. Please, delete it or change the -d option." % ref_path)
+        #
     else:
         os.mkdir(ref_path)
-
+    #
     if rrbs: # RRBS preprocessing
         rrbs_build(fasta_file, build_command, ref_path, options.low_bound, options.up_bound, options.aligner, options.cut_format)
     else: # Whole genome preprocessing
         wg_build(fasta_file, build_command, ref_path, options.aligner)
+    #
+#
 

bs_utils/utils.py

@@ -23,7 +23,7 @@ def reverse_compl_seq(strseq):
 
 def show_version() :
     print ""
-    print "     BS-Seeker2 v2.1.3 - Oct. 25, 2017"
+    print "     BS-Seeker2 v2.1.5 - Dec. 21, 2017"
     print ""