--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/bs_index/wg_build.py	Fri Jul 12 18:47:28 2013 -0400
@@ -0,0 +1,55 @@
+from bs_utils.utils import *
+
+
+def wg_build(fasta_file, build_command, ref_path, aligner):
+
+    # ref_path is a string that containts the directory where the reference genomes are stored with
+    # the input fasta filename appended
+    ref_path = os.path.join(ref_path,
+                            os.path.split(fasta_file)[1] + '_'+aligner)
+
+    clear_dir(ref_path)
+    #---------------------------------------------------------------
+    # 1. First get the complementary genome (also do the reverse)
+    # 2. Then do CT and GA conversions
+    #---------------------------------------------------------------
+
+    open_log(os.path.join(ref_path, 'log'))
+    refd = {}
+    w_c2t = open(os.path.join(ref_path, 'W_C2T.fa'),'w')
+    c_c2t = open(os.path.join(ref_path, 'C_C2T.fa'),'w')
+
+    w_g2a = open(os.path.join(ref_path, 'W_G2A.fa'),'w')
+    c_g2a = open(os.path.join(ref_path, 'C_G2A.fa'),'w')
+    for chrom_id, chrom_seq in read_fasta(fasta_file):
+        serialize(chrom_seq, os.path.join(ref_path, chrom_id))
+        refd[chrom_id] = len(chrom_seq)
+
+        w_c2t.write('>%s\n%s\n' % (chrom_id, chrom_seq.replace("C","T")))
+        w_g2a.write('>%s\n%s\n' % (chrom_id, chrom_seq.replace("G","A")))
+
+        chrom_seq = reverse_compl_seq(chrom_seq)
+
+        c_c2t.write('>%s\n%s\n' % (chrom_id, chrom_seq.replace("C","T")))
+        c_g2a.write('>%s\n%s\n' % (chrom_id, chrom_seq.replace("G","A")))
+
+        elapsed('Preprocessing '+chrom_id)
+
+    for outf in [w_c2t, c_c2t, w_g2a, c_g2a]:
+        outf.close()
+
+    serialize(refd, os.path.join(ref_path,"refname"))
+    elapsed('Genome preprocessing')
+    # append ref_path to all elements of to_bowtie
+    to_bowtie = map(lambda f: os.path.join(ref_path, f), ['W_C2T', 'W_G2A', 'C_C2T', 'C_G2A'])
+
+    # start bowtie-build for all converted genomes and wait for the processes to finish
+
+    run_in_parallel([(build_command % { 'fname' : fname }, fname+'.log') for fname in to_bowtie])
+
+    # delete fasta files of converted genomes
+    if aligner != "rmap" :
+        delete_files(f+'.fa' for f in to_bowtie)
+
+    elapsed('Done')
+