--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/bs_utils/utils.py	Fri Jul 12 18:47:28 2013 -0400
@@ -0,0 +1,332 @@
+import gzip
+import os
+
+import datetime
+import re
+import shlex
+import shutil
+import string
+import subprocess
+import types
+#from itertools import izip
+
+import marshal
+import sys
+
+
+
+_rc_trans = string.maketrans('ACGT', 'TGCA')
+def reverse_compl_seq(strseq):
+    return strseq.translate(_rc_trans)[::-1]
+
+
+
+def show_version() :
+    print ""
+    print "     BS-Seeker2 v2.0.3 - May 19, 2013     "
+    print ""
+
+
+
+"""
+IUPAC nucleotide code Base
+    A	Adenine
+    C	Cytosine
+    G	Guanine
+    T (or U)	Thymine (or Uracil)
+    R	A or G
+    Y	C or T
+    S	G or C
+    W	A or T
+    K	G or T
+    M	A or C
+    B	C or G or T
+    D	A or G or T
+    H	A or C or T
+    V	A or C or G
+    N	any base
+    . or -	gap
+"""
+
+
+def IUPAC ( nuc ) :
+    if nuc == 'R' :
+        return ('A','G')
+    elif nuc == 'Y' :
+        return ('C', 'T')
+    elif nuc == 'S' :
+        return ('G', 'C')
+    elif nuc == 'W' :
+        return ('A', 'T')
+    elif nuc == 'K' :
+        return ('G','T')
+    elif nuc == 'M' :
+        return ('A','C')
+    elif nuc == 'B' :
+        return ('C', 'G', 'T')
+    elif nuc == 'D' :
+        return ('A', 'G', 'T')
+    elif nuc == 'H' :
+        return ('A', 'C', 'T')
+    elif nuc == 'V' :
+        return ('A', 'C', 'G')
+    elif nuc == 'N' :
+        return ('A', 'C', 'G', 'T')
+    else :
+        return (nuc)
+
+
+def uniq(inlist):
+    # order preserving
+    uniques = []
+    for item in inlist:
+        if item not in uniques:
+            uniques.append(item)
+    return uniques
+
+from itertools import product
+
+def EnumerateIUPAC ( context_lst ) :
+    tag_list = []
+#    context_lst = [context]
+    for one_context in context_lst :
+        for m in product(*[ IUPAC(i) for i in list(one_context)]) :
+            tag_list.append(''.join(m))
+    return uniq(tag_list)
+
+from itertools import product
+
+# example: cut3_context="CGG"
+# return generator for : ["CGG","TGG"]
+# wild-card C to both C and T
+def Enumerate_C_to_CT ( cut3_context_lst ) :
+    tag_list = []
+    for context in cut3_context_lst :
+        for m in product(*[i if (i is not 'C') else ('C','T') for i in context]) :
+            tag_list.append(''.join(m))
+    return uniq(tag_list)
+
+#-------------------------------------------------------------------------------------
+
+# set a reasonable defaults
+def find_location(program):
+    def is_exe(fpath):
+        return os.path.exists(fpath) and os.access(fpath, os.X_OK)
+    for path in os.environ["PATH"].split(os.pathsep):
+        if is_exe(os.path.join(path, program)):
+            return path
+
+    return None
+
+BOWTIE = 'bowtie'
+BOWTIE2 = 'bowtie2'
+SOAP = 'soap'
+RMAP = 'rmap'
+
+supported_aligners = [
+                      BOWTIE,
+                      BOWTIE2,
+                      SOAP,
+                      RMAP
+                    ]
+
+aligner_options_prefixes = { BOWTIE  : '--bt-',
+                             BOWTIE2 : '--bt2-',
+                             SOAP    : '--soap-',
+                             RMAP    : '--rmap-' }
+
+aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or default_path))
+                    for aligner, default_path in
+                           [(BOWTIE,'~/bowtie-0.12.7/'),
+                            (BOWTIE2, '~/bowtie-0.12.7/'),
+                            (SOAP, '~/soap2.21release/'),
+                            (RMAP, '~/rmap_v2.05/bin')
+                            ])
+
+
+reference_genome_path = os.path.join(os.path.split(globals()['__file__'])[0],'reference_genomes')
+
+
+
+def error(msg):
+    print >> sys.stderr, 'ERROR: %s' % msg
+    exit(1)
+
+
+global_stime = datetime.datetime.now()
+def elapsed(msg = None):
+    print "[%s]" % msg if msg is not None else "+", "Last:" , datetime.datetime.now() - elapsed.stime, '\tTotal:', datetime.datetime.now() - global_stime
+
+    elapsed.stime = datetime.datetime.now()
+
+elapsed.stime = datetime.datetime.now()
+
+
+def open_log(fname):
+    open_log.logfile = open(fname, 'w', 1)
+
+def logm(message):
+    log_message = "[%s] %s\n" % (datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'), message)
+    print log_message,
+    open_log.logfile.write(log_message)
+
+def close_log():
+    open_log.logfile.close()
+
+
+
+
+def clear_dir(path):
+    """ If path does not exist, it creates a new directory.
+        If path points to a directory, it deletes all of its content.
+        If path points to a file, it raises an exception."""
+
+    if os.path.exists(path):
+        if not os.path.isdir(path):
+            error("%s is a file. Please, delete it manually!" % path)
+        else:
+            for the_file in os.listdir(path):
+                file_path = os.path.join(path, the_file)
+                try:
+                    if os.path.isfile(file_path):
+                        os.unlink(file_path)
+                    elif os.path.isdir(file_path):
+                        shutil.rmtree(file_path)
+                except Exception, e:
+                    print e
+    else:
+        os.mkdir(path)
+
+
+def delete_files(*filenames):
+#    return
+    """ Deletes a number of files. filenames can contain generator expressions and/or lists, too"""
+
+    for fname in filenames:
+        if type(fname) in [list, types.GeneratorType]:
+            delete_files(*list(fname))
+        elif os.path.isdir(fname):
+            shutil.rmtree(fname)
+        else:
+            os.remove(fname)
+
+def split_file(filename, output_prefix, nlines):
+    """ Splits a file (equivalend to UNIX split -l ) """
+    fno = 0
+    lno = 0
+    INPUT = open(filename, 'r')
+    output = None
+    for l in INPUT:
+        if lno == 0:
+            fno += 1
+            if output is not None: output.close()
+            output = open('%s%d' % (output_prefix, fno), 'w')
+            lno = nlines
+        output.write(l)
+        lno -= 1
+    output.close()
+    INPUT.close()
+
+def isplit_file(filename, output_prefix, nlines):
+    """ Splits a file (equivalend to UNIX split -l ) """
+    fno = 0
+    lno = 0
+    try :
+        input = (gzip.open if filename.endswith('.gz') else open)(filename, 'r')
+    except IOError :
+        print "[Error] Cannot find file : %s !" % filename
+        exit(-1)
+    output = None
+    output_fname = None
+    for l in input:
+        if lno == 0:
+
+            if output is not None:
+                output.close()
+                yield output_fname
+
+            fno += 1
+            output_fname = '%s%d' % (output_prefix, fno)
+#            output_fname = '%s_0' % output_prefix
+            output = open(output_fname, 'w')
+            lno = nlines
+        output.write(l)
+        lno -= 1
+    if output is not None:
+        output.close()
+    yield output_fname
+
+    input.close()
+
+def read_fasta(fasta_file):
+    """ Iterates over all sequences in a fasta file. One at a time, without reading the whole file into the main memory.
+    """
+
+    try :
+        input = (gzip.open if fasta_file.endswith('.gz') else open)(fasta_file)
+    except IOError:
+        print "[Error] Cannot find fasta file : %s !" % fasta_file
+        exit(-1)
+    sanitize = re.compile(r'[^ACTGN]')
+    sanitize_seq_id = re.compile(r'[^A-Za-z0-9]')
+
+    chrom_seq = []
+    chrom_id = None
+    seen_ids = set()
+
+    for line in input:
+        if line[0] == '>':
+            if chrom_id is not None:
+                yield chrom_id, ''.join(chrom_seq)
+
+            chrom_id = sanitize_seq_id.sub('_', line.split()[0][1:])
+
+            if chrom_id in seen_ids:
+                error('BS Seeker found identical sequence ids (id: %s) in the fasta file: %s. Please, make sure that all sequence ids are unique and contain only alphanumeric characters: A-Za-z0-9_' % (chrom_id, fasta_file))
+            seen_ids.add(chrom_id)
+
+            chrom_seq = []
+
+        else:
+            chrom_seq.append(sanitize.sub('N', line.strip().upper()))
+
+    yield chrom_id, ''.join(chrom_seq)
+
+    input.close()
+
+
+def serialize(obj, filename):
+    """ Be careful what you serialize and deseriazlize! marshal.load is not secure!
+    """
+    output = open(filename+'.data', 'w')
+    marshal.dump(obj, output)
+    output.close()
+
+def deserialize(filename):
+    """ Be careful what you serialize and deseriazlize! marshal.load is not secure!
+    """
+    try:
+        input = open(filename+'.data')
+    except IOError:
+        print "\n[Error]:\n\t Cannot find file: %s.data" % filename
+        exit(-1)
+
+    obj = marshal.load(input)
+    input.close()
+    return obj   
+
+
+
+def run_in_parallel(commands):
+
+    commands = [(cmd[0], open(cmd[1], 'w')) if type(cmd) is tuple else (cmd, None) for cmd in commands]
+
+    logm('Starting commands:\n' + '\n'.join([cmd for cmd, stdout in commands]))
+    for i, proc in enumerate([subprocess.Popen(args = shlex.split(cmd), stdout = stdout) for cmd, stdout in commands]):
+        return_code = proc.wait()
+        logm('Finished: ' + commands[i][0])
+        if return_code != 0:
+            error('%s \nexit with an error code: %d. Please, check the log files.' % (commands[i], return_code))
+    for _, stdout in commands:
+        if stdout is not None:
+            stdout.close()