# HG changeset patch
# User drosofff
# Date 1432761555 14400
# Node ID b996480cd604701f39e60f728376602d4de52a06

planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r 000000000000 -r b996480cd604 sRbowtieParser.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtieParser.py	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/python
+# python parser module to analyse sRbowtie alignments
+# version 1.0.2 - argparse implementation
+# Usage sRbowtieParser.py  <1:index source> <2:extraction directive> <3:outputL> <4:polarity> <5:6:7 filePath:FileExt:FileLabel> <.. ad  lib>
+
+import sys, argparse
+from smRtools import *
+
+def masterListGenerator(data_source):
+  for filePath, FileExt, FileLabel in data_source:
+    yield HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat)
+
+def Parser():
+  the_parser = argparse.ArgumentParser()
+  the_parser.add_argument('--IndexSource', action="store", type=str, help="Path to the index source")
+  the_parser.add_argument('--ExtractDirective', action="store", type=str, choices=["fastaSource", "bowtieIndex"], help="Extract info from fasta or bowtie index")
+  the_parser.add_argument('--output', action="store", type=str, help="path to the output")
+  the_parser.add_argument('--polarity', choices=["forward", "reverse", "both"], help="forward, reverse or both forward an reverse reads are counted")
+  the_parser.add_argument('--alignmentSource',nargs='+', help="paths to alignments files")
+  the_parser.add_argument('--alignmentFormat',nargs='+', help="Format of the bowtie alignment (tabular, sam or bam)")
+  the_parser.add_argument('--alignmentLabel',nargs='+', help="Label of the alignment")
+  args = the_parser.parse_args()
+  return args
+
+args = Parser()
+
+IndexSource = args.IndexSource
+genomeRefFormat = args.ExtractDirective
+Output = args.output
+Polarity = args.polarity
+header = ["gene"]
+
+
+FileLabelList=[label for label in args.alignmentLabel]
+header.extend(FileLabelList)
+assert (len(FileLabelList)==len(set(FileLabelList))),"You have supplied a non-unique label. Please make sure that your input files have unique names"
+
+data_source=zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel)
+master_generator=masterListGenerator(data_source)
+
+for i,window in enumerate(master_generator):
+  window=window
+  if i==0:
+    gene_count_dict={gene:[str(item.readcount(polarity=Polarity))] for gene,item in window.instanceDict.items()}
+  else:
+    [gene_count_dict[gene].append(str(item.readcount(polarity=Polarity))) for gene,item in window.instanceDict.items()]
+
+
+F = open (args.output, "w")
+# print >>F, args
+print >> F, "\t".join(header)
+
+for item in sorted(gene_count_dict.keys()):
+  line=[item]
+  line.extend(gene_count_dict[item])
+  print >> F,  "\t".join(line )
+F.close()
diff -r 000000000000 -r b996480cd604 sRbowtieParser.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtieParser.xml	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,87 @@
+<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1">
+  <description></description>
+  <requirements>
+	<requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="0.7.7">pysam</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.14">scipy</requirement>
+ </requirements>
+<command interpreter="python">
+        sRbowtieParser.py 
+	          #if $refGenomeSource.genomeSource == "history":
+                    --IndexSource $refGenomeSource.ownFile
+         	    --ExtractDirective fastaSource
+          	  #else:
+		    #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
+            	    --IndexSource $reference
+            	    --ExtractDirective bowtieIndex
+          	  #end if
+		  --output $output
+		  --polarity $polarity
+                  --alignmentSource
+		  #for $i in $refGenomeSource.input_list
+    		    $i
+		  #end for
+                  --alignmentFormat
+                  #for $i in $refGenomeSource.input_list
+                    $i.ext
+                  #end for
+                  --alignmentLabel          
+                  #for $i in $refGenomeSource.input_list
+                    "$i.name"
+                  #end for
+
+</command>
+  <inputs>
+       <conditional name="refGenomeSource">
+           <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+               <option value="indexed">Use a built-in index</option>
+               <option value="history">Use one from the history</option>
+           </param>
+           <when value="indexed">
+               <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true">
+                  <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
+               </param>
+           </when>
+           <when value="history">
+                <param name="ownFile" type="data" format="fasta"  label="Select the fasta reference" />
+	        <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
+           </when>
+       </conditional>  <!-- refGenomeSource -->
+       <param name="polarity" type="select" label="how to count sense and antisense reads">
+         <option value="both">count both sense and antisense reads</option>
+         <option value="forward">count only sense reads</option>
+         <option value="reverse">count only antisense reads</option>
+       </param>
+   </inputs>
+   <outputs>
+   <data format="tabular" name="output" label="Read Count  Lists"/>
+   </outputs>
+  <help>
+
+**What it does**
+
+Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format).
+Here a bowtie match done against an index composed of a set of items is parsed and expressed as a hit list of the corresponding items
+
+Sense, antisense or both sense and antisense alignments can be counted
+
+The library labels are infered from the input dataset names in the galaxy history.
+
+**It is thus essential that input datasets are appropriately renamed**
+
+**it is preferable that you do not put any space in this input dataset names. You may edit these names in the history**
+
+  </help>
+  <tests>
+    <test>
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value ="dme-mir-v20" ftype="fasta" />
+      <param name="input_list" value="matchedSample_1,matchedSample_2" ftype="tabular" />
+      <param name="polarity" value="forward" />
+      <output name="output" ftype="tabular" file="Read_Count_Lists.tab" />
+    </test>
+  </tests>
+</tool>
+
diff -r 000000000000 -r b996480cd604 smRtools.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smRtools.py	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,755 @@
+#!/usr/bin/python
+# version 1 7-5-2012 unification of the SmRNAwindow class
+
+import sys, subprocess
+from collections import defaultdict
+from numpy import mean, median, std
+from scipy import stats
+
+def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"):
+  '''This function will return a dictionary containing fasta identifiers as keys and the
+  sequence as values. Index must be the path to a fasta file.'''
+  p = subprocess.Popen(args=["bowtie-inspect","-a", "0", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines
+  outputlines = p.stdout.readlines()
+  p.wait()
+  item_dic = {}
+  for line in outputlines:
+    if (line[0] == ">"):
+      try:
+        item_dic[current_item] = "".join(stringlist) # to dump the sequence of the previous item - try because of the keyerror of the first item
+      except: pass
+      current_item = line[1:].rstrip().split()[0] #take the first word before space because bowtie splits headers !
+      item_dic[current_item] = ""
+      stringlist=[]
+    else:
+      stringlist.append(line.rstrip() )
+  item_dic[current_item] = "".join(stringlist) # for the last item
+  return item_dic
+
+def get_fasta_headers (index):
+  p = subprocess.Popen(args=["bowtie-inspect","-n", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines
+  outputlines = p.stdout.readlines()
+  p.wait()
+  item_dic = {}
+  for line in outputlines:
+    header = line.rstrip().split()[0] #take the first word before space because bowtie splits headers !
+    item_dic[header] = 1
+  return item_dic
+
+
+def get_file_sample (file, numberoflines):
+  '''import random to use this function'''
+  F=open(file)
+  fullfile = F.read().splitlines()
+  F.close()
+  if len(fullfile) < numberoflines:
+    return "sample size exceeds file size"
+  return random.sample(fullfile, numberoflines)
+
+def get_fasta_from_history (file):
+  F = open (file, "r")
+  item_dic = {}
+  for line in F:
+    if (line[0] == ">"):
+      try:
+        item_dic[current_item] = "".join(stringlist) # to dump the sequence of the previous item - try because of the keyerror of the first item
+      except: pass
+      current_item = line[1:-1].split()[0] #take the first word before space because bowtie splits headers !
+      item_dic[current_item] = ""
+      stringlist=[]
+    else:
+      stringlist.append(line[:-1])
+  item_dic[current_item] = "".join(stringlist) # for the last item
+  return item_dic
+
+def antipara (sequence):
+    antidict = {"A":"T", "T":"A", "G":"C", "C":"G", "N":"N"}
+    revseq = sequence[::-1]
+    return "".join([antidict[i] for i in revseq])
+
+def RNAtranslate (sequence):
+    return "".join([i if i in "AGCN" else "U" for i in sequence])
+def DNAtranslate (sequence):
+    return "".join([i if i in "AGCN" else "T" for i in sequence])
+
+def RNAfold (sequence_list):
+  thestring= "\n".join(sequence_list)
+  p = subprocess.Popen(args=["RNAfold","--noPS"], stdin= subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+  output=p.communicate(thestring)[0]
+  p.wait()
+  output=output.split("\n")
+  if not output[-1]: output = output[:-1] # nasty patch to remove last empty line
+  buffer=[]
+  for line in output:
+    if line[0] in ["N","A","T","U","G","C"]:
+      buffer.append(DNAtranslate(line))
+    if line[0] in ["(",".",")"]:
+      fields=line.split("(")
+      energy= fields[-1]
+      energy = energy[:-1] # remove the ) parenthesis
+      energy=float(energy)
+      buffer.append(str(energy))
+  return dict(zip(buffer[::2], buffer[1::2]))
+
+def extractsubinstance (start, end, instance):
+  ''' Testing whether this can be an function external to the class to save memory'''
+  subinstance = SmRNAwindow (instance.gene, instance.sequence[start-1:end], start)
+  subinstance.gene = "%s %s %s" % (subinstance.gene, subinstance.windowoffset, subinstance.windowoffset + subinstance.size - 1)
+  upcoordinate = [i for i in range(start,end+1) if instance.readDict.has_key(i) ]
+  downcoordinate = [-i for i in range(start,end+1) if instance.readDict.has_key(-i) ]
+  for i in upcoordinate:
+    subinstance.readDict[i]=instance.readDict[i]
+  for i in downcoordinate:
+    subinstance.readDict[i]=instance.readDict[i]
+  return subinstance
+
+class HandleSmRNAwindows:
+  def __init__(self, alignmentFile="~", alignmentFileFormat="tabular", genomeRefFile="~", genomeRefFormat="bowtieIndex", biosample="undetermined", size_inf=None, size_sup=1000, norm=1.0):
+    self.biosample = biosample
+    self.alignmentFile = alignmentFile
+    self.alignmentFileFormat = alignmentFileFormat # can be "tabular" or "sam"
+    self.genomeRefFile = genomeRefFile
+    self.genomeRefFormat = genomeRefFormat # can be "bowtieIndex" or "fastaSource"
+    self.alignedReads = 0
+    self.instanceDict = {}
+    self.size_inf=size_inf
+    self.size_sup=size_sup
+    self.norm=norm
+    if genomeRefFormat == "bowtieIndex":
+      self.itemDict = get_fasta (genomeRefFile)
+    elif genomeRefFormat == "fastaSource":
+      self.itemDict = get_fasta_from_history (genomeRefFile)
+    for item in self.itemDict:
+      self.instanceDict[item] = SmRNAwindow(item, sequence=self.itemDict[item], windowoffset=1, biosample=self.biosample, norm=self.norm) # create as many instances as there is items
+    self.readfile()
+
+  def readfile (self) :
+    if self.alignmentFileFormat == "tabular":
+      F = open (self.alignmentFile, "r")
+      for line in F:
+        fields = line.split()
+        polarity = fields[1]
+        gene = fields[2]
+        offset = int(fields[3])
+        size = len (fields[4])
+        if self.size_inf:
+          if (size>=self.size_inf and size<= self.size_sup):
+            self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
+            self.alignedReads += 1
+        else:
+          self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
+          self.alignedReads += 1
+      F.close()
+      return self.instanceDict
+#    elif self.alignmentFileFormat == "sam":
+#      F = open (self.alignmentFile, "r")
+#      dict = {"0":"+", "16":"-"}
+#      for line in F:
+#        if line[0]=='@':
+#            continue
+#        fields = line.split()
+#        if fields[2] == "*": continue
+#        polarity = dict[fields[1]]
+#        gene = fields[2]
+#        offset = int(fields[3])
+#        size = len (fields[9])
+#        if self.size_inf:
+#          if (size>=self.size_inf and size<= self.size_sup):
+#            self.instanceDict[gene].addread (polarity, offset, size)
+#            self.alignedReads += 1
+#       else:
+#          self.instanceDict[gene].addread (polarity, offset, size)
+#          self.alignedReads += 1
+#      F.close()
+    elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam":
+      import pysam
+      samfile = pysam.Samfile(self.alignmentFile)
+      for read in samfile:
+        if read.tid == -1:
+          continue # filter out unaligned reads
+        if read.is_reverse:
+          polarity="-"
+        else:
+          polarity="+"
+        gene = samfile.getrname(read.tid)
+        offset = read.pos
+        size = read.qlen
+        if self.size_inf:
+          if (size>=self.size_inf and size<= self.size_sup):
+            self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
+            self.alignedReads += 1
+        else:
+          self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
+          self.alignedReads += 1
+      return self.instanceDict
+
+#  def size_histogram (self):
+#    size_dict={}
+#    size_dict['F']= defaultdict (int)
+#    size_dict['R']= defaultdict (int)
+#    size_dict['both'] = defaultdict (int)
+#    for item in self.instanceDict:
+#      buffer_dict_F = self.instanceDict[item].size_histogram()['F']
+#      buffer_dict_R = self.instanceDict[item].size_histogram()['R']
+#      for size in buffer_dict_F:
+#        size_dict['F'][size] += buffer_dict_F[size]
+#      for size in buffer_dict_R:
+#        size_dict['R'][size] -= buffer_dict_R[size]
+#    allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) )
+#    for size in allSizeKeys:
+#      size_dict['both'][size] = size_dict['F'][size] + size_dict['R'][size]
+#    return size_dict
+  def size_histogram (self): # in HandleSmRNAwindows
+    '''refactored on 7-9-2014 to debug size_histogram tool'''
+    size_dict={}
+    size_dict['F']= defaultdict (float)
+    size_dict['R']= defaultdict (float)
+    size_dict['both'] = defaultdict (float)
+    for item in self.instanceDict:
+      buffer_dict = self.instanceDict[item].size_histogram()
+      for polarity in ["F", "R"]:
+        for size in buffer_dict[polarity]:
+          size_dict[polarity][size] += buffer_dict[polarity][size]
+      for size in buffer_dict["both"]:
+        size_dict["both"][size] += buffer_dict["F"][size] - buffer_dict["R"][size]
+    return size_dict
+
+  def CountFeatures (self, GFF3="path/to/file"):
+    featureDict = defaultdict(int)
+    F  = open (GFF3, "r")
+    for line in F:
+      if line[0] ==  "#": continue
+      fields = line[:-1].split()
+      chrom, feature, leftcoord, rightcoord, polarity = fields[0], fields[2], fields[3], fields[4], fields[6]
+      featureDict[feature] += self.instanceDict[chrom].readcount(upstream_coord=int(leftcoord), downstream_coord=int(rightcoord), polarity="both", method="destructive")
+    F.close()
+    return featureDict
+
+class SmRNAwindow:
+
+  def __init__(self, gene, sequence="ATGC", windowoffset=1, biosample="Undetermined", norm=1.0):
+    self.biosample = biosample
+    self.sequence = sequence
+    self.gene = gene
+    self.windowoffset = windowoffset
+    self.size = len(sequence)
+    self.readDict = defaultdict(list) # with a {+/-offset:[size1, size2, ...], ...}
+    self.matchedreadsUp = 0
+    self.matchedreadsDown = 0
+    self.norm=norm
+    
+  def addread (self, polarity, offset, size):
+    '''ATTENTION ATTENTION ATTENTION'''
+    ''' We removed the conversion from 0 to 1 based offset, as we do this now during readparsing.'''
+    if polarity == "+":
+      self.readDict[offset].append(size)
+      self.matchedreadsUp += 1
+    else:
+      self.readDict[-(offset + size -1)].append(size)
+      self.matchedreadsDown += 1
+    return
+
+  def barycenter (self, upstream_coord=None, downstream_coord=None):
+    '''refactored 24-12-2013 to save memory and introduce offset filtering see readcount method for further discussion on that
+    In this version, attempt to replace the dictionary structure by a list of tupple to save memory too'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    window_size = downstream_coord - upstream_coord +1
+    def weigthAverage (TuppleList):
+      weightSum = 0
+      PonderWeightSum = 0
+      for tuple in TuppleList:
+        PonderWeightSum += tuple[0] * tuple[1]
+        weightSum += tuple[1]
+      if weightSum > 0:
+        return PonderWeightSum / float(weightSum)
+      else:
+        return 0
+    forwardTuppleList = [(k, len(self.readDict[k])) for k in self.readDict.keys() if (k > 0 and abs(k) >= upstream_coord and abs(k) <= downstream_coord)] # both forward and in the proper offset window
+    reverseTuppleList = [(-k, len(self.readDict[k])) for k in self.readDict.keys() if (k < 0 and abs(k) >= upstream_coord and abs(k) <= downstream_coord)] # both reverse and in the proper offset window
+    Fbarycenter = (weigthAverage (forwardTuppleList) - upstream_coord) / window_size
+    Rbarycenter = (weigthAverage (reverseTuppleList) - upstream_coord) / window_size
+    return Fbarycenter, Rbarycenter
+
+  def correlation_mapper (self, reference, window_size):
+    '''to map correlation with a sliding window 26-2-2013'''
+    if window_size > self.size:
+      return []
+    F=open(reference, "r")
+    reference_forward = []
+    reference_reverse = []
+    for line in F:
+      fields=line.split()
+      reference_forward.append(int(float(fields[1])))
+      reference_reverse.append(int(float(fields[2])))
+    F.close()
+    local_object_forward=[]
+    local_object_reverse=[]
+    ## Dict to list for the local object
+    for i in range(1, self.size+1):
+      local_object_forward.append(len(self.readDict[i]))
+      local_object_reverse.append(len(self.readDict[-i]))
+    ## start compiling results by slides
+    results=[]
+    for coordinate in range(self.size - window_size):
+      local_forward=local_object_forward[coordinate:coordinate + window_size]
+      local_reverse=local_object_reverse[coordinate:coordinate + window_size]
+      if sum(local_forward) == 0 or sum(local_reverse) == 0: 
+        continue
+      try:
+        reference_to_local_cor_forward = stats.spearmanr(local_forward, reference_forward)
+        reference_to_local_cor_reverse = stats.spearmanr(local_reverse, reference_reverse)
+        if (reference_to_local_cor_forward[0] > 0.2 or  reference_to_local_cor_reverse[0]>0.2):
+          results.append([coordinate+1, reference_to_local_cor_forward[0], reference_to_local_cor_reverse[0]])
+      except:
+        pass
+    return results
+
+  def readcount (self, size_inf=0, size_sup=1000, upstream_coord=None, downstream_coord=None, polarity="both", method="conservative"):
+    '''refactored 24-12-2013 to save memory and introduce offset filtering
+    take a look at the defaut parameters that cannot be defined relatively to the instance are they are defined before instanciation
+    the trick is to pass None and then test
+    polarity parameter can take "both", "forward" or "reverse" as value'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "both":
+      return self.matchedreadsUp +  self.matchedreadsDown
+    if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "forward":
+      return self.matchedreadsUp    
+    if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "reverse":
+      return self.matchedreadsDown    
+    n=0
+    if polarity == "both":
+      for offset in xrange(upstream_coord, downstream_coord+1):
+        if self.readDict.has_key(offset):
+          for read in self.readDict[offset]:
+            if (read>=size_inf and read<= size_sup):
+              n += 1
+          if method != "conservative":
+            del self.readDict[offset] ## Carefull ! precludes re-use on the self.readDict dictionary !!!!!! TEST
+        if self.readDict.has_key(-offset):
+          for read in self.readDict[-offset]:
+            if (read>=size_inf and read<= size_sup):
+              n += 1
+          if method != "conservative":
+            del self.readDict[-offset]
+      return n
+    elif polarity == "forward":
+      for offset in xrange(upstream_coord, downstream_coord+1):
+        if self.readDict.has_key(offset):
+          for read in self.readDict[offset]:
+            if (read>=size_inf and read<= size_sup):
+              n += 1
+      return n
+    elif polarity == "reverse":
+      for offset in xrange(upstream_coord, downstream_coord+1):
+        if self.readDict.has_key(-offset):
+          for read in self.readDict[-offset]:
+            if (read>=size_inf and read<= size_sup):
+              n += 1
+      return n
+
+  def readsizes (self):
+    '''return a dictionary of number of reads by size (the keys)'''
+    dicsize = {}
+    for offset in self.readDict:
+      for size in self.readDict[offset]:
+        dicsize[size] = dicsize.get(size, 0) + 1
+    for offset in range (min(dicsize.keys()), max(dicsize.keys())+1):
+      dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
+    return dicsize
+    
+#  def size_histogram(self):
+#    norm=self.norm
+#    hist_dict={}
+#    hist_dict['F']={}
+#    hist_dict['R']={}
+#    for offset in self.readDict:
+#      for size in self.readDict[offset]:
+#        if offset < 0:
+#          hist_dict['R'][size] = hist_dict['R'].get(size, 0) - 1*norm
+#        else:
+#          hist_dict['F'][size] = hist_dict['F'].get(size, 0) + 1*norm
+#   ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !    
+#    if not (hist_dict['F']) and (not hist_dict['R']):
+#      hist_dict['F'][21] = 0
+#      hist_dict['R'][21] = 0
+#   ##
+#    return hist_dict
+
+  def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow
+    '''refactored on 7-9-2014 to debug size_histogram tool'''
+    norm=self.norm
+    size_dict={}
+    size_dict['F']= defaultdict (float)
+    size_dict['R']= defaultdict (float)
+    size_dict['both']= defaultdict (float)
+    for offset in self.readDict:
+      for size in self.readDict[offset]:
+        if offset < 0:
+          size_dict['R'][size] = size_dict['R'][size] - 1*norm
+        else:
+          size_dict['F'][size] = size_dict['F'][size] + 1*norm
+    ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !    
+    if not (size_dict['F']) and (not size_dict['R']):
+      size_dict['F'][21] = 0
+      size_dict['R'][21] = 0
+    ##
+    allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) ) 
+    for size in allSizeKeys:
+      size_dict['both'][size] = size_dict['F'][size] - size_dict['R'][size]
+    if minquery:
+      for polarity in size_dict.keys():
+        for size in xrange(minquery, maxquery+1):
+          if not size in size_dict[polarity].keys():
+            size_dict[polarity][size]=0
+    return size_dict
+
+  def statsizes (self, upstream_coord=None, downstream_coord=None):
+    ''' migration to memory saving by specifying possible subcoordinates
+    see the readcount method for further discussion'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    L = []
+    for offset in self.readDict:
+      if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
+      for size in self.readDict[offset]:
+        L.append(size)
+    meansize = mean(L)
+    stdv = std(L)
+    mediansize = median(L)         
+    return meansize, mediansize, stdv
+
+  def foldEnergy (self, upstream_coord=None, downstream_coord=None):
+    ''' migration to memory saving by specifying possible subcoordinates
+    see the readcount method for further discussion'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    Energy = RNAfold ([self.sequence[upstream_coord-1:downstream_coord] ])
+    return float(Energy[self.sequence[upstream_coord-1:downstream_coord]])
+
+  def Ufreq (self, size_scope, upstream_coord=None, downstream_coord=None):
+    ''' migration to memory saving by specifying possible subcoordinates
+    see the readcount method for further discussion. size_scope must be an interable'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    freqDic = {"A":0,"T":0,"G":0,"C":0, "N":0}
+    convertDic = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
+    for offset in self.readDict:
+      if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
+      for size in self.readDict[offset]:
+        if size in size_scope:
+          startbase = self.sequence[abs(offset)-self.windowoffset]
+          if offset < 0:
+            startbase = convertDic[startbase]
+          freqDic[startbase] += 1
+    base_sum = float ( sum( freqDic.values()) )
+    if base_sum == 0:
+      return "."
+    else:
+      return freqDic["T"] / base_sum * 100
+
+  def Ufreq_stranded (self, size_scope, upstream_coord=None, downstream_coord=None):
+    ''' migration to memory saving by specifying possible subcoordinates
+    see the readcount method for further discussion. size_scope must be an interable
+    This method is similar to the Ufreq method but take strandness into account'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    freqDic = {"Afor":0,"Tfor":0,"Gfor":0,"Cfor":0, "Nfor":0,"Arev":0,"Trev":0,"Grev":0,"Crev":0, "Nrev":0}
+    convertDic = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
+    for offset in self.readDict:
+      if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
+      for size in self.readDict[offset]:
+        if size in size_scope:
+          startbase = self.sequence[abs(offset)-self.windowoffset]
+          if offset < 0:
+            startbase = convertDic[startbase]
+            freqDic[startbase+"rev"] += 1
+          else:
+            freqDic[startbase+"for"] += 1
+    forward_sum = float ( freqDic["Afor"]+freqDic["Tfor"]+freqDic["Gfor"]+freqDic["Cfor"]+freqDic["Nfor"])
+    reverse_sum = float ( freqDic["Arev"]+freqDic["Trev"]+freqDic["Grev"]+freqDic["Crev"]+freqDic["Nrev"])
+    if forward_sum == 0 and reverse_sum == 0:
+      return ". | ."
+    elif reverse_sum == 0:
+      return "%s | ." % (freqDic["Tfor"] / forward_sum * 100)
+    elif forward_sum == 0:
+      return ". | %s" % (freqDic["Trev"] / reverse_sum * 100)
+    else:
+      return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100)
+
+    
+  def readplot (self):
+    norm=self.norm
+    readmap = {}
+    for offset in self.readDict.keys():
+      readmap[abs(offset)] = ( len(self.readDict.get(-abs(offset),[]))*norm , len(self.readDict.get(abs(offset),[]))*norm )
+    mylist = []
+    for offset in sorted(readmap):
+      if readmap[offset][1] != 0:
+        mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, readmap[offset][1], "F") )
+      if readmap[offset][0] != 0:
+        mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, -readmap[offset][0], "R") )
+    ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !
+    if not mylist:
+      mylist.append("%s\t%s\t%s\t%s" % (self.gene, 1, 0, "F") )
+    ###
+    return mylist
+
+  def readcoverage (self, upstream_coord=None, downstream_coord=None, windowName=None):
+    '''Use by MirParser tool'''
+    upstream_coord = upstream_coord or 1
+    downstream_coord = downstream_coord or self.size
+    windowName = windowName or "%s_%s_%s" % (self.gene, upstream_coord, downstream_coord)
+    forORrev_coverage = dict ([(i,0) for i in xrange(1, downstream_coord-upstream_coord+1)])
+    totalforward = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="forward")
+    totalreverse = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="reverse")
+    if totalforward > totalreverse:
+      majorcoverage = "forward"
+      for offset in self.readDict.keys():
+        if (offset > 0) and ((offset-upstream_coord+1) in forORrev_coverage.keys() ):
+          for read in self.readDict[offset]:
+            for i in xrange(read):
+              try:
+                forORrev_coverage[offset-upstream_coord+1+i] += 1
+              except KeyError:
+                continue # a sense read may span over the downstream limit
+    else:
+      majorcoverage = "reverse"
+      for offset in self.readDict.keys():
+        if (offset < 0) and (-offset-upstream_coord+1 in forORrev_coverage.keys() ):
+          for read in self.readDict[offset]:
+            for i in xrange(read):
+              try:
+                forORrev_coverage[-offset-upstream_coord-i] += 1 ## positive coordinates in the instance, with + for forward coverage and - for reverse coverage
+              except KeyError:
+                continue # an antisense read may span over the upstream limit
+    output_list = []
+    maximum = max (forORrev_coverage.values()) or 1
+    for n in sorted (forORrev_coverage):
+      output_list.append("%s\t%s\t%s\t%s\t%s\t%s\t%s" % (self.biosample, windowName, n, float(n)/(downstream_coord-upstream_coord+1), forORrev_coverage[n], float(forORrev_coverage[n])/maximum, majorcoverage))
+    return "\n".join(output_list)
+
+          
+  def signature (self, minquery, maxquery, mintarget, maxtarget, scope, zscore="no", upstream_coord=None, downstream_coord=None):
+    ''' migration to memory saving by specifying possible subcoordinates
+    see the readcount method for further discussion
+    scope must be a python iterable; scope define the *relative* offset range to be computed'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    query_range = range (minquery, maxquery+1)
+    target_range = range (mintarget, maxtarget+1)
+    Query_table = {}
+    Target_table = {}
+    frequency_table = dict ([(i, 0) for i in scope])
+    for offset in self.readDict:
+      if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
+      for size in self.readDict[offset]:
+        if size in query_range:
+          Query_table[offset] = Query_table.get(offset, 0) + 1
+        if size in target_range:
+          Target_table[offset] = Target_table.get(offset, 0) + 1
+    for offset in Query_table:
+      for i in scope:
+        frequency_table[i] += min(Query_table[offset], Target_table.get(-offset -i +1, 0))
+    if minquery==mintarget and maxquery==maxtarget: ## added to incorporate the division by 2 in the method (26/11/2013), see signature_options.py and lattice_signature.py
+      frequency_table = dict([(i,frequency_table[i]/2) for i in frequency_table])
+    if zscore == "yes":
+      z_mean = mean(frequency_table.values() )
+      z_std = std(frequency_table.values() )
+      if z_std == 0:
+        frequency_table = dict([(i,0) for i in frequency_table] )
+      else:
+        frequency_table = dict([(i, (frequency_table[i]- z_mean)/z_std) for i in frequency_table] )    
+    return frequency_table
+
+  def hannon_signature (self, minquery, maxquery, mintarget, maxtarget, scope, upstream_coord=None, downstream_coord=None):
+    ''' migration to memory saving by specifying possible subcoordinates see the readcount method for further discussion
+    note that scope must be an iterable (a list or a tuple), which specifies the relative offsets that will be computed'''
+    upstream_coord = upstream_coord or self.windowoffset
+    downstream_coord = downstream_coord or self.windowoffset+self.size-1
+    query_range = range (minquery, maxquery+1)
+    target_range = range (mintarget, maxtarget+1)
+    Query_table = {}
+    Target_table = {}
+    Total_Query_Numb = 0
+    general_frequency_table = dict ([(i,0) for i in scope])
+    ## filtering the appropriate reads for the study
+    for offset in self.readDict:
+      if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
+      for size in self.readDict[offset]:
+        if size in query_range:
+          Query_table[offset] = Query_table.get(offset, 0) + 1
+          Total_Query_Numb += 1
+        if size in target_range:
+          Target_table[offset] = Target_table.get(offset, 0) + 1
+    for offset in Query_table:
+      frequency_table = dict ([(i,0) for i in scope])
+      number_of_targets = 0
+      for i in scope:
+        frequency_table[i] += Query_table[offset] *  Target_table.get(-offset -i +1, 0)
+        number_of_targets += Target_table.get(-offset -i +1, 0)
+      for i in scope:
+        try:
+          general_frequency_table[i] += (1. / number_of_targets / Total_Query_Numb) * frequency_table[i]
+        except ZeroDivisionError :
+          continue
+    return general_frequency_table      
+
+  def phasing (self, size_range, scope):
+    ''' to calculate autocorelation like signal - scope must be an python iterable'''
+    read_table = {}
+    total_read_number = 0
+    general_frequency_table = dict ([(i, 0) for i in scope])
+    ## read input filtering
+    for offset in self.readDict:
+      for size in self.readDict[offset]:
+        if size in size_range:
+          read_table[offset] = read_table.get(offset, 0) + 1
+          total_read_number += 1
+    ## per offset read phasing computing
+    for offset in read_table:
+      frequency_table = dict ([(i, 0) for i in scope]) # local frequency table
+      number_of_targets = 0
+      for i in scope:
+        if offset > 0:
+          frequency_table[i] += read_table[offset] *  read_table.get(offset + i, 0)
+          number_of_targets += read_table.get(offset + i, 0)
+        else:
+          frequency_table[i] += read_table[offset] *  read_table.get(offset - i, 0)
+          number_of_targets += read_table.get(offset - i, 0)
+    ## inclusion of local frequency table in the general frequency table (all offsets average)
+      for i in scope:
+        try:
+          general_frequency_table[i] += (1. / number_of_targets / total_read_number) * frequency_table[i]
+        except ZeroDivisionError :
+          continue
+    return general_frequency_table
+
+
+
+  def z_signature (self, minquery, maxquery, mintarget, maxtarget, scope):
+    '''Must do: from numpy import mean, std, to use this method; scope must be a python iterable and defines the relative offsets to compute'''
+    frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope)
+    z_table = {}
+    frequency_list = [frequency_table[i] for i in sorted (frequency_table)]
+    if std(frequency_list):
+      meanlist = mean(frequency_list)
+      stdlist = std(frequency_list)
+      z_list = [(i-meanlist)/stdlist for i in frequency_list]
+      return dict (zip (sorted(frequency_table), z_list) ) 
+    else:
+      return dict (zip (sorted(frequency_table), [0 for i in frequency_table]) )
+
+  def percent_signature (self, minquery, maxquery, mintarget, maxtarget, scope):
+    frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope)
+    total = float(sum ([self.readsizes().get(i,0) for i in set(range(minquery,maxquery)+range(mintarget,maxtarget))]) )
+    if total == 0:
+      return dict( [(i,0) for i in scope])
+    return dict( [(i, frequency_table[i]/total*100) for i in scope])
+
+  def pairer (self, overlap, minquery, maxquery, mintarget, maxtarget):
+    queryhash = defaultdict(list)
+    targethash = defaultdict(list)
+    query_range = range (int(minquery), int(maxquery)+1)
+    target_range = range (int(mintarget), int(maxtarget)+1)
+    paired_sequences = []
+    for offset in self.readDict: # selection of data
+      for size in self.readDict[offset]:
+        if size in query_range:
+          queryhash[offset].append(size)
+        if size in target_range:
+          targethash[offset].append(size)
+    for offset in queryhash:
+      if offset >= 0: matched_offset = -offset - overlap + 1
+      else: matched_offset = -offset - overlap + 1
+      if targethash[matched_offset]:
+        paired = min ( len(queryhash[offset]), len(targethash[matched_offset]) )
+        if offset >= 0:
+          for i in range (paired):
+            paired_sequences.append("+%s" % RNAtranslate ( self.sequence[offset:offset+queryhash[offset][i]]) )
+            paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-targethash[matched_offset][i]+1:-matched_offset+1]) ) )
+        if offset < 0:
+          for i in range (paired):
+            paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-offset-queryhash[offset][i]+1:-offset+1]) ) )
+            paired_sequences.append("+%s" % RNAtranslate (self.sequence[matched_offset:matched_offset+targethash[matched_offset][i]] ) )
+    return paired_sequences
+
+  def pairable (self, overlap, minquery, maxquery, mintarget, maxtarget):
+    queryhash = defaultdict(list)
+    targethash = defaultdict(list)
+    query_range = range (int(minquery), int(maxquery)+1)
+    target_range = range (int(mintarget), int(maxtarget)+1)
+    paired_sequences = []
+
+    for offset in self.readDict: # selection of data
+      for size in self.readDict[offset]:
+        if size in query_range:
+          queryhash[offset].append(size)
+        if size in target_range:
+          targethash[offset].append(size)
+
+    for offset in queryhash:
+      matched_offset = -offset - overlap + 1
+      if targethash[matched_offset]:
+        if offset >= 0:
+          for i in queryhash[offset]:
+            paired_sequences.append("+%s" % RNAtranslate (self.sequence[offset:offset+i]) )
+          for i in targethash[matched_offset]:
+            paired_sequences.append( "-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-i+1:-matched_offset+1]) ) )
+        if offset < 0:
+          for i in queryhash[offset]:
+            paired_sequences.append("-%s" %  RNAtranslate (antipara (self.sequence[-offset-i+1:-offset+1]) ) )
+          for i in targethash[matched_offset]:
+            paired_sequences.append("+%s" %  RNAtranslate (self.sequence[matched_offset:matched_offset+i] ) )
+    return paired_sequences
+
+  def newpairable_bowtie (self, overlap, minquery, maxquery, mintarget, maxtarget):
+    ''' revision of pairable on 3-12-2012, with focus on the offset shift problem (bowtie is 1-based cooordinates whereas python strings are 0-based coordinates'''
+    queryhash = defaultdict(list)
+    targethash = defaultdict(list)
+    query_range = range (int(minquery), int(maxquery)+1)
+    target_range = range (int(mintarget), int(maxtarget)+1)
+    bowtie_output = []
+
+    for offset in self.readDict: # selection of data
+      for size in self.readDict[offset]:
+        if size in query_range:
+          queryhash[offset].append(size)
+        if size in target_range:
+          targethash[offset].append(size)
+    counter = 0
+    for offset in queryhash:
+      matched_offset = -offset - overlap + 1
+      if targethash[matched_offset]:
+        if offset >= 0:
+          for i in queryhash[offset]:
+            counter += 1
+            bowtie_output.append("%s\t%s\t%s\t%s\t%s" % (counter, "+", self.gene, offset-1, self.sequence[offset-1:offset-1+i]) ) # attention a la base 1-0 de l'offset 
+        if offset < 0:
+          for i in queryhash[offset]:
+            counter += 1
+            bowtie_output.append("%s\t%s\t%s\t%s\t%s" % (counter, "-", self.gene, -offset-i, self.sequence[-offset-i:-offset])) # attention a la base 1-0 de l'offset
+    return bowtie_output
+
+
+def __main__(bowtie_index_path, bowtie_output_path):
+  sequenceDic = get_fasta (bowtie_index_path)
+  objDic = {}
+  F = open (bowtie_output_path, "r") # F is the bowtie output taken as input
+  for line in F:
+    fields = line.split()
+    polarity = fields[1]
+    gene = fields[2]
+    offset = int(fields[3])
+    size = len (fields[4])
+    try:
+      objDic[gene].addread (polarity, offset, size)
+    except KeyError:
+      objDic[gene] = SmRNAwindow(gene, sequenceDic[gene])
+      objDic[gene].addread (polarity, offset, size)
+  F.close()
+  for gene in objDic:
+    print gene, objDic[gene].pairer(19,19,23,19,23)
+
+if __name__ == "__main__" : __main__(sys.argv[1], sys.argv[2]) 
diff -r 000000000000 -r b996480cd604 test-data/Read_Count_Lists.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Read_Count_Lists.tab	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,239 @@
+gene	matchedSample_1	matchedSample_2
+dme-bantam	1	1
+dme-let-7	0	0
+dme-mir-1	72	0
+dme-mir-10	0	20
+dme-mir-100	0	1
+dme-mir-1000	0	0
+dme-mir-1001	0	0
+dme-mir-1002	0	0
+dme-mir-1003	0	0
+dme-mir-1004	0	0
+dme-mir-1005	0	0
+dme-mir-1006	0	0
+dme-mir-1007	0	0
+dme-mir-1008	0	0
+dme-mir-1009	0	0
+dme-mir-1010	0	0
+dme-mir-1011	0	0
+dme-mir-1012	0	0
+dme-mir-1013	0	0
+dme-mir-1014	0	0
+dme-mir-1015	0	0
+dme-mir-1016	0	0
+dme-mir-1017	0	0
+dme-mir-11	1	2
+dme-mir-12	2	0
+dme-mir-124	0	0
+dme-mir-125	0	1
+dme-mir-133	0	0
+dme-mir-137	0	0
+dme-mir-13a	0	0
+dme-mir-13b-1	0	0
+dme-mir-13b-2	0	0
+dme-mir-14	7	7
+dme-mir-184	146	111
+dme-mir-190	0	0
+dme-mir-193	0	0
+dme-mir-210	0	0
+dme-mir-219	0	0
+dme-mir-2279	0	0
+dme-mir-2280	0	0
+dme-mir-2281	0	0
+dme-mir-2282	0	0
+dme-mir-2283	0	0
+dme-mir-2489	0	0
+dme-mir-2490	0	0
+dme-mir-2491	0	0
+dme-mir-2492	0	0
+dme-mir-2493	0	0
+dme-mir-2494	0	0
+dme-mir-2495	0	0
+dme-mir-2496	0	0
+dme-mir-2497	0	0
+dme-mir-2498	0	0
+dme-mir-2499	0	0
+dme-mir-2500	0	0
+dme-mir-2501	0	0
+dme-mir-252	0	0
+dme-mir-2535b	0	0
+dme-mir-263a	12	2
+dme-mir-263b	0	0
+dme-mir-274	0	0
+dme-mir-275	7	0
+dme-mir-276a	7	5
+dme-mir-276b	1	0
+dme-mir-277	0	1
+dme-mir-278	0	0
+dme-mir-279	8	0
+dme-mir-280	0	0
+dme-mir-281-1	0	3
+dme-mir-281-2	1	28
+dme-mir-282	0	0
+dme-mir-283	0	0
+dme-mir-284	0	0
+dme-mir-285	0	0
+dme-mir-286	0	0
+dme-mir-287	0	0
+dme-mir-288	0	0
+dme-mir-289	0	0
+dme-mir-2a-1	1	0
+dme-mir-2a-2	0	0
+dme-mir-2b-1	0	0
+dme-mir-2b-2	0	1
+dme-mir-2c	0	0
+dme-mir-3	0	0
+dme-mir-303	0	0
+dme-mir-304	0	0
+dme-mir-305	10	2
+dme-mir-306	0	0
+dme-mir-307a	0	0
+dme-mir-307b	0	0
+dme-mir-308	0	0
+dme-mir-309	0	0
+dme-mir-310	0	0
+dme-mir-311	0	0
+dme-mir-312	1	0
+dme-mir-313	0	0
+dme-mir-314	0	0
+dme-mir-315	0	0
+dme-mir-316	1	0
+dme-mir-317	0	0
+dme-mir-318	1	0
+dme-mir-31a	2	22
+dme-mir-31b	1	0
+dme-mir-33	0	0
+dme-mir-34	0	0
+dme-mir-3641	0	0
+dme-mir-3642	0	0
+dme-mir-3643	0	0
+dme-mir-3644	0	0
+dme-mir-3645	0	0
+dme-mir-375	0	0
+dme-mir-4	0	0
+dme-mir-4908	0	0
+dme-mir-4909	0	0
+dme-mir-4910	0	0
+dme-mir-4911	0	0
+dme-mir-4912	0	0
+dme-mir-4913	0	0
+dme-mir-4914	0	0
+dme-mir-4915	0	0
+dme-mir-4916	0	0
+dme-mir-4917	0	0
+dme-mir-4918	0	0
+dme-mir-4919	0	0
+dme-mir-4939	0	0
+dme-mir-4940	0	0
+dme-mir-4941	0	0
+dme-mir-4942	0	0
+dme-mir-4943	0	0
+dme-mir-4944	0	0
+dme-mir-4945	0	0
+dme-mir-4946	0	0
+dme-mir-4947	0	0
+dme-mir-4948	0	0
+dme-mir-4949	0	0
+dme-mir-4950	0	0
+dme-mir-4951	0	0
+dme-mir-4952	0	0
+dme-mir-4953	0	0
+dme-mir-4954	0	0
+dme-mir-4955	0	0
+dme-mir-4956	0	0
+dme-mir-4957	0	0
+dme-mir-4958	0	0
+dme-mir-4959	0	0
+dme-mir-4960	0	0
+dme-mir-4961	0	0
+dme-mir-4962	0	0
+dme-mir-4963	0	0
+dme-mir-4964	0	0
+dme-mir-4965	0	0
+dme-mir-4966	0	0
+dme-mir-4967	0	0
+dme-mir-4968	0	0
+dme-mir-4969	0	0
+dme-mir-4970	0	0
+dme-mir-4971	0	0
+dme-mir-4972	0	0
+dme-mir-4973	0	0
+dme-mir-4974	0	0
+dme-mir-4975	0	0
+dme-mir-4976	0	0
+dme-mir-4977	0	0
+dme-mir-4978	0	0
+dme-mir-4979	0	0
+dme-mir-4980	0	0
+dme-mir-4981	0	0
+dme-mir-4982	0	0
+dme-mir-4983	0	0
+dme-mir-4984	0	0
+dme-mir-4985	0	0
+dme-mir-4986	0	0
+dme-mir-4987	0	0
+dme-mir-5	0	0
+dme-mir-6-1	0	0
+dme-mir-6-2	0	0
+dme-mir-6-3	0	0
+dme-mir-7	0	0
+dme-mir-79	7	0
+dme-mir-8	1	4
+dme-mir-87	0	0
+dme-mir-927	0	0
+dme-mir-929	0	0
+dme-mir-92a	1	0
+dme-mir-92b	2	32
+dme-mir-932	0	0
+dme-mir-954	0	0
+dme-mir-955	0	0
+dme-mir-956	0	51
+dme-mir-957	0	0
+dme-mir-958	0	0
+dme-mir-959	0	1
+dme-mir-960	1	0
+dme-mir-961	0	0
+dme-mir-962	0	0
+dme-mir-963	0	0
+dme-mir-964	0	0
+dme-mir-965	0	1
+dme-mir-966	0	0
+dme-mir-967	0	0
+dme-mir-968	0	0
+dme-mir-969	0	0
+dme-mir-970	0	0
+dme-mir-971	0	0
+dme-mir-972	0	0
+dme-mir-973	0	0
+dme-mir-974	0	0
+dme-mir-975	0	0
+dme-mir-976	0	0
+dme-mir-977	0	0
+dme-mir-978	0	0
+dme-mir-979	0	0
+dme-mir-980	0	0
+dme-mir-981	0	0
+dme-mir-982	1	0
+dme-mir-983-1	0	0
+dme-mir-983-2	0	0
+dme-mir-984	0	0
+dme-mir-985	0	0
+dme-mir-986	0	0
+dme-mir-987	0	0
+dme-mir-988	0	0
+dme-mir-989	2	1
+dme-mir-990	0	0
+dme-mir-991	0	1
+dme-mir-992	0	0
+dme-mir-993	0	0
+dme-mir-994	2	0
+dme-mir-995	0	1
+dme-mir-996	1	0
+dme-mir-997	0	0
+dme-mir-998	0	0
+dme-mir-999	0	1
+dme-mir-9a	0	0
+dme-mir-9b	0	0
+dme-mir-9c	0	0
+dme-mir-iab-4	0	0
+dme-mir-iab-8	0	0
diff -r 000000000000 -r b996480cd604 test-data/dme-mir-v20
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dme-mir-v20	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,476 @@
+>dme-bantam
+ATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAA
+>dme-let-7
+TCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGA
+>dme-mir-1
+TTCAGCCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTTATATTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAG
+>dme-mir-2a-1
+GCTGGGCTCTCAAAGTGGTTGTGAAATGCATTTCCGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGC
+>dme-mir-2a-2
+ATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGAT
+>dme-mir-2b-1
+CTTCAACTGTCTTCAAAGTGGCAGTGACATGTTGTCAACAATATTCATATCACAGCCAGCTTTGAGGAGCGTTGCGG
+>dme-mir-2b-2
+TTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGA
+>dme-mir-2c
+TCGTATCTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCGA
+>dme-mir-3
+GATCCTGGGATGCATCTTGTGCAGTTATGTTTCAATCTCACATCACTGGGCAAAGTGTGTCTCAAGATC
+>dme-mir-4
+TTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTTTCCGGTCATAAAGCTAGACAACCATTGAAGTTCGTTGTGG
+>dme-mir-5
+GCTAAAAGGAACGATCGTTGTGATATGAGTTGTTTCCTAACATATCACAGTGATTTTCCTTTATAACGC
+>dme-mir-6-1
+TTTAATGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACCATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAA
+>dme-mir-6-2
+TAACCCAAGGGAACTTCTGCTGCTGATATATTATTGAAAAACTACTATATCACAGTGGCTGTTCTTTTTGGTTG
+>dme-mir-6-3
+CAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTTGAAACTCTCACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTG
+>dme-mir-7
+GAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTT
+>dme-mir-8
+AAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCTTTTTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT
+>dme-mir-9a
+GCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGC
+>dme-mir-9b
+TGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTTTATGTATATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCA
+>dme-mir-9c
+ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAAT
+>dme-mir-10
+CCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCTTTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGG
+>dme-mir-11
+GCACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACTTAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC
+>dme-mir-12
+TACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTG
+>dme-mir-13a
+TACGTAACTCCTCAAAGGGTTGTGAAATGTCGACTATTATCTACTCATATCACAGCCATTTTGATGAGTTTCGTG
+>dme-mir-13b-1
+CCATGTCGTTAAAATGTTTGTGAACTTATGTATTCACAATCATATCACAGCCATTTTGACGAGTTTGG
+>dme-mir-13b-2
+TATTAACGCGTCAAAATGACTGTGAGCTATGTGGATTTGACTTCATATCACAGCCATTTTGACGAGTTTG
+>dme-mir-14
+TGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATA
+>dme-mir-31a
+TCCGTTGGTAAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTTGAAGAGCGCTATGCTGCATCTAGTCAGTTGTTCAATGGA
+>dme-mir-31b
+CAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAGCACAGCGGATCGAACATTTTATCGTCCGAAAAAATGTGATTATTTTTGAAAAGCGGCTATGCCTCATCTAGTCAATTGCATTACTTTG
+>dme-mir-33
+CTCTTCCTCTGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTCCCAATTGCTTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCAC
+>dme-mir-34
+AATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAATTATTGCCGTTGACAATTCACAGCCACTATCTTCACTGCCGCCGCGACAAGC
+>dme-mir-79
+TGAAGCTGACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAGGTCA
+>dme-mir-87
+AACACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCCATTATGGCCAACGATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCA
+>dme-mir-92a
+AATATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAATAAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAATAAACA
+>dme-mir-92b
+TAAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCATTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAATGAGTGTCGCAGTCGAC
+>dme-mir-100
+CCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACTGGTTTTTGGCA
+>dme-mir-124
+TCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAAAT
+>dme-mir-125
+GACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTT
+>dme-mir-133
+ACCTGCAACACTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTTTTCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGACAAC
+>dme-mir-137
+CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAATCCAAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTT
+>dme-mir-184
+GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCACTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATC
+>dme-mir-190
+CGAACTAATTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGC
+>dme-mir-193
+TGTGTGCCCTTATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCATATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAA
+>dme-mir-210
+AAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAGCC
+>dme-mir-219
+TAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATATTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAAC
+>dme-mir-252
+ACCAAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGT
+>dme-mir-263a
+TAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTATACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAA
+>dme-mir-263b
+TTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTATTATTCTGTGGTTCTGCGGGTGCCAAAACTTAAAAACCGGCTT
+>dme-mir-274
+TCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGCCGCCAGGATTACTCGTTTTTGCGATCACAAATTATGAAATTGCAGCAA
+>dme-mir-275
+TGTAAAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTTTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCAGACATATAT
+>dme-mir-276a
+CCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACCAAG
+>dme-mir-276b
+AAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTATATTCAGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACC
+>dme-mir-277
+TTGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGAAGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTT
+>dme-mir-278
+GTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTGTCATTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGA
+>dme-mir-279
+GGAATTCATACTACTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTC
+>dme-mir-280
+TGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATATGCAAGTCGAGGTCCTCCACACTG
+>dme-mir-281-1
+CGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGAAACTATTTAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCG
+>dme-mir-281-2
+CGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTTAAGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCG
+>dme-mir-282
+AGTTTCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAAAGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACA
+>dme-mir-283
+CTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATATGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATT
+>dme-mir-284
+GTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGCAAGGCTTGAATAATGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGA
+>dme-mir-285
+TCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAGGAGAACCCACTCAATTTAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAAC
+>dme-mir-286
+TTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCAAAGAAAGGTTTCGATTAAGCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAAT
+>dme-mir-287
+GGACGCCGGGGATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACGACTGTGA
+>dme-mir-288
+CGGCCATGTCGTAATTAGCGGAGCACGGCATCGCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCG
+>dme-mir-289
+GAGTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGACTTCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGAC
+>dme-mir-303
+TCTTGGTTTAGGTTTCACAGGAAACTGGTTTAATAACGAAAACTAGTTTCCTCTAAAATCCTAATCAAGA
+>dme-mir-304
+GCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTTTAAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGC
+>dme-mir-305
+CATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTCTCGTAACCCGGCACATGTTGAAGTACACTCAATATG
+>dme-mir-306
+GTCCACTCGATGGCTCAGGTACTTAGTGACTCTCAATGCTTTTGACATTTTGGGGGTCACTCTGTGCCTGTGCTGCCAGTGGGAC
+>dme-mir-307a
+TGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTTCGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACA
+>dme-mir-307b
+TAGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCGAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAATGCTGCTAACTT
+>dme-mir-308
+CTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAATCCAAATCACAGGATTATACTGTGAG
+>dme-mir-309
+ATTATACGACAAACCTTGTTCGGTTTTGCCAATTTCCAAGCCAGCACTGGGTAAAGTTTGTCCTATAAT
+>dme-mir-310
+AACATAAACATTTGCAGGGCGGGTCGTGTGTCAGTGTATTTATATCTTAGCTATATTGCACACTTCCCGGCCTTTAAATGTCCAATGTT
+>dme-mir-311
+TCTAGATCATTTTTCGGACGGTATATGGGTTAATATTTCATTTGTCGAATATATTGCACATTCACCGGCCTGAAAATATCAAGA
+>dme-mir-312
+GATTTGGTTCGTCACAAGGGCAATTCTGCATTTTTTAACTAGTATTGCACTTGAGACGGCCTGATT
+>dme-mir-313
+ATTTTCTGCTGCGGATGGGGGCAGTACTGTTTTTTTAACATTGAGTATTGCACTTTTCACAGCCCGAAAAT
+>dme-mir-314
+TCGTAACTTGTGTGGCTTCGAACTTACCTAGTTGAGGAAAACTCCCATGTCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGG
+>dme-mir-315
+CACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTCATTGTTTACCAGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTG
+>dme-mir-316
+AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCAATTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTT
+>dme-mir-317
+ATGCAACTGCCATTGGGATACACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTGGCAT
+>dme-mir-318
+TTTATGGGATACACACAGTTCAGTTTTGTCACACTTCAAGCATCACTGGGCTTTGTTTATCTCATGAG
+>dme-mir-375
+CCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTGATCATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCGACT
+>dme-mir-927
+TGGTTGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTGGCATACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTACCGATCCATTA
+>dme-mir-929
+AGTCCTGGTGGAGCTCAAATTGACTCTAGTAGGGAGTCCTTTAATGAGCGACTCCCTAACGGAGTCAGATTGAGCTGCAAAGGAGCGA
+>dme-mir-932
+TTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTTTCATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTC
+>dme-mir-954
+TACAAACACAAGATTTTCTGGGTGTTGCGTTGTGTGTACCTGTGTACAGGCGTATTCACATGCAACATCCCTTACATCTTGCTTGAT
+>dme-mir-955
+GGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTGTTTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAA
+>dme-mir-956
+GATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCGGCTCACTGGCCCAAATGCAGTTTGCCCGGAGACGCCGGTTAACCCAGCACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTT
+>dme-mir-957
+TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAGTTCTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGTGAGGCGC
+>dme-mir-958
+GGCGTGTCTATGGCAAGTAGAATAGCAGGCTTATCACATGTTTAATTCAATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAACACCCGT
+>dme-mir-959
+TTAACTTTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCTTCAGGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAA
+>dme-mir-960
+GGGTTTTGTACCACATTCTGAGTATTCCAGATTGCATAGCTTTGTGCTACTATTGCTATACGGTCTGGGACACTTTTAACATGGTATCAAATC
+>dme-mir-961
+TCAAGGGCCGAGTTACCTTTGATCACCAGTAACTGAGATTGTTTCTGATACGGTTTCGTTTTCTGGCAATCAAAAGAACTTGGACTCGA
+>dme-mir-962
+GATGGGGCACTCAGGCTATAAGGTAGAGAAATTGATGCTGTCTACACTATTCAGACTTCAGTTTCATTACCTTTCAATTTGTTTGCCCCCAT
+>dme-mir-963
+TTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTCGATCGAAACATCTGTATATACCTTTGTTCCGATTGGACAAAA
+>dme-mir-964
+CAATAACATATTGGTCCAACTTGCCTTAGAATAGGGGAGCTTAACTTATGTTTTTGATGTTTAAGTTAAAAGCCTCTGTTCTAAGACAATTTGATGATCA
+>dme-mir-965
+GACAATATTGCTCAACATTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCTGTGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAA
+>dme-mir-966
+AACCTGATCCGCTGCTGTGGGTTGTGGGCTGTGTGGCTGTGGTATAGGTGCCGCCAGTTGATAACCCCCAGCGTGGGCACGGACCCA
+>dme-mir-967
+CTTGGAGAGCAGAGATACCTCTGGAGAAGCGCGTGACCTGACCCCAGCAGGAGAACCCAACCCGCTTTTCCACCTAGGTGTCTCTCTCTCTCTTTAT
+>dme-mir-968
+TGATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATGCAAATCAACCTTTTGATGTACTACTTTAAGAATCTCCAGTTA
+>dme-mir-969
+AGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGTTTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGATGGACT
+>dme-mir-970
+GAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGTAATGATTTGAATCTATCATAAGACACACGCGGCTATAACCGTTGTCTAAG
+>dme-mir-971
+TCCGTGGCTGGCATCGCTCGCTGTAAATTGTAATCATCAAAGCGTTTTCTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCCGTA
+>dme-mir-972
+AGAATGATAGGGAAATTGCTAAATATTTTTTTTGTATAAATAACTTTTAACTTTTGTACAATACGAATATTTAGGCATTTCTCAAATCAAA
+>dme-mir-973
+ACCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTTAAGTATTTAAATAAAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCACGCAAAGG
+>dme-mir-974
+CAATTGTCACCGGTCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTGTTTCCAAGAGCAAATATAACTTCATTGGAAGCTAAGTGGATTTGCCCAAAT
+>dme-mir-975
+TTGAATTTTTGATTTTAAACACTTCCTACATCCTGTATGTGTTTTGCATCCGGTACAGATGTGGGAGTCGTTTGCACTCAGAGATTTCACA
+>dme-mir-976
+CATCGCCATGCAGTGCCGCGGCATTGGTGAGGCCATCTCCAATGGATTAGTTCTCAACATTGGATTAGTTATCATCAATGCCGGTGCACTGCACCTA
+>dme-mir-977
+CGAATCAACAAACAAGGTATGCTTTAGATAACTCGAATATCACATCTTCAGTGTTCGAAATCTGATGAGATATTCACGTTGTCTAAATCATGTTTTGTA
+>dme-mir-978
+GTTGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGCAATCGAAAATCGTGTCCAGTGCCGTAAATTGCAGTTGTGTGAACGCAAA
+>dme-mir-979
+TACATGTGAGGATGTCACAAATACACTGAATTTGGGGGGAATTCTTATGTATATACAAATTCTTCCCGAACTCAGGCTAATTTTGTGGCATCCGT
+>dme-mir-980
+AGTTGATTGTATGTCAGTTTTTCATTTGGCCTGGCTAGCTTACTCCTTTTTAAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTC
+>dme-mir-981
+AAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAATTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGTGGAAAAT
+>dme-mir-982
+CGAAATCATGTTAGATCCTGGACAAATATGAAGTAAATTGTTTTTATGCATCAATTACTTGATATTCATCCTTGAACTAAATGGTTTTAGAGC
+>dme-mir-983-1
+TATATTGCAATAATTAAATAATACGTTTCGAACTAATGATTTTCAGTTCATTCATTAGGTAGTTACGCATTATCTAGTTGTTGTAAACATT
+>dme-mir-983-2
+TATTATATTGCAATAATTAAATAATACGTTTCGAACTAATGATTTTCAGTTCATTCATTAGGTAGTTACGCATTATCTAGTTGTTGTAAACATTCAACT
+>dme-mir-984
+AGAAACAAATTTCATTGAGGTAAATACGGTTGGAATTTTGTCTTTTAACTATAAATCCAACCGAATTTGGCTCGGCGAAATTTTTCAGTT
+>dme-mir-985
+TATATAATAGCACTGCTGGCTCATTGGTACATTTCATAAGTACCTTATCAAATGTTCCAATGGTCGGGCAGAGCTATTATTTGTCC
+>dme-mir-986
+CACACCTGAAATTACCCATCTCGAATAGCGTTGTGACTGAGGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCAAGTAAGGTTATTTTGGGCC
+>dme-mir-987
+TGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGTTGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAA
+>dme-mir-988
+GACGGCGGTACCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATTTGATCATCCCCTTGTTGCAAACCTCACGCCAAAGATGATCTGCGA
+>dme-mir-989
+AAAGATTTTGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACACAGGTGACACTGATCCGGATTTGGTAGTTGACAAATCCTCCATGCCGAGATTAGTTTCATTTTGCGTCTTTTGAATTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTACA
+>dme-mir-990
+TCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGCTTCGGTGCCATTTCACCCCGAGCAC
+>dme-mir-991
+TATCACTGCAGTTTCAGGCTTTTCCCAACTACACCTATTAATACATATTTTAACGTCCTATTAAAGTTGTAGTTTGGAAAGTTTTGGTTTTGCATT
+>dme-mir-992
+ATTTTCCCAAGTGCCTGGTATCAGCAAAGTGTTATTTTTTATGTTTATGTAAAGTACACGTTTCTGGTACTAAGTACTTCGAGAAAGTTACC
+>dme-mir-993
+AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTTAAATGGCGTTCGGCACATTGTCGGACTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAA
+>dme-mir-994
+TATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAGAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGT
+>dme-mir-995
+CACCTGCACCCCGCAGCCCGAATTATGTGGGAGCTGCGCCGTTTCCGTAATCCGTAGCACCACATGATTCGGCTTCGTGGTACAGGATAT
+>dme-mir-996
+TCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGTGGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAG
+>dme-mir-997
+TTATGGATCCTCTTTCAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAAGAGCGACAGTCCTGGAGAAGTTATCAGAGCCAAAAAAATTCATATGATGATGCATTTTCCGTCTCTGAAAACGTCTTCAGCAGAAGTTGTTTTTAGCGAAGTGAAACTCATTCGATTTTGATCATACTAACGACATTGGATGCTTGGATCGGCA
+>dme-mir-998
+CCTCGTGTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTGACCGCTCCAGGGCAAATTGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCAT
+>dme-mir-999
+AAGGATGCCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCCCAGCCAC
+>dme-mir-1000
+GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATTATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCA
+>dme-mir-1001
+AAGCTGGCCTGTCCCTGGGTAAACTCCCAAGGATCAGGTGGAGATTGAATCCCGATCCTTGGGTTTCTGCTCTCGGGCAAGGTCAGTAGT
+>dme-mir-1002
+TAGAAATTATATATTTAAGTAGTGGATACAAAGGGCGATTTGATATAAAAGTGTCGCATTGTATGACCTACTTAACTAGCTGATTTTGT
+>dme-mir-1003
+GTGGGTATCTGGATGTGGTTGGCTCTGGCGGTCCTCTCACATTTACATATTCACAG
+>dme-mir-1004
+GTTGGGGGACATTGATCTCGGAGACGGCGGTTTAACTGATCCATTCTCTCACATCACTTCCCTCACAG
+>dme-mir-1005
+GTGAGTTGATCGATTTCGAGGTTTTGGCACACGAATATAATCTGGAATCTTTAATTCGCAG
+>dme-mir-1006
+GTGAGTTTGAAATTGAAATGCGTAAATTGTTTGGTACAATTTAAATTCGATTTCTTATTCATAG
+>dme-mir-1007
+GTAAGCAGTGTTTGAACTCGATCTTGGTTCTTGGACTCTTGATAAGCTCAATTAACTGTTTGCAG
+>dme-mir-1008
+GTAAATATCTAAAGTTGAACTTGGCCAATGGCAAGTCACAGCTTTTTGTGTTTACAG
+>dme-mir-1009
+GTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATTGTTACATTTCAG
+>dme-mir-1010
+GTAAGTGGTGTAGATGAAACAAATTTACCAACAATTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAG
+>dme-mir-1011
+GTGAGTTTTTGAGCCAGGAATATAGTTCTTATTATTGGTTCAAATCGCTCGCAG
+>dme-mir-1012
+GTGGGTAGAACTTTGATTAATATTGCTTGAAAAATATTAGTCAAAGATTTTCCCCATAG
+>dme-mir-1013
+GTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAAAAGTATGCCGAACTCGCAG
+>dme-mir-1014
+GTATAATGGAAATAGATTTTAATCGCAGGCGCGTCAGTGGTTGAATTAAAATTCATTTTCATTTGCAG
+>dme-mir-1015
+GTGAGTGATGCTCCAGTTAGCTTGGCTGAGTGAGGATTTAAGTCCTGGGACATCTCTCTTGCAG
+>dme-mir-1016
+GTAAGTATAGAGAGGATGTGATTGGTAAATTCCAAAGTTCACCTCTCTCCATACTTAG
+>dme-mir-1017
+GTGAGTTTAGTGGAGTTTAAAGCTTCCCATCGCCAGCAATTACGCGAAAGCTCTACCCAAACTCATCCCCC
+>dme-mir-2279
+CGGGAGAGGATTATGAAAGACAATTTGAAATTAAATATCTGTGTGTGAAATTATTTAAAAGATTAATTTCACGCGAAGATATTTATTTTTACATTTGTCCCTATAATAACCGG
+>dme-mir-2280
+TCGTTTAAGATGCTGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAATATTATTCACAGAAACTAGTAATTTACTTCCAAGCTAACTGAAGGGGATATTCAGTGCAACCACGGA
+>dme-mir-2281
+GGATGTCGAGCAGTACACGTATTATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCAGTATTGCAGTATCGCTGCTTTATTCATATCC
+>dme-mir-2282
+GCCTGCATAACGCTGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCCTTGTGCTTCGTTGGAAAATCGGTGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAAGGG
+>dme-mir-2283
+AGCTGCTCCGAAAATATCATGAATACGACAATTATGTGCACATCATTTAGTATACGTGATATTTTAGGAGCAGCTA
+>dme-mir-2489
+GCAATAAGTTAGACGTGAGTATGGCTATACAAATCATCTGGAACGTAAGTTCTAATGTATGTATTGTATGTTGTATTTGCAGTTTTATGATAGCA
+>dme-mir-2490
+GAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGCTTTGCTCTTACTTTATCGCTTAAACTCGCAA
+>dme-mir-2491
+CGCGAACCACTTTGTGCCGCTGTTGCCTTTGCAGTTGCTGTTTTCCATGTTGCTACTGCGGCCAATTGTTGCGCATCAGCAACATCAACAACATCAACAACAGCAGCAGCAACTGCAGTAGCAGCACTCGTGATTCACTTTCGA
+>dme-mir-2492
+GAATTTTTTTGGGATCTCTTTATAAAGCGTTTATTATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAAATTCA
+>dme-mir-2493
+CGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCATGTGCATGGAGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGC
+>dme-mir-2494
+TCCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATTGGGAATAACCTTCAAAAGCTGCAACTTAAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGA
+>dme-mir-2495
+TGTATGATCACATTGGCTTGTGGGCGTGGCACTTCAATTGGGCTGACTTTGCCTGGCTGGAAAAGCGGCACCTAATTGAAATGCCCGCCGATCAGTGCTCGATTACGATCGACAC
+>dme-mir-2496
+GTGCGCCGGTGTGCGTGTGTGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGCGGGGCACTCACACACGCATATTCAGCCGCAC
+>dme-mir-2497
+GCACGTCATCGTAAGCATTGCAAAATGTAGTTGTTAAATTCGCTCTTCAATCATTAACAACATTTACAATGTTTGCAGGCTGTCAACGTTGATGGC
+>dme-mir-2498
+CACATTTGCCATAATCTCCTTAAAATAGTAAAGGCTGTTATGCTTATTTTTGTGTTTTTTACAAAACTGGCATTCCCGTCTTACTTATTTTCAGAAAACTTACACCAAAGTG
+>dme-mir-2499
+TCCTTGCTGTGGGTGTGGTTGCGTGCGTAGACGTCAGCGCAATGCCTTTGTTTGGCGGCATGCGGATGACATTCACGTCCGTATCCGCACACACAT
+>dme-mir-2500
+GTAAGGAACACACATATACAATACCGTTTGAATTTCAAATAATCAGGATTTTGTGTGTGGACCTCAGA
+>dme-mir-2501
+GTAAGTTTGGAGTGCCTGGGCTAAGAACTTCCATTCTGAAACTTAACTCTTGCAATCAAACTTTCTTTCAG
+>dme-mir-2535b
+GTAAGTGACTATGCCGGGATTGTGGTTATTGAACTTAGCGTCTCCACTCACGGCATTTCATTCACTTGCAG
+>dme-mir-3641
+GTGAGTGTCCTGTTTACAGCTGGTATATTTTTCGAAAAGCCCTCTAAACTGGTCACTTCCACTCTACAG
+>dme-mir-3642
+GTGAGTGGGTCGCACGGAGCGTCATTTGGAATTCCCATGGCTGACGAAACGTTCACTCTGCTCTTCTCGATTACAG
+>dme-mir-3643
+GTGAGTTTATCTAAATATGCCCATTTATCAATAGTCATACTTATTTATGCTCCTTTAACTCCTTGCAG
+>dme-mir-3644
+GTGAGTGATTATGGTTTAAGTAATACGAATTACATAAACTATATTTAACCACTATTCTTAG
+>dme-mir-3645
+GTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTACTGTTTACGATCGCACTGGAAGTGCGCTTTCCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCTTCATTGTTTTCCTTTCTTTCCCCTCTCTCTCTCCCCGCAG
+>dme-mir-4908
+GTAGGATTTTAAGCATTAAGCATGTATATAGTTTTTGCTGTGCTCATAAAGTTCTATAG
+>dme-mir-4909
+GTAGGTTGAAATCGGATACAACTAAAAGTTATTTTTAATTGTATCCGGTCTTCATTTTAG
+>dme-mir-4910
+GTTTGTATGGAATTCCATGAGCTTCAAAGTAATGCTTCTAACTCTGTGGTTTTTCATATTTCCCAG
+>dme-mir-4911
+GTGAGGAGGAGCAAAGTGGCGCCACAATTTACTAGAAACTAATTGCATCTTTTTGTCCCCCCGCGTAG
+>dme-mir-4912
+GTGAGTAGTCGTATGTTTATTAAGATTTACTTTCTATAAATTAATGTCCACTACTTTTAG
+>dme-mir-4913
+GTGAGTTCGATTGGAAAATTTAAATTTAATGTTTAATTAACCAATTCGAATTGCTTAG
+>dme-mir-4914
+GTGAGTGAGAGCGAGTTCCAATGTGGTCCTCGAAACCAGTTGTGCTTCGATCAGATTCCAAAATTGACACATTCCGACCTTGAATCACCCACAG
+>dme-mir-4915
+GTGAGAAAAAGTAGTAAATTAAGCATATCACGCAAGGACAAACATTAAGTTAAGGCCTAGTTCCTATTATACTAGGAATACTCAATCCTACTTATGCCTCTTATTCTTCTTTTCTCAG
+>dme-mir-4916
+GTGGGTGTTCTTGGAAATTCGCCTCGATCGGTAGCTAAATTTCTGATTACTCCTAAAAG
+>dme-mir-4917
+GTGAGTAGCGATGGGGGTCAGATGGCCGTGGAAGATATGTGACGATTGCCCCCTTACTACTATCGTCTGCTCAACAG
+>dme-mir-4918
+GTGAGCACGATGGCCACATTTATTGGGCAACCAATGAATTCCCGCCTGCCCACAG
+>dme-mir-4919
+GTGAGTCTCTAGGGGATTAGCAAGCTATAATTTCTCACTTAATCCCTGAACGACTTGCAG
+>dme-mir-4939
+GCATCATGCTTCTGCGATCTCTACCAATTTTCCTTGCACTCTTTGTCCTTTCCAAAAGTGACACGGGTGCAGGTGAAGATTCGGAAGAGGACGACGAAAACGACTGCAA
+>dme-mir-4940
+TTATCGCAACTTATCGATCGGGTGGCGGATATAGATCATTGGTTATCCCTTAATTAAAGCAAACAAGATTTGTTTCGGCCGCCCGATTTTACATACAACGACACG
+>dme-mir-4941
+ATGACCGGCGAGGAGATGCGATTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACA
+>dme-mir-4942
+TATGAATACATATATTTTTATGTTTGAGTCAACATCGAGTTGCCGATGTTTGGAAAACATCGATGACATCGCTGTTGGCATCGAAATATGTCCATATCTAATATATAGTT
+>dme-mir-4943
+TTCGGATCGTTTGAATGACCAATTTTGTCTTTTATTTTCTCTGTGTTTTCAGTTAATGAAAGATAGTGAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACCCAAG
+>dme-mir-4944
+AAAAGTAACTTTCGTAATCGAAAAAGTTTCGCTTTTTTTTCTGCTTCTGCCGCTGAGCAAGTTTTAAATATTACCGCTTAGTTACAGCTGCAGGAAGAAAAGTTATAATTATGGACTACGTACATAAAT
+>dme-mir-4945
+GTGATGGTGCTGGTGGTGGTGCCTTCATTGTTTTTCTCTTCTTTTTGTTGTTTGACTTTTACACTTTTGAACAACAAGCCGAAAGGAAAAAGCATGAAGGAATGCAAAGTATTCG
+>dme-mir-4946
+GCTCGATTGCTGCAACTAAGAAACAAATATTTTCAGTTGTTCATTGCAAATTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCTAGGCTTATCAGCTGCA
+>dme-mir-4947
+AAAGCGACCCACCCATTCCCCTTCCGCCCATATTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGTGGGCGGAGCACGGAATTCGGGGGCGTGGCG
+>dme-mir-4948
+GTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTC
+>dme-mir-4949
+ATAATGCGCCGCCATCTTGCGGCACACTCGCACACACACACGTGTGCCATTCTGGTTTTGCAGTGGTGTGCGTGTGTGCCTCGAGTCGTTGCGTCACTG
+>dme-mir-4950
+TAATGCACATAATAAATGCCAACCATTCATCATGAAATTATAAATAGTATCATTTCAAGATGCATGGTAAGGCTTTATTTTGTTTTGCAATC
+>dme-mir-4951
+TTTTCGTACGTACAAAAAAGCATCAGGTTTTCGGGTGAGGTTTCTGATGCTTTGTCTCTTAAGTTTTTCCTAACAATTAAACCCTATGTCGGTATTACGAATACCATCAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA
+>dme-mir-4952
+TCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGT
+>dme-mir-4953
+TAAAGTTCACAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGTTTTATTTTTTATTGAAGGTCATGGACATCCTTGAACCGATT
+>dme-mir-4954
+TTGGCGCTTGGAATCGATACCCGAGCCATGATAGATTGAAGTCAACCCAATCGATCGCGGTTCGAGTGCTCGAGTCTTGTGCGCCGGCATG
+>dme-mir-4955
+CACCGATTTGCTTCCCCTTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATCTCTGTCTCTGTCTAACGCTTAATTGTTGCTCAATTGCGAATTAATGTCTGGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCT
+>dme-mir-4956
+AGGGGGCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATGAACGATCCTCGGGC
+>dme-mir-4957
+TCGTTGTATTTTACGCACTCTGCTGGCAGCGCTGTCGGCGTCGCTGCCAGCTGCCAGCAGCGAGCGGTACACTTGCAACTATCC
+>dme-mir-4958
+TCTCTGGCAGCTGCAGTTCCGTTTCCGGAGCGGGATCTGGAACGGGCTCTGGTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTACCGCTCCAGGTCCCGTTCCCGGAAACGGTGCCACCGCCAATGCA
+>dme-mir-4959
+TGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCG
+>dme-mir-4960
+ACACAAGGCCTGCCGCCCAAGAAACGCAAGCCCAGAAGTCCGGCAGTCGAGAATCACGAGGGACTGGGACCTTGGGCTTACGGTTCTCAGTTTGGCTTGAC
+>dme-mir-4961
+CGATATCCAATAGTAGCCAACTCTCTCGCTCTCTATGTGTATGTATGTATCTTGCTATCCATATATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGATATAACCCGAAACCACACTGGCCA
+>dme-mir-4962
+TCCTTTCTTTTCTCTCCGTCTCTCTCTTTCCCTCTCTCTGTTTACATTGAGCTGTTTTGTCCGTGCACGTGCTAGACGATGTAGAGAGTGAGGGAGAGAGCGAATAGAATAACAGCTCATTGTG
+>dme-mir-4963
+CTGTAGGAAATTTTTTGGGGTACTTCTGGTTTCATAACGCAGAGAATCATCAGCGTGAAGGAATGATTCTCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTA
+>dme-mir-4964
+ATTTTTGAATGGTCCTTTTCATGCCCAAGGCGAATAAATATGTATTTATGTATATTTTTTTATATGGTACGTATTTATTTGTCTGCAAATGGCTGCCAAGGAGTGCTACATA
+>dme-mir-4965
+CACAAGGTGATCGATGGGAGATGAGCGCCTGATGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCAGGTTTCATCC
+>dme-mir-4966
+GCTGTGTGACAACAAACTTGTCGGCACTGGAGTACTAAATATATTGCACATGTTCATGCATGTTCAACATATTTAGCACTCAAGTACCGAAAAATGAACAACGAAACGAAAAATAACACGAACATCA
+>dme-mir-4967
+CTATAGCGTTGTCTCTTGCGCAAATTGCATTTTCTCTCTGTTAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAATGTGTGAGTCAGCAAACCGCATCCG
+>dme-mir-4968
+TTTTCCTCAGAGCCGCGACTGCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAACAGCAGCAGCAGCAGAAGCAACAGCAACTAACTGCAGAGGAGCAATAGCAGCTGAGAGTTC
+>dme-mir-4969
+GTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCTGCCATTGTTTGGTTGATAAGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGATGCGACATCATCAT
+>dme-mir-4970
+CCAAAGGTGGGCGACAAGGGCTGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGCTGCTCTTCCGTGGGTTGCTCTTGCTCCTGACCCTCCTCTTCCTCCGCTT
+>dme-mir-4971
+TCGGCCCTCGACACGGTGGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATC
+>dme-mir-4972
+AATCAAAAGCGCCGTAGGCCTCCACCTCGGCTTTACAGATATATATATATATATCGTGTATATATCTGTGCGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTT
+>dme-mir-4973
+CTCGTTCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAGCTCCGTTTGGACTGCTCCTCCTCCAACTACTACTGCGGCCGCTGCTGCTGCTGCTGCGGCTGCTGCATCCGCCTGCAACCTGCAACACTCACACCACGGCAACAG
+>dme-mir-4974
+TTCTTTGTTTTTATTCCCTGTCAGAGAGTATATTGATTTTAGGTGGACATTTGCGACCATATAAAATATATATATTCCTGATAAAGAATATTTAATATATCT
+>dme-mir-4975
+GGGCAAATAAAGCACGTTGCTCCCTGTTTACTTGGGTTTTCTGTTCATTTCGCCTATCGAACGTTGAACTTAAAAAGCCACGATCAGTTGTTTAACATACAGATATCTCTG
+>dme-mir-4976
+GTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCT
+>dme-mir-4977
+TAACCCTCCGCTCGAGAACGTGGTTTCTTTTGCGACGTGCAATACTCTGTGGCAGAAGTCTTGCACCGTTCCAAAAGAGAGCAGCACGTGGAGCGACGAGAACGG
+>dme-mir-4978
+GGACTTTCCACTTTTCGTTTGGCTGGCCTGGAAAAGCTCTCTTTCTCTATTGCCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAAAGCCTGGCAAGCACACA
+>dme-mir-4979
+CATAGGTGTTATATCTAGGCCAAATATATATACTTGTTCTATGTATTAGTTATTTGCAAAGGAATACATGTGCCTGTATATATATTCGGTAAAATCACATCTTTGAATT
+>dme-mir-4980
+GAAGAGGCTGAGAGCGGGAAAGTGAGAAGTAGAGAGCGCAGATAGGGAGTGGGAGCTTATACCGTTATAAAGCCAACTTCCGTTCTGCGTTTCGTTCCAACCCCCCACCTCTCTTTCCCTCT
+>dme-mir-4981
+TGGCCACGTGCCCGCAAGACGCCTTCGGCCGGCGCAAAGTTTCAATTTGATATTCCTTGGCCGGTCGAGCAGCGTCTTGGGGTTGTTCGTGGATT
+>dme-mir-4982
+CCAACTTTGCTGGCATTCGGTGGCCAATAATGCAATTGCATGTCCTTGTTGCTGTTGCAATGTTGCAGCTGGAATTGCAATTGCATTTCTAGTTGCCGCTGCTGCTGCTCGAGTGGCAA
+>dme-mir-4983
+GGCTGGCTGTCTTGACCCACTTGCTCGTTTGCATTTCTGAAAAATGTATACGCAAAAACCAAAATCAGAAATTCTTTTGAGCAAGTGTGTCATGAAATTGCCATTCGT
+>dme-mir-4984
+CTTCGCTCGAGGTGTGAAAACCTTTTGGCCAGCGAATACGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTCGCCATGTTTTGCG
+>dme-mir-4985
+TTGGGGGCGCTGCACTGGCATTGAAAAGTGAATTACATTGATCGTGACATGGGAATGGAAAATGTCGCCGAGCCATGTAAATCGTTTGGCCTACCCGTCTA
+>dme-mir-4986
+TTCTGCCGCTTTTGCTGTGGCTTCTCTGCATGGGATTCCCCATTCTGCATGGCGCCGATCTCTGCCAGCCCATCGGATGGCGGAACTTCCAGTGCAGCGAGGTCGCTTCTCTGCAGGATCTG
+>dme-mir-4987
+GCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGA
+>dme-mir-iab-4
+TCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGA
+>dme-mir-iab-8
+TCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGA
diff -r 000000000000 -r b996480cd604 test-data/matchedSample_1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matchedSample_1	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,300 @@
+58	+	dme-mir-305	45	CGGCACATGTTGAATTACACTCA
+109	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+156	+	dme-mir-14	40	TCAGTCTTTTTTTCTCTCCTA
+158	+	dme-mir-184	61	GGACGGAGAACTGATAAGGGCA
+170	+	dme-mir-79	58	ATAAAGCTAGATTACCAAAGCAT
+199	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+217	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+228	+	dme-mir-184	61	GGACGGAGAACTGATAATGGC
+276	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+295	+	dme-mir-982	15	TCCTGGACAAATATGAATTAAATT
+294	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+315	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+341	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+340	+	dme-mir-31a	13	TGGCAAGATGTCGGCATATCT
+359	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+392	+	dme-mir-184	60	TGGACGGAGAACTGATAAGG
+398	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+408	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+417	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+425	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+451	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+464	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+460	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+481	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+500	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCTT
+516	+	dme-mir-279	66	TGACTAGATCCACACTCATTA
+521	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+522	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+537	+	dme-mir-275	58	TCAGGTACCTGAAGTAGCGCGCG
+567	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGTC
+570	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+573	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+544	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+557	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+603	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+601	+	dme-mir-79	59	TAAAGCTAGATTACCAAAGCAT
+591	+	dme-mir-996	60	TGACTAGATTTCATGCTCTTC
+612	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+620	+	dme-mir-276a	53	TAGGAACTTCATACCGTTCTCT
+628	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+656	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+653	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAGT
+663	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+666	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+647	+	dme-mir-184	60	TGGACGGAGAACTGATAAGG
+668	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACG
+681	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+683	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+684	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+688	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+689	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGA
+702	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+706	+	dme-mir-184	60	TGGACGGAGAACTTATAAGGGC
+715	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+719	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+730	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+738	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+752	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+753	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+765	+	dme-mir-14	3	GGGAGCGAGACGGGGACTCAC
+766	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+773	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+797	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+795	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGTC
+803	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+804	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+816	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGTC
+808	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+821	+	dme-mir-12	6	TGAGTATTACATCAGGTACT
+837	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+842	+	dme-mir-92a	16	AGGACGGGAAGGTGTCAACGT
+859	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+863	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+864	+	dme-mir-279	66	TGACTAGATCCACACTCATTAAA
+862	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+873	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+885	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+883	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+893	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+902	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+903	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+906	+	dme-mir-279	66	TGACTAGATCCACACTCATTAA
+922	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+940	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+944	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+951	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+957	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+953	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCTA
+964	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+968	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+974	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+979	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+983	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+990	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGTC
+1030	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1058	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1037	+	dme-mir-1	55	TGGAATGTAAAGAAGGATGGAG
+1061	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1065	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1076	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1075	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1077	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1082	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+1098	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1101	+	dme-mir-279	66	TGACTAGATCCACACTCATTAA
+1091	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGTC
+1110	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAGT
+1123	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+1150	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCC
+1153	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCT
+1164	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1171	+	dme-mir-279	66	TGACTAGATCCACACTCATTAA
+1187	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1185	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1190	+	dme-mir-92b	60	ATTGCACTAGTCCCGGCCTG
+1197	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1206	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+1194	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1219	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1213	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1221	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1233	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGA
+1239	+	dme-mir-184	60	TGGACGGAGAACTGATAAGG
+1252	+	dme-mir-279	66	TGACTAGATCCACACTCATTA
+1259	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1262	+	dme-mir-316	53	ACAGGAAAGGGAAAAAGGCGTA
+1265	+	dme-mir-275	58	TCAGGTACCTGAAGTAGCGCGCG
+1273	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1275	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1296	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1298	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1302	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGA
+1305	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1306	+	dme-mir-14	3	GGGAGCGAGACGGGGACTCACT
+1317	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1321	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1324	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1337	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1340	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1352	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1357	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+1356	+	dme-mir-184	60	TAGACGGAGAACTGATAAGGGC
+1360	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1366	+	dme-mir-184	60	TGGACGGAGAACGGATAAGGGC
+1374	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGA
+1383	+	dme-mir-184	60	TGGACGGAGAACTTATAAGG
+1381	+	dme-mir-14	3	GGGAGCGAGACGGGGACTCACT
+1389	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1401	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1417	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCT
+1420	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1426	+	dme-mir-275	58	TCAGGTACCTGAAGTAGCGCGCG
+1427	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1444	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+1438	+	dme-mir-14	3	GGGAGCGAGACGGGGACTCACT
+1449	+	dme-mir-318	42	TCACTGGGCTTTGTTTATCTC
+1455	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1454	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1473	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1505	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGG
+1510	+	dme-mir-994	11	CTAAGGAAATAGTAGCCGTGA
+1512	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1517	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGTC
+1526	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1522	+	dme-bantam	51	TGAGATCATTTTGAAAGCTGATT
+1530	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+1524	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+1533	+	dme-mir-79	59	TAAAGCTAGATTACCAAAGCAT
+1538	+	dme-mir-989	138	TGTGATGTGACGTAGTGGAA
+1550	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1554	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1555	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+1558	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1563	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1564	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+1570	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1587	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1591	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAGA
+1601	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1609	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1610	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+1625	+	dme-mir-79	59	TAAAGCTAGATTACCAAAGCAT
+1630	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1657	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1655	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1664	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1670	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1689	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1705	+	dme-mir-275	58	TCAGGTACCTGAAGTAGCGCGCG
+1704	+	dme-mir-276b	23	AGCGAGGTATAGAGTTCCTACG
+1721	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1715	+	dme-mir-276a	53	TAGGAACTTCATACCGTTCTCTT
+1733	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1732	+	dme-mir-279	66	TGACTAGATCCACACTCATTAA
+1729	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGA
+1750	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGA
+1747	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGG
+1757	+	dme-mir-994	12	TAAGGAAATAGTAGTCGTGATT
+1760	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1762	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1770	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGG
+1780	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1800	+	dme-mir-12	6	TGAGTATTACATCAGGTACTGGT
+1795	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1799	+	dme-mir-960	56	CATACGGTCTGGGACACTTTTA
+1807	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGTC
+1821	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1823	+	dme-mir-2a-1	48	TATCACAGCCAGCTTTTATGAGCT
+1866	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1879	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+1914	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1928	+	dme-mir-279	66	TGACTAGATTCACACTCATTA
+1938	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1946	+	dme-mir-8	52	TAATACTGTCAGGTAAAGATGTC
+1955	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+1961	+	dme-mir-184	60	TGGACGGAGAACTGATAATGGC
+1965	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+1971	+	dme-mir-275	58	TCAGGTACCTGAAGTAGCGCGCGA
+1974	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+1978	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1988	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2011	+	dme-mir-14	3	GGGAGCGAGACGGGGACTCACT
+2023	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2021	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2033	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+2040	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2045	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2048	+	dme-mir-989	138	TGTGATGTGACGTAGTGGAA
+2061	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2053	+	dme-mir-14	3	GGGAGCGAGACGGGGACTCAC
+2062	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2070	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2072	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2098	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2104	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2123	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+2131	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2177	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2173	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2172	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2179	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2186	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2190	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2191	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2198	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2194	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2223	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2227	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+2254	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2259	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2278	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCT
+2274	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2297	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2301	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2307	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2299	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2337	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2359	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2382	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2391	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2399	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2400	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2413	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2437	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2445	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2448	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2461	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+2463	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+2473	+	dme-mir-275	58	TCAGGTACCTTAAGTAGCGCG
+2483	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGGG
+2491	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2520	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2550	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAG
+2556	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2568	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTG
+2591	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2602	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2598	+	dme-mir-79	59	TAAAGCTAGATTACCAAAGCAT
+2601	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGA
+2614	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2613	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2625	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+2652	+	dme-mir-312	42	TATTGCACTTGAGACGGCCTTA
+2662	+	dme-mir-1	55	TGGAATGTAAAGAAGTATGGAGT
+2671	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2675	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2672	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2693	+	dme-mir-31b	13	TGGCAAGATGTCGGAATAGCT
+2705	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+2711	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2716	+	dme-mir-79	59	TAAAGCTAGATTACCAAAGCAT
+2725	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+2735	+	dme-mir-79	59	TAAAGCTAGATTACCAAAGCAT
+2739	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+2749	+	dme-mir-275	58	TCAGGTACCTGAAGTAGCGCGCG
+2748	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+2756	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2771	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+2790	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+2811	+	dme-mir-11	47	CATCACAGTCTGAGTTCTTGCT
diff -r 000000000000 -r b996480cd604 test-data/matchedSample_2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matchedSample_2	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,300 @@
+22	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+16	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+14	+	dme-mir-281-1	13	AAAGAGAGCTGTCCGTCGACA
+26	+	dme-mir-281-2	15	AGAGAGCTATCCGTCGACAGT
+28	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+32	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+34	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+41	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+42	+	dme-mir-14	3	GGGAGCGAGACGGGGACTC
+43	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+61	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+65	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+67	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+69	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGTC
+79	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+84	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+89	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+96	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+103	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+108	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+110	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+112	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+117	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+120	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+123	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+124	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+125	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+129	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTG
+140	+	dme-mir-100	11	AACCCGTAAATCCGAACTTG
+141	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+143	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+147	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+157	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+159	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+164	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+166	+	dme-mir-8	52	TAATACTGTCAGGTAAAGATGTC
+181	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+17	+	dme-mir-92b	59	AATTGCACTAGACCCGGCCTGC
+190	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTG
+189	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+194	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+197	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+203	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+205	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+215	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+206	+	dme-mir-956	117	TTCGAGACCACTCTAATCCAT
+230	+	dme-mir-956	117	TTCGAGACCACTCTAATCCAT
+218	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+236	+	dme-mir-14	40	TCAGTCTTTTTCTCTCTCCT
+245	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+248	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+247	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCT
+253	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGT
+251	+	dme-mir-281-2	59	TGTCATGGAATTGCTCTCTTTG
+264	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+270	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCC
+275	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+274	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+280	+	dme-mir-10	48	CAAATTCGGTTCTAGAGAGGTT
+278	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGTC
+287	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+291	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+306	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+310	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+315	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+322	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+323	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+324	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+331	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+342	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+346	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+350	+	dme-mir-995	54	TAGCACCACATGATTCGGCTT
+347	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+352	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+358	+	dme-mir-305	45	CGGCACATGTTGAAGTACACTCA
+363	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTG
+369	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+392	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+395	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+400	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+401	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+406	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+414	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGTC
+419	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+425	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+435	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+432	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+437	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+439	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+442	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+453	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+450	+	dme-mir-989	138	TGTGATGTGACGTAGTGGAACA
+451	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+463	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+466	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+467	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+470	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCT
+483	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+484	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+485	+	dme-mir-11	47	CATCACAGTCTGAGTTCTTGCT
+487	+	dme-bantam	51	TGAGATCATTTTGAAAGCTGATT
+494	+	dme-mir-125	28	TCCCTGAGACCCTAACTTGTG
+502	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+507	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+510	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+518	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+520	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+526	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+528	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+529	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAG
+540	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+542	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+547	+	dme-mir-14	40	TCAGTCTTTTTCTCTCTCCT
+544	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+552	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+553	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+563	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+566	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+568	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+564	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACA
+569	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+575	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+584	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+586	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+589	+	dme-mir-14	40	TCAGTCTTTTTCTCTCTCCT
+592	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+598	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+3	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+6	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+608	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+614	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+618	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+641	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+642	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+646	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+648	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGT
+651	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+650	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+658	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+673	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACA
+683	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+696	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+694	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+692	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAG
+697	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTTT
+713	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+718	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGT
+709	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+700	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGTC
+744	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+737	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+720	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+750	+	dme-mir-8	52	TAATACTGTCAGGTAAAGATGTC
+756	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGT
+751	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+761	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+760	+	dme-mir-956	116	TTTCGAGACCACACTAATCCATT
+769	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+763	+	dme-mir-8	52	TAATACTGTCAGGTAAAGATGTC
+771	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGC
+770	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+783	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+792	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+805	+	dme-mir-184	60	TGGACGGAGAACTGATAAGG
+806	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+810	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+818	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+815	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+823	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGG
+822	+	dme-mir-281-1	13	AAAGAGAGCTGTCCGTCGACA
+836	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+842	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+848	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+843	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+865	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+863	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+864	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGTT
+876	+	dme-mir-277	58	TAAATGCACTATCTGGTACGAC
+866	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+881	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+880	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+889	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+901	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+899	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGCA
+904	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+912	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+910	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+917	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+914	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+924	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+927	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+919	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+922	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+931	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGT
+930	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+944	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+946	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+950	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+948	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+963	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+960	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+965	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+968	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+964	+	dme-mir-184	60	TGGACAGAGAACTGATAAGGG
+969	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+978	+	dme-mir-965	65	TAAGCGTATAGCTTTTCCCCTT
+971	+	dme-mir-959	60	TTGTCATCGGGGGTATTATGAA
+985	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+983	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+993	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+995	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+1002	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1013	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1011	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1004	+	dme-mir-281-1	13	AAAGAGAGCTGTCCGTCGACA
+1022	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1033	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1035	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+1046	+	dme-mir-276a	53	TAGGAACTTCATACCGTGCTCT
+1061	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1057	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1070	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1067	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+1066	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1073	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+1071	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1072	+	dme-mir-11	8	CAAGAACTTTCTCTGTGACCCG
+1065	+	dme-mir-2b-2	53	TATCACAGCCAGCTTTGAGGAG
+1081	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+1103	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1108	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1106	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+1115	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+1128	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+1127	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+1135	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+1138	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1139	+	dme-mir-14	40	TCAGTCTTTTTCTCTCTCCT
+1151	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+1158	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1170	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1177	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+1175	+	dme-mir-956	117	TTCGAGACCACTCTAATCCAT
+1197	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGT
+1186	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1199	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1201	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGTC
+1216	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+1221	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1230	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1234	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+1233	+	dme-mir-14	40	TCAGTCTTTTTCTCTCTCCT
+1243	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1235	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+1240	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTG
+1246	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1248	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+1241	+	dme-mir-8	52	TAATACTGTCAGGTAAAGATGTC
+1254	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+1255	+	dme-mir-956	117	TTCGAGACCACTCTAATCCATT
+1266	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1262	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAG
+1272	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+1281	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1277	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTG
+1288	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1291	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+1297	+	dme-mir-305	45	CGGCACATGTTGAAGTACACT
+1302	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+1300	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+1304	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1314	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1326	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGG
+1334	+	dme-mir-92b	59	AATTGCACTAGTCCCGGCCTGC
+1343	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1342	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCAT
+1349	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1337	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+1352	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+1361	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTG
+1364	+	dme-mir-999	61	TGTTAACTGTAAGACTGTGTCT
+1365	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCT
+1357	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAG
+1370	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1379	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+1389	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1388	+	dme-mir-991	60	TTAAAGTTGTAGTTTGGAAAGT
+1384	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+1403	+	dme-mir-14	40	CCAGTCTTTTTCTCTCTCCT
+1406	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGT
+1420	+	dme-mir-956	116	TTTCGAGACCACTCTAATCCATT
+1422	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1414	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCT
+1424	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
+1427	+	dme-mir-263a	17	AATGGCACTGGAAGAATTCACGG
+1440	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGT
+1439	+	dme-mir-10	8	ACCCTGTAGATCCGAATTTGTT
+1442	+	dme-mir-281-2	14	AAGAGAGCTATCCGTCGACAGTC
+1444	+	dme-mir-31a	13	TGGCAAGATGTCGGCATAGCTGA
+1452	+	dme-mir-184	60	TGGACGGAGAACTGATAAGGGC
diff -r 000000000000 -r b996480cd604 tool-data/bowtie_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices.loc.sample	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon	 hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full	 hg18	hg18 Full	 /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19	hg19	hg19	 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r b996480cd604 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie_indices.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r b996480cd604 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bowtie" version="0.12.7">
+      <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.18">
+      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.7.7">
+      <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository changeset_revision="d470054f3a5d" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>