Mercurial > repos > drosofff > msp_sr_bowtie_parser
changeset 0:b996480cd604 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Wed, 27 May 2015 17:19:15 -0400 |
| parents | |
| children | ca3845fb0b31 |
| files | sRbowtieParser.py sRbowtieParser.xml smRtools.py test-data/Read_Count_Lists.tab test-data/dme-mir-v20 test-data/matchedSample_1 test-data/matchedSample_2 tool-data/bowtie_indices.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 10 files changed, 2277 insertions(+), 0 deletions(-) [+] |
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--- /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()
--- /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> +
--- /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])
--- /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
--- /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
--- /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
--- /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
--- /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. +#
--- /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>
--- /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>