Mercurial > repos > tyty > structurefold

changeset 70:f76deb490f06 draft

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Deleted selected files
author tyty
date Tue, 09 Dec 2014 02:49:03 -0500
parents bd02fcf26f7a
children b6bdd41440f3
files Iterative_mapping/.DS_Store Iterative_mapping/iterative_map.py Iterative_mapping/iterative_map.xml Iterative_mapping/log.txt Iterative_mapping/map_ex.py Iterative_mapping/rRNA.txt Iterative_mapping/read_file.py Iterative_mapping/read_s_file.py Iterative_mapping/remove_map.py Iterative_mapping/sample.fasta Iterative_mapping/seq_track.py Iterative_mapping/truncate.py Iterative_mapping/unmap.py get_reads/.DS_Store get_reads/get_read.py get_reads/get_read.xml get_reads/read_file.py get_reads/test.bam predict/.DS_Store predict/id_list_test.txt predict/log.txt predict/parse_dis_pac.py predict/predict_RNAs.py predict/predict_RNAs.xml predict/rRNA.txt predict/read_file.py predict/rtts_plot.py predict/test_reactivity.txt predict/test_reference.fa reactivity_cal/dis_f_N1Am_rrna.txt reactivity_cal/dis_f_N1Ap_rrna.txt reactivity_cal/parse_dis_react.py reactivity_cal/rRNA.txt reactivity_cal/react_cal.py reactivity_cal/react_norm_function.py reactivity_cal/reactivity_calculation.xml reactivity_cal/read_file.py
diffstat 37 files changed, 0 insertions(+), 2259 deletions(-) [+]
line wrap: on
line diff
Binary file Iterative_mapping/.DS_Store has changed
--- a/Iterative_mapping/iterative_map.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-import os
-from read_file import *
-from read_s_file import *
-import random
-import string
-
-type_input = sys.argv[1]
-seq_file = sys.argv[2]
-ref_file = sys.argv[3]
-shift = sys.argv[4]
-length = sys.argv[5]
-t_end = sys.argv[6]
-map_type = sys.argv[7]
-output_file = sys.argv[8]
-
-
-if map_type!="default":
-    s = ""
-    sm = ""
-    s = s+"-v "+sys.argv[9]
-    sm = sm+"-v "+sys.argv[9]
-    sm = sm+" -5 "+sys.argv[10]
-    sm = sm+" -3 "+sys.argv[11]
-    s = s+" -k "+sys.argv[12]
-    sm = sm+" -k "+sys.argv[12]
-    if sys.argv[13]:
-        s = s+" -a"
-        sm = sm+" -a"
-    if int(sys.argv[14])>=1:
-        s = s+" -m "+sys.argv[14]
-        sm = sm+" -m "+sys.argv[14]
-    if sys.argv[15]:
-        s = s+" --best --strata "
-        sm = sm+" --best --strata "
-    
-else:
-    s = "-v 3 -a --best --strata "
-    sm = "-v 3 -a --best --strata "
-
-ospath = os.path.realpath(sys.argv[0])
-ost = ospath.split('/')
-syspath = ""
-for i in range(len(ost)-1):
-    syspath = syspath+ost[i].strip()
-    syspath = syspath+'/'
-
-syspathrs = os.getcwd()
-
-os.system("bowtie-build -f "+ref_file+" "+syspathrs+"ref > "+syspathrs+"log.txt")
-
-os.system("cp "+seq_file+" "+syspathrs+"seq0.fa")
-
-if type_input == "fasta":
-    tp = 'fasta'
-if type_input == "fastq":
-    tp = 'fastq'
-
-k = 0
-
-if type_input == "fasta":
-    os.system("bowtie "+sm+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
-if type_input == "fastq":
-    os.system("bowtie "+sm+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
-
-while(True):
-    os.system("samtools view -Sb -F 0xfff "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"mapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get mapped reads
-    os.system("samtools view -Sb -f 0x4 "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"umapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get unmapped reads
-    os.system("samtools view -Sb -f 0x10 "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"rmapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get reversed mapped reads
-    os.system("samtools merge -f "+syspathrs+"unmapped"+str(k)+".bam "+syspathrs+"umapped"+str(k)+".bam "+syspathrs+"rmapped"+str(k)+".bam") #get reversed mapped reads
-    os.system("samtools view -h -o "+syspathrs+"unmapped"+str(k)+".sam "+syspathrs+"unmapped"+str(k)+".bam") #get reversed mapped reads
-    if k>0:
-        os.system("samtools view -h -o "+syspathrs+"mapped"+str(k)+".sam "+syspathrs+"mapped"+str(k)+".bam") #get reversed mapped reads
-        os.system("cut -f 1 "+syspathrs+"unmapped"+str(k)+".sam > "+syspathrs+"unmapped"+str(k)+".txt")
-        os.system("cut -f 1 "+syspathrs+"mapped"+str(k)+".sam > "+syspathrs+"mapped"+str(k)+".txt")
-        os.system("python "+syspath+"remove_map.py "+syspathrs+"unmapped"+str(k)+".txt "+syspathrs+"mapped"+str(k)+".txt "+syspathrs+"runmapped"+str(k)+".txt")
-        os.system("rm "+syspathrs+"mapped"+str(k)+".sam")
-        os.system("rm "+syspathrs+"mapped"+str(k)+".txt")
-        os.system("rm "+syspathrs+"unmapped"+str(k)+".txt")
-    else:
-        os.system("cut -f 1 "+syspathrs+"unmapped"+str(k)+".sam > "+syspathrs+"runmapped"+str(k)+".txt")
-    
-    os.system("rm "+syspathrs+"unmapped"+str(k)+".bam")
-    os.system("rm "+syspathrs+"umapped"+str(k)+".bam")
-    os.system("rm "+syspathrs+"rmapped"+str(k)+".bam")
-    os.system("python "+syspath+"seq_track.py "+syspathrs+"runmapped"+str(k)+".txt "+syspathrs+"seq"+str(k)+".fa "+syspathrs+"unmap_seq"+str(k)+".fa "+tp) #get unmapped sequence
-    os.system("python "+syspath+"truncate.py "+syspathrs+"unmap_seq"+str(k)+".fa "+shift+" "+syspathrs+"seq"+str(k+1)+".fa "+length+" "+t_end) #truncate unmapped sequence
-    os.system("rm "+syspathrs+"seq"+str(k)+".fa") #Remove sequences being mapped
-    os.system("rm "+syspathrs+"map"+str(k)+".sam") #Remove mapping file
-    os.system("rm "+syspathrs+"unmap_seq"+str(k)+".fa") #Remove unmapped sequnce
-    os.system("rm "+syspathrs+"runmapped"+str(k)+".txt")
-    os.system("rm "+syspathrs+"unmapped"+str(k)+".sam")
-    
-    os.system("wc -l "+syspathrs+"seq"+str(k+1)+".fa > "+syspathrs+"count"+str(k+1)+".txt")
-    c = read_sp_file(syspathrs+"count"+str(k+1)+".txt")
-    if c[0][0] == '0': #If no reads is in the sequence file, stop
-        os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
-        os.system("rm "+syspathrs+"seq"+str(k+1)+".fa")
-        break
-    os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
-    k = k+1
-    if type_input == "fasta":
-        os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
-    if type_input == "fastq":
-        os.system("bowtie "+s+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
-
-
-ss = ""
-for i in range(0,k+1):
-    ss = ss+" "+syspathrs+"mapped"+str(i)+".bam"
-
-
-os.system("samtools merge -f "+output_file+" "+ss)
-#print("samtools merge mapped_all.bam"+ss)
-os.system("rm "+syspathrs+"mapped*.bam")
-os.system("rm "+syspathrs+"ref*")
-#os.system("rm -r "+syspathrs)
-
-
--- a/Iterative_mapping/iterative_map.xml	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-<tool id="iterative_map_pipeline" name="Iterative Mapping" version="1.0">
-	<description></description>
-	<command interpreter="python">
-        #if $mapping_file.type == "user"
-            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output $mapping_file.param_v $mapping_file.param_five $mapping_file.param_three $mapping_file.param_k $mapping_file.param_a $mapping_file.param_m $mapping_file.param_best  
-        #else
-            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output
-        #end if
-    </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-                <requirement type="package" version="1.7.1">numpy</requirement>
-                <requirement type="package" version="0.1.18">samtools</requirement>
-                <requirement type="package" version="0.12.7">bowtie</requirement>
-        </requirements>
-	<inputs>
-                <conditional name="file_format">
-                  <param name="type" type="select" label="File format of the reads (Default FASTQ)">
-                    <option value="fastq">FASTQ</option>
-                    <option value="fasta">FASTA</option>
-                  </param>
-                  <when value="fastq">
-                    <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
-                  </when>
-                  <when value="fasta">
-                    <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
-                  </when>
-                </conditional>
-		        <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
-                <param name="shift" type="integer" value="1" label="Number of nucleotides trimmed each round"/>
-                <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
-                <param name="t_end" type="select" label="Trim from 5' or 3' end">
-                    <option value="five_end">5' end</option>
-                    <option value="three_end">3' end</option>
-                </param>
-                
-                <conditional name="mapping_file">
-                  <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
-                    <option value="default">Default</option>
-                    <option value="user">User specified</option>
-                  </param>
-                  <when value="default"/>
-                  <when value="user"> 
-                    <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
-                    <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
-                    <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
-                    <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
-                    <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
-                    <param name="param_m" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m), -1 for unlimited"/>
-                    <param name="param_best" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best --strata)"/>
-                  </when>
-                </conditional>
-
-	</inputs>
-	<outputs>
-		<data name="output" type="data" format="bam"/>
-	</outputs>
-    <tests>
-        <test>
-            <param name="file_format.type" value="fasta" />
-            <param name="file_format.seq_file" value="sample.fasta" />
-	        <param name="reference_file" value="rRNA.txt" />
-            <param name="shift" value="1" />
-            <param name="length" value="21" />
-            <param name="mapping_file.type" value="default" />
-	        <output name="output" file="mapped.out" />
-        </test>
-    </tests>
-
-	<help>
-
-
-**TIPS**:
-
------
-
-**Input**:
-
-* 1. Sequence file type (FASTA/FASTQ)
-* 2. Sequence file (fasta/fastq format)
-* 3. Reference file (fasta) used to map the reads to
-* 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
-* 5. “Length” (The minimum length of the reads for mapping after trimming)
-* [Optional]
-* 1. Bowtie mapping flags (options) [Default: -v 0 -a --best --strata] (-v flag indicates the number of allowed mismatches. Use -5/-3 flag to trim the nucleotides from 5'/3' end of the reads)
-
------
-
-**Output**:
-
-A bam file with all of the reads that are mapped	
-
-
-
-	</help>
-</tool>
--- a/Iterative_mapping/log.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-[samopen] SAM header is present: 4 sequences.
--- a/Iterative_mapping/map_ex.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-map_file = sys.argv[1]
-result_file = sys.argv[2]
-
-
-#reads = read_t_file(read_file);
-
-f = open(map_file);
-h = file(result_file, 'w')
-
-for aline in f.readlines():
-    tline = aline.strip();
-    tl = tline.split('\t');
-    if len(tl)>4:
-        if int(tl[1].strip())== 0:
-            h.write(tline)
-            h.write('\n')
-
-
-f.close();
-h.close()
-
-
-
-
--- a/Iterative_mapping/rRNA.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->25s rRNA 3375nts
-GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACTAACAAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAGAGCCCAGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGGAAAGGGGCGCCAGAGAGGGTGAGAGCCCGTCGTGCCCGGACCCTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGCAGCCCCAATCGGGCGGTAAATTCCGTCCAAGGCTAAATACGGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGTAAAGATGAAAAGGACTTTGAAAAGAGAGTCAAAGAGTGCTTGAAATTGTCGGGAGGGAAGCGGATGGGGGCCGGCGATGCGTCCTGGTCGGATGCGGAACGGAGCAATCCGGTCCGCCGATCGATTCGGGGCGTGGACCGACGCGGATTACGGTGGCGGCCTAAGCCCGGGCTTTTGATACGCTTGTGGAGACGTCGCTGCCGTGATCGTGGTCTGCAGCACGCGCCTAACGGCGTGCCTCGGCATCAGCGTGCTCCGGGCGTCGGCCTGTGGGCTCCCCATTCGACCCGTCTTGAAACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTGGCGGGATCCTCGCGGGTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGTGAGCATGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGTAAAGCCAGAGGAAACTCTGGTGGAAGCCCGCAGCGATACTGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGGACGCGAGTTCTATCGGGTAAAGCCAATGATTAGAGGCATTGGGGGCGCAACGCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACGTGTCGGCTGCTTTGTTGAGCCGTCACACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGGAAGCCGGGTTACGGTGCCCAACTGCGCGCTAACCTAGAACCCACAAAGGGTGTTGGTCGATTAAGACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATGGCGCTTAAGCGCGACCTATACCCGGCCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGGGCGCGGCGGTCGCTGCAAAACCTAGGGCGCGAGGCGCGGAGCGGCCGTCGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGGCGCCCTTGAAAATCCGGAGGACCGAGTGCCGCTCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTTCCGAACCCGTCGGCTGTCAGCGGACTGCTCGAGCTGCTTCCGCGGCGAGAGCGGGTCGCCGGCTGCCGGCCGGGGGACGACTGGGAACGGCTCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGCAAGTGAAATACCACTACTTTTAACGTTATTTTACTTACTCCGTGAATCGGAGGCCGGGGTACAACCCCTGTTTTTGGTCCCAAGGCTCGCTTCGGCGGGTCGATCCGGGCGGAGGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGTGTTGGATTGTTCACCCACCAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGCCCGCGTCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGAAGCGACGCATGCGCCCGCCGCCCGATTGCCGACCCTCAGTAGGAGCTTAGGCTCCAAAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAACGGTCGTTCGGACCGCCTTGAATTATAATTACCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAAGTGGCAGAGTGGCCTTGCTGCCACGATCCACTGAGATTCAGCCCTTTGTCGCTAAGATTCGA
->gi|20197903:2706-4513 Arabidopsis thaliana chromosome 2 BAC F23H14 genomic sequence, complete sequence
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACGAATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTAACTACTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGGCCTACCATGGTGGTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATAAATAACAATACTGGGCTCTTTCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCCCTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTATAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAATGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAGGCATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTTTAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAGTGTTCGGATCGCGGCGACGTGGGTGGTTCGCCGCCCGCGACGTCGCGAGAAGTCCACTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTG
->Arabidopsis thaliana 1
-GGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCATCCCTC
->gi|186498419|ref|NR_022453.1| Arabidopsis thaliana (AT2G01020) rRNA
-AAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAA
\ No newline at end of file
--- a/Iterative_mapping/read_file.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_t_file(in_file):
-    f = open(in_file);
-    result = [];
-    for aline in f.readlines():
-        temp = [];
-        tline = aline.strip();
-        tl = tline.split('\t');
-        for i in range(0, len(tl)):
-            temp.append(tl[i].strip());
-        result.append(temp);
-    f.close();
-    return result;
-
-
--- a/Iterative_mapping/read_s_file.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_sp_file(in_file):
-    f = open(in_file);
-    result = [];
-    for aline in f.readlines():
-        temp = [];
-        tline = aline.strip();
-        tl = tline.split(' ');
-        for i in range(0, len(tl)):
-            if len(tl[i].strip())>0:
-                temp.append(tl[i].strip());
-        result.append(temp);
-    f.close();
-    return result;
-
-
--- a/Iterative_mapping/remove_map.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-
-
-unmap_file = sys.argv[1]
-map_file = sys.argv[2]
-result_file = sys.argv[3]
-
-
-unmap = read_t_file(unmap_file)
-mapped = read_t_file(map_file)
-h = file(result_file, 'w')
-
-maps = set()
-for i in range(len(mapped)):
-    maps.add(mapped[i][0])
-
-
-for i in range(len(unmap)):
-    name = unmap[i][0]
-    if name not in maps:
-        h.write(name)
-        h.write('\n')
-
-
-h.close()
--- a/Iterative_mapping/sample.fasta	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1000 +0,0 @@
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1415:1662#0/1
-TCATTCATCCATTTCCAGTGCTCAGCTAACCCCAACT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1359:1735#0/1
-TGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1469:1743#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1750:1642#0/1
-AACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1899:1627#0/1
-AAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1859:1668#0/1
-TACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCCCCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1830:1700#0/1
-ATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2000:1705#0/1
-TTAATGATTAACAGGGACAGTCGGGGGCATTCGTATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2149:1632#0/1
-GATCATACATTACTGACTAAAAGAAGCAAAATCTTGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2052:1637#0/1
-AGAACATGAAACCGTAAGCTCCCAAGCAGTGGGAGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2036:1706#0/1
-AAAACTTAGCTGAGACGACGCAGAAACAGGTGAGATC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2183:1706#0/1
-TTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2068:1721#0/1
-AAGTAGCACGTCCCTCAGGAAAGAAGCTCTTCAGATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2162:1740#0/1
-ATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2339:1628#0/1
-TGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCCGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2338:1670#0/1
-TCGCGCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2459:1678#0/1
-CCTCGTCGCTGCGTCTCTCTCCCGCAACCTTCGATTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2492:1685#0/1
-AAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2286:1687#0/1
-AAGGCGGTGGAGGCCGCCCAGCATTGCCCGCACCTAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2283:1704#0/1
-ACTCTTGTTACAATGATTGTATGACATTCCTGATGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2475:1719#0/1
-TTATGCAGAAATTGCTATAAGAAGAAACCTAAACTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2299:1733#0/1
-CTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2464:1744#0/1
-GTGTTTTTATCCAAATCCGGGGATAAACACATTTTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2547:1662#0/1
-AGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2512:1664#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2675:1664#0/1
-GTACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2694:1675#0/1
-ACTACGAGAGGAACCGTTGATTCGCACAATTGGTCAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2558:1692#0/1
-ATCTTTCATATCCAGAGAGAGAGAAAGAGAACAAAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2587:1709#0/1
-CAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2560:1727#0/1
-TTTCCGAGAGTATGCAGATTTTGTTTTCCAAGAATAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2960:1646#0/1
-CTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2981:1669#0/1
-GATTCATCCCAAAACATTACAAAACGTTACAATGGCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2884:1740#0/1
-TCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3172:1696#0/1
-TCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3046:1703#0/1
-AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3218:1717#0/1
-TCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3140:1732#0/1
-ATAAGAAGGTTATTGATTTGGTTAAAGAATACAATGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3212:1744#0/1
-TCCTGGTCTTAATTGGCCGGGTCGTGGCCCCCGCGCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3277:1654#0/1
-TACTCGGATAACCGTAGTAATTCTAGAGCTAATACGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3373:1695#0/1
-CGTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3255:1702#0/1
-ACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3391:1733#0/1
-AAATAGAAGGGTCAAAAGCTAAGGAAGAAAAGAAAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3606:1635#0/1
-TTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3710:1652#0/1
-CCCCGTGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3551:1662#0/1
-AGAACATGAAACCGTAAGCTCCCAAGCAGTGGGAGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3696:1663#0/1
-ACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3679:1667#0/1
-ACGGGGGGCAGCAGTGGGGAATCTTGGACAATGGGCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3622:1671#0/1
-TCATCCAATTGGAGACGAATCATATCGAGCGATGGAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3506:1682#0/1
-TGCGTTGTGGAAGTCGAAGAGGTTGATGAATATTGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3540:1687#0/1
-AAATTAAACCTCACCGACGGATTCAATTCTCTCGTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3627:1725#0/1
-TCATCCAGATCTCAACTTTCTCTCATCTTCAAATTAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3710:1735#0/1
-GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3787:1636#0/1
-AGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3996:1694#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3942:1696#0/1
-TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4104:1635#0/1
-AGGTCGGCGGTTCCATCACCACAACGCCGGACGACAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4243:1713#0/1
-AGATACTCCTTTGACCGAAGAAACCATAACGGAAGCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4091:1714#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4229:1733#0/1
-GGGCCTGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4060:1745#0/1
-TGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4308:1693#0/1
-TCCTCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4384:1697#0/1
-AAAATTTCATCGTGATGGGGATAGATCATTGCAATTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4506:1651#0/1
-GATAATAAAGAGATGGAGATTGTTTTGGAGCAACGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4535:1654#0/1
-AAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4592:1677#0/1
-CTACCTGGTTAATCCTGCCAGTAGTCATATGCTTGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4726:1686#0/1
-TATGTTTTTGTTTGTTCGTAAATTCTTGACATCACTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4544:1694#0/1
-TGGAGCTCCGCTGAATTTTCTTTGCTCCATTTCCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4604:1707#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4996:1665#0/1
-CTTATTTTACGAAGCTCCCCTCGGTTACAGCATTGAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4860:1668#0/1
-AGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4786:1671#0/1
-TATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4889:1691#0/1
-ATGGGGGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4843:1693#0/1
-AGGCAGTCCGATCCAACGGCTAGGCACTTACATGGCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4977:1703#0/1
-ATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4791:1723#0/1
-TTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5019:1686#0/1
-ACAATGGAGCAACCACTCCTTCCGGCCTCGTCGCCGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5134:1686#0/1
-TCTGCTGTTGTAGAGCCTTACAACAGTGTGCTTTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5307:1664#0/1
-ACGTGCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5278:1674#0/1
-GCATCAAAATCCTCCGACGATGACAACCATAGCTGCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5486:1715#0/1
-TTGTGGTGGCGACGCATCATTCAAATTTCTGCCCTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5541:1641#0/1
-TTCTCCCCGAAATGCGTTGAGGCGCAGCAGTTGACTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5706:1646#0/1
-ACGAGGATCCATTGGAGGGCAAGTCTGGTGCCTGCAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5593:1651#0/1
-AAGGGGCTTCTTGTCATTGATGATGAGCTAGCCACCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5503:1695#0/1
-GAGAGGGAACTAATCATAAGAGATGCAATGAGTGTGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5581:1706#0/1
-ATAAAAACCAGAAGAATCCGTATAAATTATCCTAACA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5713:1729#0/1
-TCTCTTGGAGAGTTCGATCCTGGCTCAGGATGAACGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5831:1656#0/1
-TTCACGTGGCTCAAGTCACTAGCAATGCTCTTGCTTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5942:1680#0/1
-TCCGGTGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5772:1711#0/1
-AGCGCGAACTTCGAAAGGGGATCTGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5957:1723#0/1
-TTACAATAAGTCTGCCTATAGTGGGAGAGGTGACAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5981:1739#0/1
-GAGAAATTTGGAGTTTCGCCGGAATCTTCCTCTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6231:1644#0/1
-AATTGGAAAAGGTGGAGGAGTTGGCGGTGGCATCGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6152:1724#0/1
-TGCAATTCTACCACGACCTCATCGACGAGCTCATAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6100:1731#0/1
-TCCTCTGCGTTTTCACGAAACAGAGAACCTTATCGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6174:1733#0/1
-TCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6310:1648#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6287:1659#0/1
-TCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6332:1666#0/1
-TTTGGGTTCTCTCCTTATAGTTTGATGAACATTGTTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6295:1704#0/1
-AGATAATCGGAACCTTCGTCCTTGTCTACACGGTCTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6590:1655#0/1
-AGAAGCCACCTCCGGTTCCGGTTTACAAGCCCCCGCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6585:1691#0/1
-CTTTTCCCAGAGAAGAAGCAATGACGGTATCTGGGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6722:1719#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6820:1642#0/1
-AAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7000:1662#0/1
-GGGAAGCGTTGAGGCTTCACCCTCCACTCATCGTGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6873:1673#0/1
-AGCACTTTAGGATGGCATAGCCTTAAAGTTAAGGGTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6770:1699#0/1
-AACTGTCTACAAAATCATTGAAGATCTACCCAAAAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6782:1735#0/1
-GATCCGTCAAATTCAATTGATCCTCTCTCCAAATCAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7159:1658#0/1
-ACCCACCTCCGGTTCCGGTTTACAAGCCACCGCCAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7183:1660#0/1
-ATTTCATCGTGATGGGGATAGATCATTGCAATTGTTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7167:1679#0/1
-TTCTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7223:1688#0/1
-TTGGACGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7410:1647#0/1
-ACCATGCAGTATCGGTTTATATAACATCCACATTGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7387:1710#0/1
-TCTTCGAGTTTTGCTACTTGTATGGGATGATAAGACT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7397:1741#0/1
-TTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7624:1680#0/1
-AATTGTTGTTGTTATCTTCAACGATAGCGTTGTGCTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7600:1744#0/1
-AGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7789:1676#0/1
-ACCCGTCTGATAGCGCTTAAGCGCGAACTTCGAAAGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7950:1684#0/1
-TGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7926:1706#0/1
-ACGGTATCTGGGGAATAAGCATCGGCTAACTCTGTGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7757:1711#0/1
-TTGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:7970:1747#0/1
-TCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8054:1672#0/1
-CGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8245:1672#0/1
-GATATATAATCATAGATTCCAGAATTTGACATTTTCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8088:1710#0/1
-GAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8244:1713#0/1
-GGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8069:1727#0/1
-TCGTCTACACCGTCTACGCCACAGCCGTTGACCCCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8018:1745#0/1
-TTCTCTACTGGATTGCTCAGCTTCTTGGCTCCGTCGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8394:1647#0/1
-CTACAAGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8475:1658#0/1
-ACACTTGATCGGAATAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8367:1664#0/1
-GGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8488:1695#0/1
-GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8442:1727#0/1
-CGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8328:1744#0/1
-TTGTCATTCTCTTCGCCGGAATCTAATCTCTCTCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8520:1660#0/1
-TTGGCCGTTGTTTCCTTCTTCTTCTTCTTCTTCTTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8563:1665#0/1
-AATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8739:1667#0/1
-TCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8596:1682#0/1
-TAGCCCACGAATGCGGTCACAACGCATTCAGCGACTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8643:1688#0/1
-TTGCACGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8727:1745#0/1
-AGGGAGAGCTAATGCTTCTTGGGTATTTAGGTTTGAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8767:1649#0/1
-TCGGTACCAAATCGAGGCAAACTCTGAATACTAGATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8932:1656#0/1
-GCTGGCGACGCATCATTCAAATTTCTGCCCTATCAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8841:1666#0/1
-TCAAACGAGGAAAGGCTTACGGTGGATACCTAGGCAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8951:1673#0/1
-TGGTGGAGCTGGAGGAGGATTTGGTGGAGGAGCTGGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8876:1674#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:8993:1737#0/1
-TTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9241:1664#0/1
-AAGTCACTCTTTCTTGTTGCCTTACTTGTCGGCTCTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9095:1710#0/1
-AGAACGAAAGTTGGGGGCTCGAAGACGATAAGATACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9231:1716#0/1
-TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9171:1733#0/1
-AAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9471:1658#0/1
-GACACATACACACATAGCCATGGCCTCTTCTTTCTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9383:1680#0/1
-TTCAGTGTTGATTCGTCTTCCTTCACGCCGTTCTTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9627:1730#0/1
-ATTGTTTGTAAAGGGTGAGAGATTATTTTTCAGTGAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9921:1680#0/1
-ATGGCTTCTCCGGTGAGATACCTGACTCGATTGGTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:9931:1727#0/1
-AAAGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10235:1668#0/1
-AAAAATCTTGAGTAAAAACAAATTTTCCTGTATCTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10040:1686#0/1
-AAAACCCGTCTGATAGCGCTTAAGCGCGAACTTCGAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10169:1689#0/1
-ACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10213:1743#0/1
-GGCGCTTAAGCGCGCGACCTATACCCGGCCGTCGGGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10021:1744#0/1
-CAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10294:1712#0/1
-TTCTCTCTCTAACATTCTTCAGAGAGGGAGACTTTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10392:1736#0/1
-TAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10582:1655#0/1
-ACGGTACTGGACAATGTGGAAGCTTCCCTTGTTCGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10777:1673#0/1
-CACTCTCACCCACAAGTTAGTCATAAAAAAAAAAAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10980:1714#0/1
-GTGGAGAGACTGAAAACCGCGAAGAGGATGTGAATGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:10931:1720#0/1
-TTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11171:1717#0/1
-TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11458:1668#0/1
-GATCACAAGTTTTAAGCAGTATTTGTAAGAAAATGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11388:1696#0/1
-TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11317:1701#0/1
-ACAACTCAAGCTTCCATCAACTTGACCCACACCGAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11403:1706#0/1
-TAGATAACATCAAGACAACAACCGTCGGTCCCGGAAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11291:1739#0/1
-GAAAATCAAATCTTTTCATTTACAATTATCTTTCTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11593:1673#0/1
-TCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11537:1726#0/1
-CCATCTCCGTATTGTCTTCTACGTAGACAATGTGCCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11709:1733#0/1
-CGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11851:1657#0/1
-TAATCAAGATCGAAAGTTGGGGGCTCGAAGACGATCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11822:1687#0/1
-TTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11950:1691#0/1
-TTATGTTTACAGCTCTCCTCCTCCTCCGGTGAAGTCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11752:1704#0/1
-TGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11895:1708#0/1
-TTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:11756:1739#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12136:1709#0/1
-ATGCGAAAAGTGTAAAGGTGGGAAGATCGGAATTGCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12070:1715#0/1
-ACGAGCAGCTCCCAACCACAGACTACTGAATTAATCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12204:1724#0/1
-GAAAATTTTCCCCATTAAACAAAAAAAAATCAAATCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12140:1746#0/1
-ACTACTCTCTCCACTAAACAAAAACACTAGAGTTAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12332:1664#0/1
-GCGAAAGCATTTGCCAAGGATGCTTTCATTAATCAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12455:1665#0/1
-ACAAGTCTTGTCTCTCGAGTGTTCTTCAAATGTTAGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12252:1728#0/1
-GGAACTCCATGCGAATATGAAGCGCATGGATACAAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12315:1747#0/1
-TGGACCGGTAATTTCATTACATCGCCGGACGGCCGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12640:1665#0/1
-TCTCTTCTACAGTAAACAAAAAATGGCAATGAATGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12666:1668#0/1
-TTATTCTGCACTTGGAAGAAGAACTAGAAAAAGGAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12735:1728#0/1
-ATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12751:1677#0/1
-TCCTCCTGTTTACAAGTCCCCACCACCACCGGTTAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12821:1679#0/1
-TCTTCTCCGGTGATTTACTTACTTAACAATCATGGCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12935:1691#0/1
-ACTGCCTTCGGATTTGATTTGGTTCGTGGCACCAAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:12996:1719#0/1
-TAATCTCTCTGTTTAATCTTATGATCTGCTGTTTTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13223:1661#0/1
-GTTGATGTGTTTATTCCCAGAGATCGAAGGACTGGTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13442:1665#0/1
-TTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13331:1684#0/1
-GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13451:1685#0/1
-TGCTCAAATTTCTTCTTTAGAAGATTAAAAATCTTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13309:1690#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13312:1742#0/1
-AAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13704:1696#0/1
-GACTCGGAGCAGAGATTTAGGGTCTGTAATTTGTATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13563:1703#0/1
-TATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13735:1728#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13899:1667#0/1
-CGTTATTTTACTTACTCCGTGAATCGGAGGCGGGGTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13836:1707#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13886:1718#0/1
-GAACAGAAAATAGAAAGAAGTAACAAAACCAAAGCAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13866:1724#0/1
-TCAATGAGCCATGGGTTTTCTCGCACGCTGGCTATGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:13943:1728#0/1
-TCGAAGACGATCAGATACCGTCCTAGTCTCAACCATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14097:1712#0/1
-CCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14116:1729#0/1
-GTTCTCACGTTCGAAGACCATTTCTTGTTCTTTGGAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14699:1669#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14594:1718#0/1
-AATTTCCTCATGTTGAGAGGTACTTCTGGACTGTGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14743:1729#0/1
-AACTCACCTGCCGAATCAACTAGCCCCGAAAATGGAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14510:1734#0/1
-TTCACCCACCGCAGCTTCACCACCGGCACCTCCGACG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14821:1705#0/1
-AACTGGCTAACACGTATTGGGTTGAGTATCTCTCTAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14892:1717#0/1
-CTTTCGGATATTCCACCAGTCTCTCGCAATCTTCGCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:14835:1743#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15239:1702#0/1
-TCTGACGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15059:1717#0/1
-TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15152:1718#0/1
-GGGCAGGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15444:1702#0/1
-GATATCTATTTATTCAATAACCCTTACAACACCGAAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15407:1747#0/1
-TCGGATACGGGTCGGGCTTCTTAGCTGTTTGAAGAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15681:1670#0/1
-AATTGCCACAACATGGGCGTTCTTCTTAGCAAGAATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15630:1695#0/1
-TTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGGTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15506:1715#0/1
-TTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15976:1688#0/1
-ATCATCCATCACATCTCCTCTTGCAAACCAACGTAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:15940:1745#0/1
-AACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16043:1680#0/1
-ACGTATGTGGCAAAATACGGGGATGACTTGTGGCTAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16175:1683#0/1
-ATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16074:1695#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16238:1700#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16229:1727#0/1
-TCGAAGACGATCAGATACCGTCCTAGTCTCAACCATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16025:1727#0/1
-CCGGGAAGGACGCACCTCTGGTGTACCAGTTATCGTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16429:1678#0/1
-ACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16255:1695#0/1
-CTAAGAAAGTTGATCCACCGCCGGTGCCAGTCCACAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16494:1739#0/1
-AGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16656:1687#0/1
-TTAAATCAGTTATAGTTTGTTTGATGGTAACTACTAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16685:1715#0/1
-TAAAACGTCGTGGACTTTTTGAGTCTGACGCTGCATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16885:1690#0/1
-CTCAGGATCGGAAGAGCACACGTCTGAACTCCAGTCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16994:1709#0/1
-ATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16768:1715#0/1
-TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:16899:1742#0/1
-GGTAAACTTCGAGCCTGTCCGACCCAGAAGGCACAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17201:1693#0/1
-TCTTTGGATAACAATATCCCAAACTGAAAATGGCTAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17179:1704#0/1
-TTAAGTCCTCCGCTGCCTTCCCAGCCACCCGCAAGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17158:1711#0/1
-ACTAATGTAAAGGAAGCCTGTGCTTGGCTTGGATATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17051:1725#0/1
-ATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17448:1685#0/1
-ACAATGACTGGGCCTCCACCTGCCATGGTGATGCCTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17551:1710#0/1
-GGTTTGTCTTCAAAATCGTCAGAAGAAGAAGAAGAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17662:1746#0/1
-GCAACACGGGGAAACTTACCAGGTCCAGACATAGTAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17823:1706#0/1
-TCCCCCGGTTGGATTGAAGGGTTGAAAAAATTAGACA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:17951:1723#0/1
-TGATCGGAGGATGTTGCGACGGAGCCGTCCTTTGACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18174:1676#0/1
-ATTAAATCCTAAAATCCATTATTGATTGAATCTTCGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18241:1694#0/1
-CCAAATCTAATAAATCTAAGTGTAGTTTTCGGTGTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18095:1727#0/1
-ACAAGCAACGGCGGAAGAGTTAACTGCATGCAGGTGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18074:1746#0/1
-ACCACCAAATCGCCGCCATGTTTAAACAAGCTTCTCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18318:1679#0/1
-GAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18410:1680#0/1
-GCAAGCCTACGCTCTGGATACATTAGCATGGGATAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18290:1681#0/1
-TCAGGCCTTGGAGGACCGAACCCACGTATGTGGCAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18280:1722#0/1
-GAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18429:1742#0/1
-TAGACTACGGATGGGACACCGCCGGACTTTCAGCTGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18675:1682#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18535:1684#0/1
-CCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18657:1722#0/1
-GAGAAGATAAAGAGATAAAGGAAAGACTAACGTTAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18618:1729#0/1
-TGAACACACACAAACACACACACACACAGCCTTTTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:18823:1701#0/1
-ACCTGACCCAGATAGCGAGAAGTTTCATGGATAAGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19063:1699#0/1
-ACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19104:1705#0/1
-AAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19019:1718#0/1
-AGACGATCAGATACCGTCCTGGTCTCAACCATAAACG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19433:1728#0/1
-AAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19355:1731#0/1
-AATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19500:1683#0/1
-TTGTAACACGGACCAAGGAGTCTGACATGTGTGCGAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19657:1698#0/1
-GGGATTGGCTTTGGGCTTTTCCTGCGCAGCTTAGGTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19640:1749#0/1
-TTTAATTAATAACAATAAATGTTCTTTTTCAGTTTTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19866:1690#0/1
-AAGCCCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:19966:1707#0/1
-AAAATGCCAAGACGGACGATCAGGATACGAGGCTTAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20090:1682#0/1
-CAGGTCCCCGAGTGGCTCACACGATATGCTTCACGTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20183:1689#0/1
-GATATCGAGCGATGGATTTGGCAGAACTGTGGGCGAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20206:1747#0/1
-TCGAAAGTTGGGGGCTCGAAGACGATCAGATGCCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20292:1695#0/1
-AGGAACGGAGACGGCAGGAACGATGAGTTCTATAGTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20306:1713#0/1
-CCGATGGTTGTGGACAACATGTATTATAAGAACATCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20402:1713#0/1
-TTACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20275:1726#0/1
-AACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20403:1737#0/1
-AAATAAGAAGACATATTTATCAACTTGATCAACTTGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20539:1702#0/1
-CCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20612:1731#0/1
-AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20566:1745#0/1
-AGTTCGGTCTCTCTGCCGGAGTCGGATCATTAAACGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20889:1691#0/1
-CTTTCATTTCAGAGTCTTGGTGTTGTTTATGGTGATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20841:1709#0/1
-TTTGCTGGCATAATGGGAATGGGTTTTCCACCTTACA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:20980:1742#0/1
-TCCACTACTTTTAACGTTATTTTACTTACTCCGTGAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:21184:1708#0/1
-CGATCAGATACCGTCCTAGTCTCAACCATAAACGATG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:21173:1745#0/1
-TCGGTTGCTAATGGTTTGATCAATTTCCTCAACATAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:21427:1722#0/1
-CGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1449:1766#0/1
-TCAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1303:1793#0/1
-TAACCATAAACGATGCCGACCAGGGATCAGCGGATGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1430:1865#0/1
-TCTTCATCCTCGTCTACTGCACCGCCGGTATCTCTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1450:1892#0/1
-AGCAACTGCCAAAGCACCCGCAACAAAATTATAAAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1342:1935#0/1
-ATTGATGATGTCTTTACTTCTTCAAGAGGATCTACCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1406:1941#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1676:1764#0/1
-TGGTGAGACAAAAACGACGATATTTTCCTCTTCCTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1512:1774#0/1
-AAAAACAATAAACGAAAACTGAGAGAGAGATTGAAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1677:1808#0/1
-ATTGGATCACTTTCAATGAGCCATGGGTTTTCTCGCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1579:1824#0/1
-TTTTGTGTTTGTCCACCACCTCCTCCATGTTATTCTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1744:1840#0/1
-GGGTGAGAGCCCCGTTGTGCCCGGACCCTGTCGCACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1579:1852#0/1
-AGAAGAAGAAGAAGAAAAAGTGGAGCAAGCTTCGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1550:1869#0/1
-AACTCTGTGCCAGCAGCCGCGGTAATACAGAGGATGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1565:1898#0/1
-AGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1738:1918#0/1
-ACATTCCTCACCAAACCCTCTCCAAAACACACCCACA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1547:1922#0/1
-TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1732:1964#0/1
-TCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1654:1991#0/1
-GATTATATAAGGGAATGTTCAGTTCCAGTGACTGAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1518:1992#0/1
-GGTGGAGGTTTACAAACACCACCAATCTTCTCTCTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1865:1796#0/1
-GATTCATCCCAAAACATTACAAAACGTTACAATGGCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1886:1815#0/1
-GGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTCCGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1855:1840#0/1
-TGGTATCGGTGGACTCGGCGGTGCAGGTGGGCTAGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1960:1855#0/1
-ACCTCACTGCCGCCGATTAGACTCCGCCGGATGCAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1808:1879#0/1
-TTACCATAAACGATGCCGACCAGGGATCAGCGGATGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1869:1890#0/1
-TGCTTCTTGGGTATTTAGGTTTGACACAGCTTCACAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1898:1925#0/1
-TCCCATGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:1765:1950#0/1
-AACTCATATCAACCTTCGCCGGAAATAATGGCTTTCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2096:1773#0/1
-ATAGCACCGATAACAATCTACTCTCTTTAAAAGAAAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2186:1774#0/1
-TTGAGAAAATAAACGAGGAGGTGGCTCATCCTGAGAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2019:1774#0/1
-AAGACGATCAGATACCGTCCTAGTCTCAACCATAAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2236:1797#0/1
-GTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2218:1825#0/1
-ACCTATCTCACTCTAAAATCTCTCTCTGCCAATCTCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2067:1830#0/1
-ACATGTCTGTGAAGATGCGGACTACCTGCACCTGGAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2183:1833#0/1
-AGGGCGCGAGCCCGGGCGGAGCGGCCGTCGGTGCAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2095:1843#0/1
-GACACAACACACCTCAAGCTTTATAACTTCTAAAACA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2184:1923#0/1
-AAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2086:1933#0/1
-AAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2134:1944#0/1
-AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2220:1966#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2066:1971#0/1
-TGAAGCATTTTCCAAAGAGAAAGAGAGAGAAATGGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2239:1991#0/1
-ATTATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2113:1996#0/1
-TTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2369:1755#0/1
-TGATCCTTTCGTCTTTTTCTGACTCTTCAATCTCTCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2281:1791#0/1
-TTAATTCCGGAACCGGGACGTGGCGGTTGACGGCAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2431:1837#0/1
-AAAATTTCATCGTGATGGGGATAGATCATTGCAATTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2272:1843#0/1
-GGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2316:1843#0/1
-TGGCTTGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2451:1850#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2264:1872#0/1
-ATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2443:1872#0/1
-ACAGGTCTGTGATGCCCTTAGATGTTCTGGGTCGCAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2297:1890#0/1
-ATAACATCATAGGATTTCGATCCTATTGTGTTGGCCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2472:1986#0/1
-ACTACCACTCTCCACCTCCTCCGGCGAAGTCCCCACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2564:1768#0/1
-GGGGCCTGATAGGCGGTGGTTTACCCTGTGGCGGATG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2674:1786#0/1
-TAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2648:1802#0/1
-GCGATAATACAGAGGATGCAAGCGTTATCCGGAATGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2691:1831#0/1
-CAGTATAATCAATCAGAAAACAAGTAGAAACTTTAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2560:1839#0/1
-TCGAAGACGATCAGATACCGTCCTAGTCTCGACCATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2612:1876#0/1
-TCTTGGGCCTTTGCCACCAACTTTGTTCCCGGAAAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2503:1919#0/1
-TCAGACGAGGAAAGGCTTACGGTGGATACCTAGGCAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2640:1953#0/1
-CACCGGGAGAAAATCCTCCTCCGCTGTCGTGAGAGCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2553:1969#0/1
-GATCATCACCTTCCCCACTAATACTCTATAGTTTGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2669:1987#0/1
-GGATCGTGAGACTCCGATGGTTGTGGACAACATGTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2782:1800#0/1
-GACATTTTCTGTTTCCGTCTACAAGAACCACTTTGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2957:1811#0/1
-ATTAATTCACATTTAAACACTTCTCTGCATATATTTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2990:1818#0/1
-TATTTTACTTACTCCGTGAATCGGAGGCGGGGTACAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2806:1852#0/1
-TGAAAATAAGCGTAGATCCGGAGATTCCCGAATAGGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2899:1856#0/1
-ACTGATGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2903:1882#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2913:1931#0/1
-TTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2816:1932#0/1
-GCATCAGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2795:1958#0/1
-TCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:2993:1984#0/1
-GACGATCAGATACCGTCCTAGTCTCAACCATAAACGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3163:1754#0/1
-AGGCAAGAGACAACCTGGCGAACTGAAACATCTTAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3082:1793#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3054:1825#0/1
-TAGATGTTGAGACTCTAATCCCTAACCACAATGACTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3100:1835#0/1
-CTATCTTAAAACTTCTTACCTAAAATAGAAATTTGAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3199:1865#0/1
-TTTCTTAAAAATTGGATTTTGTGTTGGGTTTTTCTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3032:1907#0/1
-AGAGAGAAGAAGTAGGCAGACAAAGAAGAAGAAGAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3232:1919#0/1
-ATCACAAGCAAACAAGAGAAAACATTTTATTGTTATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3075:1937#0/1
-ACAGACTGTGAAACTGCGAATGGCTCATTAAATCAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3005:1941#0/1
-TTTTAAGTCCGCCGTCAAATCCCAGGGCTCAACCCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3026:1990#0/1
-AAGAAAGAGATTCCCCCGCCGGTTCCGGTTTACGATC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3131:1992#0/1
-GGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3319:1777#0/1
-GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3337:1789#0/1
-GACGCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3416:1846#0/1
-AACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3292:1846#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3491:1888#0/1
-ATCTTTTCGAAGAGCGGAAGCTAAGGAGAGGCGAATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3266:1903#0/1
-TATAGAAATGGCCAAAGACGTGGAAGGACCTGAGGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3339:1904#0/1
-GTGAAGACACCAGAGACGCCTAGTTTGGTGGGAAAGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3435:1918#0/1
-AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3478:1938#0/1
-CCGGAGAATAATATCCGATCTGCTAGTGCGGTTAATA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3381:1938#0/1
-ATCAGCGACTCTCCCACTCGCTCGTGTCGTCGAAGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3311:1972#0/1
-ACATTCATCCCAAAACATTACAAAACGTTACAATGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3471:1996#0/1
-CCCATGTCCACCTAAATACAGTCCTCCTGTGGAGGTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3408:1998#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3714:1760#0/1
-TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3734:1790#0/1
-ATACAGCAGCTGAAGCTGTGTATCGGAAAGCTCAATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3699:1795#0/1
-ACAAAAGACAAGTTTTTAAACTGCAGAACCGCATTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3651:1798#0/1
-TCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3557:1799#0/1
-TGATAGTGCTTAAGCGCGAACTTCGAAAGGGGATCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3531:1811#0/1
-TACAGACACACACGTGGCTCATCACCTGTTCTCGACA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3526:1856#0/1
-TCTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3693:1860#0/1
-AAAACAACTCTGCTTCACTCTCTATCTTTCTTAAGTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3616:1916#0/1
-AGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3599:1930#0/1
-AGACGATCAGATACCGTCCTAGTCTCAACCATAAACG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3620:1956#0/1
-GAATCTCTCTGTGTTTTTTCTATCTCTCTCTTTCTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3596:1973#0/1
-TGTAAGAGCTAGGCAGCAGGGATTATGTGTACGCAAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3721:1974#0/1
-AAGCCTGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3507:1998#0/1
-ACAAGGTGCTGGTGCTGGAGGAGGATATGGAGGTGGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3756:1769#0/1
-ACGCCCTCGACCTATTCTCAAACTTTAAATAGGTAGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3901:1846#0/1
-TACAAGTCTCCTCCGCCACCAACTCCGACATATGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3892:1871#0/1
-ATCACCGCCTCCATATTCTTTCGCGTCTTTTGCTTCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3765:1925#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3842:1953#0/1
-TCGAGCATTTTTGACGCCAAGGCTGGAATTGCATTCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3758:1970#0/1
-AACCCCGACTTATGGAAGGGACGCATTTATTAGATAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3931:1972#0/1
-CTCCGTGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:3828:1991#0/1
-CCTTCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4152:1771#0/1
-TCCTGAGATTTTTTATATATTTTCTCCAGATCTGCTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4212:1780#0/1
-GACTCAACCAATTTCTTCTCAGGTAATACTCGTAAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4130:1806#0/1
-TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4183:1813#0/1
-AAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4010:1857#0/1
-ACTCTGCTTCACTCTCTATCTTTCTTAAGTAAACAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4206:1859#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4051:1895#0/1
-TCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4226:1939#0/1
-TGATCATCACTTTCACAATCTTCTTCATCGATTTCTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4381:1809#0/1
-GCAGCATCAGCAACAACAGAGCAGTCCTGGCTTTCTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4456:1814#0/1
-TTCATGGACGTTGATAAGATCTTTCCATTTAGCAGCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4311:1831#0/1
-AAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4464:1844#0/1
-TACGCTTGGGCCTTCGTCGCCAAGACTTCTCAAGTTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4254:1850#0/1
-AAAAGGAGGTAGGGGTGCAGAGACAGCCAGGAGGTTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4286:1883#0/1
-ATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4465:1887#0/1
-AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4329:1895#0/1
-CCGTTCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4379:1906#0/1
-ACTACTCTCTCCACTAAACAAAAACACTAGAGTTAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4486:1907#0/1
-TAAGAGCCAAAGGTTGAGAATGTGACTCTTGGACCAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4456:1996#0/1
-GAGGATGCGAAAAGATACATCCGGCAACTTCCCAACT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4674:1782#0/1
-TTTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4634:1791#0/1
-GAATCACTTCACTCTCTCTAATCAAAAAGCTTTTAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4501:1806#0/1
-TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4629:1820#0/1
-TGATCGTTCTTATTGACCCTAGCCGCTACACACTTTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4590:1838#0/1
-ATTCATTTCAATCAATCTTCTTCTTCTTCTTCTTCTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4741:1847#0/1
-AACGACTCTCGGCAACGGATATCTCGGCTCTCGCATC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4708:1892#0/1
-TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4508:1902#0/1
-TTAGCATGGGATAACATCATAGGATTTCGATCCTATT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4691:1903#0/1
-AGTGAAATACCACTACTTTTTACGTTATTTTACTTAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4648:1966#0/1
-AAATTTCAAAATCAGATCCAACAAATCTTCTTCTTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4963:1798#0/1
-AGACGTCGGCGGGGGCCTCGGAAAGAGTTATCTTTTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4766:1882#0/1
-CTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4860:1888#0/1
-ATACTCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4947:1899#0/1
-CATCAATACTCCTGTGAGAACAAAATGAAGCTTTCTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4982:1926#0/1
-AGACTCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4879:1942#0/1
-TCGAGTCAGGTAATTGGAATGAGTACAATCTAAATCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:4914:1944#0/1
-GTGCAAAGGTTTCCTCGGGCCGGACGGAGATTGGCCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5091:1754#0/1
-TTTATGTTTCTCATTATTACTGCGGGAATTTCAATTA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5145:1756#0/1
-TATCGGTAGGGGAGCGTTCCGCCTTAGGGGGAAGCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5015:1781#0/1
-TTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5166:1833#0/1
-TTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5035:1836#0/1
-TGGCGACGCATCATTCAAATTTCTGCCCTATCAACTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5195:1862#0/1
-TTCACCCATTTCTTGGCTTACAACAACAAATCTTAAA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5062:1871#0/1
-TTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5235:1878#0/1
-ACGGAAATGTCTTCATGGGTTCTTCCGAACATGTTCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5231:1897#0/1
-GGAACGAACACACCACCTTCTCTCCAATCTGGATCTG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5168:1901#0/1
-ACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5220:1915#0/1
-CCACCTCCGGTTCCGGTTTACAAGCCCCCGCCAAAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5013:1950#0/1
-ACTTTCAATGAGCCATGGGTTTTCTCGCACGCTGGCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5175:1985#0/1
-CGTGAAATACCACTACTTTTAACGTTATTTTACTTAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5145:1985#0/1
-ATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5453:1770#0/1
-CATCAAAACCCAGACGCTGTATGGTTATGGGGAATGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5412:1781#0/1
-ATGTCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5412:1816#0/1
-TAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5496:1822#0/1
-AAAAACCTAAAACAAAAAAAATCTCTTTCCTTCTTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5346:1823#0/1
-AAGCCACCACCAAAGGTGGAGCTTCCACCGCCTATTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5333:1831#0/1
-TCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5305:1833#0/1
-AGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5371:1867#0/1
-GTAGCGTCCTCAGCAACGGACCGGGCCTAAGTTCCCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5374:1893#0/1
-ATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5377:1943#0/1
-TGTTCGGGAAACATTGACGACAAAGGAAAGTTTGGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5313:1973#0/1
-TGTATACAAGTCTCCTCCGCCACCAACTCCGACATAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5620:1756#0/1
-AAAAACTTTCTCTCAATTCTCTCTACCGTGATCAAGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5716:1779#0/1
-TCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5667:1857#0/1
-GTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5654:1887#0/1
-GTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5636:1908#0/1
-TTCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5715:1927#0/1
-CCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5610:1936#0/1
-GAAGAAGCAATGACGGTATCTGGGGAATAAGCATCGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5832:1784#0/1
-GCCCGGATCGGAAGAGCACACGTCTGAACTCCAGTCA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5917:1794#0/1
-AGTCGCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5769:1883#0/1
-AGCAAAGTTTTATGTAATCAAATCGTACAGTGAAGAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5796:1889#0/1
-TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5992:1905#0/1
-ATGTGTGTATTAATTTATCTTCTTGTTTTAAAGAGAC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5885:1923#0/1
-AAGAAGAGCCAATGGCGATGAAGACATCACATGTTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5976:1937#0/1
-AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:5957:1978#0/1
-TTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6197:1781#0/1
-ACTTAGGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6180:1789#0/1
-ATTTTGGCTGGTGCTGAATACGGTAGTGGAAGTTCTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6038:1789#0/1
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6177:1825#0/1
-TTGATCCCGAGACTGAAGCTATGACCAGGAGAATTGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6159:1830#0/1
-CGGGCCGATCGGAAGAGCACACGTCTGAACTCCAGTC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6151:1878#0/1
-ATACGGTGTATGAATCCGAATTACACAGAGTTCAAGT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6123:1878#0/1
-AGCGCTAACTTCGAAAGGGGATCCGGTTAAAATTCCG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6196:1879#0/1
-ATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGG
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6237:1895#0/1
-AAGATCCCAGACGAAATGGCTCAGAAAGTGGTGCTGA
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6023:1896#0/1
-ACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6123:1904#0/1
-ATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGC
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6125:1922#0/1
-ATGGATCGTTGCACGTCGTCGTTTTTGCTTCCCACAT
->DGM97JN1_120925_0255_AD166MACXX:4:1101:6184:1926#0/1
-GATCATCAAAAAACACCTCAAAGAATTATTCATTCAG
--- a/Iterative_mapping/seq_track.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-unmap_file = sys.argv[1]
-reads_file = sys.argv[2]
-result_file = sys.argv[3]
-tp = sys.argv[4]
-
-
-unmap = read_t_file(unmap_file);
-
-h = file(result_file, 'w')
-
-reads = SeqIO.parse(reads_file,tp)
-um = set()
-for i in range(0, len(unmap)):
-    id_r = unmap[i][0]
-    um.add(id_r)
-
-for read in reads:
-    if read.id in um:
-        h.write('>')
-        h.write(read.id)
-        h.write('\n')
-        h.write(read.seq.tostring())
-        h.write('\n')
-    
-
-
-h.close()
-
-
-
-
--- a/Iterative_mapping/truncate.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from Bio import SeqIO
-
-fasta_file = sys.argv[1]
-shift_in = sys.argv[2]
-result_file = sys.argv[3]
-length = sys.argv[4]
-t_end = sys.argv[5]
-
-shift = int(shift_in)
-    
-fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
-h = file(result_file,'w')
-for seq in fasta_sequences:
-        nuc = seq.id;
-        sequence = seq.seq.tostring();
-        if (len(sequence)-shift)>=int(length):
-                h.write('>'+nuc)
-                h.write('\n')
-                if t_end == 'three_end':
-                        h.write(sequence[0:(len(sequence)-shift)])
-                if t_end == 'five_end':
-                        h.write(sequence[(shift):(len(sequence))])
-                h.write('\n')
-
-
-
-
-h.close()
-
-
-
-
--- a/Iterative_mapping/unmap.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-map_file = sys.argv[1]
-result_file = sys.argv[2]
-
-
-#reads = read_t_file(read_file);
-
-f = open(map_file);
-h = file(result_file, 'w')
-
-for aline in f.readlines():
-    tline = aline.strip();
-    tl = tline.split('\t');
-    if len(tl)>4:
-        if int(tl[1].strip()) != 0:
-            h.write(tl[0].strip());
-            h.write('\n');
-
-
-f.close();
-h.close()
-
-
-
-
Binary file get_reads/.DS_Store has changed
--- a/get_reads/get_read.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from Bio import SeqIO
-import os
-from read_file import *
-import random
-import string
-
-fasta_file = sys.argv[1]
-map_file = sys.argv[2]
-result_file = sys.argv[3]
-
-syspathrs = os.getcwd()
-
-os.system("samtools view -F 0xfff "+map_file+"|cut -f 3,4 > "+syspathrs+"map_info.txt") 
-
-fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
-length_seq = {};
-for seq in fasta_sequences:
-        nuc = seq.id;
-        length_seq[nuc] = len(seq.seq.tostring());
-
-
-
-mapping = {}
-transcripts = []
-
-f = open(syspathrs+"map_info.txt");
-for aline in f.readlines():
-    tline = aline.strip();
-    tl = tline.split('\t');
-    if tl[0].strip() not in transcripts:
-        transcripts.append(tl[0].strip());
-        mapping[tl[0].strip()] = [];
-
-    mapping[tl[0].strip()].append(tl[1].strip());
-
-distribution = {};
-coverage = {};
-for transcript in length_seq:
-    distribution[transcript] = [];
-    for i in range(0, length_seq[transcript]):
-        distribution[transcript].append(0);
-    sum_count = float(0);
-    if transcript in mapping:
-        for j in range(0, len(mapping[transcript])):
-            index = mapping[transcript][j];
-            #count = reads[mapping[transcript][j][0]];
-            sum_count = sum_count + 1;
-            distribution[transcript][int(index)-1] = distribution[transcript][int(index)-1] + 1;
-            coverage[transcript] = float(sum_count)/float(length_seq[transcript]);
-    else:
-        coverage[transcript] = 0
-
-        
-        
-    
-
-h = file(result_file, 'w')
-for transcript in length_seq:
-    h.write(transcript);
-    h.write('\n')
-    for i in range(0, length_seq[transcript]):
-        h.write(str(distribution[transcript][i]))
-        h.write('\t')
-    h.write('\n')
-    h.write('\n')
-
-#os.system("rm -r "+syspathrs)
-
-    
-
-f.close();
-h.close()
-
-
-
-
--- a/get_reads/get_read.xml	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-<tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0">
-	<description></description>
-	<command interpreter="python">get_read.py $lib_file $map_file $output </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-                <requirement type="package" version="1.7.1">numpy</requirement>
-                <requirement type="package" version="0.1.18">samtools</requirement>
-        </requirements>
-	<inputs>
-                <param name="lib_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
-		<param name="map_file" type="data" format="bam" label="Mapped file"/>
-	</inputs>
-	<outputs>
-		<data name="output" format="txt"/>
-	</outputs>
-    <tests>
-        <test>
-            <param name="lib_file" value="test.bam" />
-	        <param name="map_file" value="com_rna.txt" />
-	        <output name="output" file="get_RT_stop_test.out" /> 
-        </test>
-    </tests>
-	<help>
-
-
-**TIPS**:
-
------
-
-**Input**
-
-* 1. A mapped (bam) file from Bowtie (or any other mapping program)
-* 2. Reference library sequences (fasta) used to map the reads to
-
------
-
-**Output**:
-
-A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file)
-
-
-
-	</help>
-</tool>
--- a/get_reads/read_file.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_t_file(in_file):
-    f = open(in_file);
-    result = [];
-    for aline in f.readlines():
-        temp = [];
-        tline = aline.strip();
-        tl = tline.split('\t');
-        for i in range(0, len(tl)):
-            temp.append(tl[i].strip());
-        result.append(temp);
-    f.close();
-    return result;
-
-
Binary file get_reads/test.bam has changed
Binary file predict/.DS_Store has changed
--- a/predict/id_list_test.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-AT3G05880.1
--- a/predict/log.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-a /Users/yintang/Project/galaxy/galaxy-dist/tools/pipeline_programs/predict/output_qicbsuLr/AT3G05880.1.ct
-a /Users/yintang/Project/galaxy/galaxy-dist/tools/pipeline_programs/predict/output_qicbsuLr/AT3G05880.1.ps
-a /Users/yintang/Project/galaxy/galaxy-dist/tools/pipeline_programs/predict/output_qicbsuLr/AT3G05880.1.tif
--- a/predict/parse_dis_pac.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-#parse reactivity file into a dictionary
-
-import sys
-
-def parse_dist(in_file):
-    result = []
-    distribution = {}
-    name = []
-    f = open(in_file)
-    for aline in f.readlines():
-        line = aline.strip()
-        dis = line.strip()
-        dist = dis.split('\t') #split the line and the reactivites or reads are in a list
-        if len(dist) > 0:
-            if len(dist) == 1:
-                if dist[0].strip().find('coverage')==-1:
-                    name.append(line) #add the name in the name list
-                    flag = 1
-                    t_name = line
-            else:
-                distri = []
-                for i in range(0, len(dist)):
-                    distri.append(dist[i].strip())
-                distribution[t_name] = distri #add the list of reactivities into a dictionary
-    result.append(name)
-    result.append(distribution) #Output the dictionary
-    f.close()
-    return result
-                
-                
-
-
-
-
-
-
-
-        
-
-
-
-
-
--- a/predict/predict_RNAs.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-#RNA structure prediction & Output and illustrate reactivities
-
-import sys
-import shlex
-import subprocess
-import tarfile
-from parse_dis_pac import *
-from read_file import *
-from Bio import SeqIO
-import os
-from rtts_plot import *
-import random
-import string
-
-
-id_file = sys.argv[1]
-seq_file = sys.argv[2]
-output_file = sys.argv[4]
-
-
-flag = False
-if sys.argv[3]!='None': #input reactivity file if provided
-    react_file = sys.argv[3]
-    react = parse_dist(react_file)
-    react = react[1]
-    flag = True
-
-syspath = os.getcwd()
-
-ids = read_t_file(id_file)
-sequences = SeqIO.parse(seq_file, 'fasta')
-
-
-seqs = {}
-for seq in sequences:
-    seqs[seq.id] = seq.seq.tostring()
-
-if len(ids)>100: #setup a limit of the number of sequence to be predicted
-    print("Number of sequences exceeds limitation!")
-    sys.exit(0)
-    
-
-#predict RNA structures
-output_directory = os.path.join(syspath, "output_files")
-if not os.path.exists(output_directory):
-    os.makedirs(output_directory)
-for i in range(len(ids)):
-    id_s = ids[i][0]
-    print(id_s)
-    #Put RNA sequence and reactivities into files
-    if id_s in seqs:
-        fh = file(os.path.join(syspath,"temp.txt"), 'w')        
-        fh.write('>'+id_s)
-        fh.write('\n')
-        fh.write(seqs[id_s])
-        fh.close()
-        if not flag:
-            command = shlex.split('Fold %s %s' % (os.path.join(syspath, 'temp.txt'), os.path.join(output_directory, '%s.ct' % id_s)))
-            subprocess.call(command)
-        else:
-            if id_s in react:
-                fh = file(os.path.join(syspath, "constraint.txt"), 'w')
-                make_plot(react[id_s], id_s, output_directory) #make a plot of the distribution of the reactivites of the input RNA
-                for j in range(0, (len(react[id_s]))):
-                    if react[id_s][j]!='NA':
-                        fh.write(str(j+1))
-                        fh.write('\t')
-                        fh.write(str(react[id_s][j]))
-                        fh.write('\n')
-                    #h.write(str(react[id_s][j])) #Output the reactivities
-                    #h.write('\t')
-                fh.close()
-                #h.write('\n')
-                #h.write('\n')
-                command = shlex.split("Fold %s -sh %s %s" % (os.path.join(syspath, "temp.txt"), 
-                                                             os.path.join(syspath, "constraint.txt"),
-                                                             os.path.join(output_directory, "%s.ct" % id_s)))
-                subprocess.call(command)
-            else:
-                print(id_s+" not in the data of react!")
-        command = shlex.split('draw %s.ct %s.ps' % (os.path.join(output_directory, id_s), os.path.join(output_directory, id_s)))
-        subprocess.call(command)
-    else:
-        print(id_s+" not in the data of sequences!")
-
-#Remove the unnecessary files
-tarball = tarfile.open(output_file, 'w:')
-for filename in os.listdir(output_directory):
-    filepath = os.path.join(output_directory, filename)
-    print filepath
-    tarball.add(filepath, arcname=filename)
-print os.listdir(syspath)
-print os.listdir(output_directory)
-# tarball.add('%s.tif' % os.path.join(syspath, id_s), arcname='%s.tif' % id_s)
-tarball.close()
\ No newline at end of file
--- a/predict/predict_RNAs.xml	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0">
-	<description></description>
-	<command interpreter="python">predict_RNAs.py $rna_list $reference_file $reactivity_file $output </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-                <requirement type="package" version="1.7.1">numpy</requirement>
-                <requirement type="package" version="1.2.1">matplotlib</requirement>
-        </requirements>
-	<inputs>
-        <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/>
-        <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
-        <param name="reactivity_file" type="data" optional = "true" label="Reactivity file"/>
-	
-	</inputs>
-	<outputs>
-		<data name="output" format=".tgz"/>
-	</outputs>
-    <tests>
-        <test>
-            <param name="rna_list" value="id_list_test.txt" />
-	        <param name="reference_file" value="cdna.txt" />
-            <param name="reactivity_file" value="mRNA_react_test2.txt" />
-	        <output name="output" file="structures.out" />
-        </test>
-    </tests>
-	<help>
-
-
-**TIPS**:
-
------
-
-**Input**:
-
-* 1. A file with transcript Ids (Max num. 20), (each ID one line)
-* 2. Reference file (fasta) used to map the reads to
-* [Optional]:
-* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided
-
------
-
-**Output**:
-
-* 1. .ct files with predicted RNA structures [transciptID.ct]
-* 2. .ps files which depict the predicted RNA structures [[transciptID.ps]
-* [Optional]
-* 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png]
-* 4. A .txt file that includes the reactivities of all the nucleotides on the transcripts of interest. [transciptID.txt]
-
------
-
-**Attention**
-
-Make sure any of the transcript Ids does not contain "|" or space!	
-
-
-
-	</help>
-</tool>
--- a/predict/rRNA.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->25s rRNA 3375nts
-GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACTAACAAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAGAGCCCAGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGGAAAGGGGCGCCAGAGAGGGTGAGAGCCCGTCGTGCCCGGACCCTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGCAGCCCCAATCGGGCGGTAAATTCCGTCCAAGGCTAAATACGGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGTAAAGATGAAAAGGACTTTGAAAAGAGAGTCAAAGAGTGCTTGAAATTGTCGGGAGGGAAGCGGATGGGGGCCGGCGATGCGTCCTGGTCGGATGCGGAACGGAGCAATCCGGTCCGCCGATCGATTCGGGGCGTGGACCGACGCGGATTACGGTGGCGGCCTAAGCCCGGGCTTTTGATACGCTTGTGGAGACGTCGCTGCCGTGATCGTGGTCTGCAGCACGCGCCTAACGGCGTGCCTCGGCATCAGCGTGCTCCGGGCGTCGGCCTGTGGGCTCCCCATTCGACCCGTCTTGAAACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTGGCGGGATCCTCGCGGGTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGTGAGCATGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGTAAAGCCAGAGGAAACTCTGGTGGAAGCCCGCAGCGATACTGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGGACGCGAGTTCTATCGGGTAAAGCCAATGATTAGAGGCATTGGGGGCGCAACGCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACGTGTCGGCTGCTTTGTTGAGCCGTCACACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGGAAGCCGGGTTACGGTGCCCAACTGCGCGCTAACCTAGAACCCACAAAGGGTGTTGGTCGATTAAGACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATGGCGCTTAAGCGCGACCTATACCCGGCCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGGGCGCGGCGGTCGCTGCAAAACCTAGGGCGCGAGGCGCGGAGCGGCCGTCGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGGCGCCCTTGAAAATCCGGAGGACCGAGTGCCGCTCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTTCCGAACCCGTCGGCTGTCAGCGGACTGCTCGAGCTGCTTCCGCGGCGAGAGCGGGTCGCCGGCTGCCGGCCGGGGGACGACTGGGAACGGCTCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGCAAGTGAAATACCACTACTTTTAACGTTATTTTACTTACTCCGTGAATCGGAGGCCGGGGTACAACCCCTGTTTTTGGTCCCAAGGCTCGCTTCGGCGGGTCGATCCGGGCGGAGGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGTGTTGGATTGTTCACCCACCAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGCCCGCGTCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGAAGCGACGCATGCGCCCGCCGCCCGATTGCCGACCCTCAGTAGGAGCTTAGGCTCCAAAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAACGGTCGTTCGGACCGCCTTGAATTATAATTACCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAAGTGGCAGAGTGGCCTTGCTGCCACGATCCACTGAGATTCAGCCCTTTGTCGCTAAGATTCGA
->gi|20197903:2706-4513 Arabidopsis thaliana chromosome 2 BAC F23H14 genomic sequence, complete sequence
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACGAATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTAACTACTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGGCCTACCATGGTGGTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATAAATAACAATACTGGGCTCTTTCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCCCTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTATAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAATGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAGGCATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTTTAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAGTGTTCGGATCGCGGCGACGTGGGTGGTTCGCCGCCCGCGACGTCGCGAGAAGTCCACTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTG
->Arabidopsis thaliana 1
-GGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCATCCCTC
->gi|186498419|ref|NR_022453.1| Arabidopsis thaliana (AT2G01020) rRNA
-AAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAA
\ No newline at end of file
--- a/predict/read_file.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_t_file(in_file):
-    f = open(in_file);
-    result = [];
-    for aline in f.readlines():
-        temp = [];
-        tline = aline.strip();
-        tl = tline.split('\t');
-        for i in range(0, len(tl)):
-            temp.append(tl[i].strip());
-        result.append(temp);
-    f.close();
-    return result;
-
-
--- a/predict/rtts_plot.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-#!/usr/bin/env python
-#Make a plot of reactivity distribution
-
-import sys
-import os
-import numpy as np
-import matplotlib
-from pylab import *
-import math
-
-#Convert the reactivities (Make NA to 0)
-def convert_react(a):
-    r = []
-    for i in range(len(a)):
-        if a[i]!='NA':
-            r.append(float(a[i]))
-        else:
-            r.append(float(0))
-    return r
-        
-
-#Make a plot of the distribution
-def make_plot(ar,id_s,path):
-    N = len(ar)
-    a = convert_react(ar)
-    w = 1
-    ind = np.arange(N)
-
-    fig = figure()
-    fig, ax = subplots()
-    ax.bar(ind+w, a, width = w, color = 'r',edgecolor = 'r')
-    ax.set_ylabel('Structural Reactivity')
-    ax.set_xlabel('Nucleotide Index')
-
-    
-    mag = int(math.log(N,10))-1
-    tail = 10**mag
-
-    intervel = int(math.ceil(float(N)/tail/5))
-    print(N)
-    print(intervel)
-    tl = []
-    k = 0
-    upmax = int(math.ceil(float(N)/intervel/tail)*intervel*tail)+1
-    ax.set_xticks(np.arange(0,upmax,intervel*tail))
-    print(np.arange(0,upmax,intervel*tail))
-    ax.set_xticklabels(np.arange(0,upmax,intervel*tail))
-
-    ax.set_title(id_s+" reactivity distribution")
-    savefig(os.path.join(path, id_s+'.tif'))
-
-
-
-    
-    
-    
-
-
--- a/predict/test_reactivity.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-AT3G05880.1
-0.943887685769	0.421815158787	NA	1.01455360981	NA	NA	NA	NA	0.503726666615	NA	0.562759466181	0.53286496306	NA	0.452307806554	NA	NA	NA	NA	0.234006609126	NA	0.356521303582	0.3345952334	NA	0.938455477986	0.961629159648	0.58445845106	0.277563382428	NA	NA	NA	0.381285618597	0.510385809404	0.263300197836	0.351983737127	NA	0.478451311944	NA	0.0	NA	NA	0.249061701962	NA	0.602014314955	0.768409570219	0.479108914417	0.609654847688	0.395147907741	NA	NA	0.316409963987	NA	NA	1.01642560569	0.178529288881	1.1258499175	NA	0.102264245055	NA	0.588862283199	0.675885983569	NA	NA	NA	0.0	NA	NA	NA	NA	0.8152009763	NA	0.730574123452	NA	NA	0.196012732449	NA	NA	0.748188202713	NA	0.0	NA	0.925269643553	0.0	0.506395998703	NA	0.511028818599	0.354285255052	NA	1.01563235674	NA	NA	NA	0.602118316823	0.486534824365	NA	0.266635693932	0.176995791343	0.887089878761	0.654802870139	NA	0.24940376078	NA	NA	NA	NA	NA	0.835049477972	NA	NA	NA	0.230188979227	NA	0.145932219541	0.510982455489	NA	0.70545494854	NA	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	NA	NA	0.0607994838688	NA	NA	NA	NA	NA	NA	NA	0.0	NA	0.510982455489	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.805809423851	0.214474701586	NA	0.320112197187	NA	0.886851602907	0.0	NA	NA	NA	NA	NA	NA	0.173824155265	NA	0.499351609605	NA	NA	0.119452482914	0.0	NA	NA	NA	NA	0.985352919102	NA	0.0	0.0	NA	0.925509063242	NA	0.54084940725	0.0	NA	0.622064968928	0.285526636999	0.373974554632	NA	NA	NA	0.0	NA	NA	NA	0.0	0.369187155673	NA	0.644843692277	0.0	0.0	0.0	0.0	0.155248951804	0.0	NA	NA	0.0	NA	NA	NA	0.0	0.0	0.0464264694222	0.0	NA	0.0	NA	0.250790026642	NA	0.11120052998	0.0299680537584	NA	0.0723351276735	0.0	NA	0.069968383925	NA	0.394969636508	0.0	NA	NA	NA	0.270970925021	0.0436999866019	0.0	0.172881011784	NA	1.24794080936	NA	NA	NA	NA	0.0	0.0	NA	NA	0.241516034212	NA	NA	NA	NA	NA	0.19903265234	NA	0.289893769912	0.835049477972	NA	0.83678872047	NA	0.769301566905	NA	NA	NA	NA	NA	NA	0.486001309495	1.00671172955	NA	NA	0.392970275151	NA	NA	0.369187155673	0.0330308799953	NA	0.0	NA	NA	NA	NA	0.322006332632	NA	NA	NA	NA	NA	1.10146992643	NA	NA	NA	0.602394928175	0.052285391313	NA	0.0	0.474447727012	NA	0.258266798648	NA	NA	NA	NA	NA	NA	0.173824155265	NA	NA	NA	NA	NA	0.435796833817	0.341824194398	0.0	NA	NA	0.971161850563	0.0	NA	NA	NA	0.594354216766	0.0	NA	NA	0.0	0.0666024493389	NA	0.36331086056	0.0	NA	0.838839492047	0.078362328999	0.54084940725	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	NA	NA	NA	NA	0.454308208169	NA	0.0	NA	0.0	0.653920441757	0.369187155673	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	0.0	0.0	0.602118316823	0.0	NA	0.0	0.0	NA	0.0	NA	0.0	NA	0.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	0.0	0.0	0.0	0.0	NA	0.0	NA	0.0	NA	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	0.0	0.0	0.465862322301	0.0	NA	0.0	0.0	0.0	NA	NA	NA	NA	0.0	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	0.0	NA	0.0	0.0	0.0	0.0	NA	NA	0.0	0.0	0.0	0.0	0.0	0.0	0.0	NA	NA	0.0	0.0	0.0	0.0	0.0	NA
--- a/predict/test_reference.fa	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->AT3G05880.1 | Symbols: RCI2A | Low temperature and salt responsive protein family | chr3:1755497-1756540 REVERSE LENGTH=495
-AAGCTTTTATAATATTTTCTCAGAAACTTTCAAAGAGCTTAGAAAAATGAGTACAGCTACTTTCGTTGATATTATTATCG
-CCATCCTCTTGCCTCCACTCGGTGTCTTTCTCAGATTTGGTTGCGGGGTTGAGTTTTGGATATGTTTGGTTTTGACGCTA
-CTTGGGTATATTCCTGGGATCATATACGCCATTTATGTCCTCACCAAATGATTTACCATCTATCATCATCTCCTTGAACA
-GCTGTTCCGTCGTGTTCTCCTATCTTTGTGACTGATTCAGCGTTTCTTTTTCTTTCATCAGAGTTTTTATGTTTCAAGTA
-ATTTAATTAATCATCACTGTTGTGTTTGCATTGTTATATAAATGTTGTGTTGATATAAAAGAAGAGAGCGTTGGTTTGTA
-CTTTGTGTGAAGATTTTTTAAAAATATAGTTGGTTTATTACAATAAATTGGAAATTGTGTTGCCTTGGTGGATCACAGGA
-CCACCATTAACCATT
--- a/reactivity_cal/dis_f_N1Am_rrna.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-gi|186498419|ref|NR_022453.1|
-146241	38142	180120	134243	5639	6848	2492	1596	695	104	1741	160	1505	3009	210	1349	2366	197	353	97	3173	453	4575	656	218	3344	196	19655	540	360	303	351	1377	300	2479	445	3882	2244	293	272	3155	540	218	1849	1902	292	1037	15050	641	989	470	770	949	177	907	927	748	2819	796	490	117	237	272	723	994	173	162	157	86	147	65	296	86	342	115	1694	380	83	205	159	332	357	255	1017	697	80	599	217	474	673	246	170	327	468	47	818	403	25	100	57	84	527	158	349	409	220	94	111	177	27	207	64	770	309	108	92	47	63	17	6	25	10	33	4	117	35	64	27	1	69	42	43	163	12	9	133	81	44	213	125	136	106	26	1349	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverage:3826.28048781
-25s
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-coverage:3967.112
-Arabidopsis
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--- a/reactivity_cal/dis_f_N1Ap_rrna.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-gi|186498419|ref|NR_022453.1|
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-coverage:6327.99377778
-Arabidopsis
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-coverage:43.1900826446
-gi|20197903:2706-4513
-918451	43069	4973	6069	5424	764	1308	1439	883	907	987	3034	389	406	952	935	228	1164	4117	891	3486	1385	2729	4818	1258	26713	4029	5575	4375	1242	1070	2107	920	1244	1091	1165	4373	1897	5508	17168	30987	6744	39793	35181	2869	4645	4692	3044	1437	1272	3410	3227	3218	950	11595	1582	3975	4126	3534	2904	9622	9201	2662	5093	17776	53180	1503	5034	36896	3073	2696	12752	92843	89306	51420	20625	12112	19628	14536	7588	16552	7625	2887	5143	2395	77142	8914	1213	1504	2871	807	9425	1820	12549	1146	1756	873	702	4748	1983	28475	12593	4907	15539	18662	26723	5381	1232	6179	7188	7257	11050	8482	3815	5990	5082	1806	1922	2605	1940	1266	5733	1528	1833	4406	5121	2372	5536	3055	7605	63077	12644	78932	88354	15542	70445	7243	6242	120346	2540	1657	3245	25109	5755	1160	8889	5851	2503	876	7493	5714	9802	13634	8462	14457	8287	7986	2320	4129	8613	1888	5304	4607	2516	6019	15661	9337	2463	7209	1824	3285	2368	4304	947	36403	95330	40526	20022	54545	77764	3922	2515	3015	414	1370	14283	58088	11847	6695	24021	59631	6958	3539	4469	16242	340311	7244	1837	18429	8372	18021	5639	41746	21583	14255	9732	18318	11221	6535	10615	10301	40428	533599	326270	55341	36178	28527	8780	4316	27359	1402	2267	21704	3585	2449	2389	1205	6044	1632	2498	21387	25280	15320	4162	1764	3727	2635	19546	22097	8739	4664	21700	11278	21131	48044	2632	42293	5936	3669	21387	10312	18637	1858	25311	159741	5693	23447	3845	15343	7781	1209	18376	1883	2889	15421	5395	5221	589	16571	255673	5036	4649	4379	14806	6242	1153	6334	1207	2127	15500	269146	206619	25198	83043	13150	15591	7979	9163	13341	1153	2181	21654	3397	11882	2120	25839	34277	8235	17713	14707	33769	34611	23409	16045	46807	10245	7192	5440	2570	1530	629	5093	2209	1933	4632	13485	118398	3529	13894	12849	5579	3313	3197	12455	2575	1353	4839	1286	818	418	463	855	938	549	6614	4199	3176	3182	462	311	873	513	175	195	2569	689	217	3286	1004	486	365	683	978	2539	987	1931	14123	358	1065	201	1443	638	861	7076	735	494	607	1394	4512	5974	12877	3584	1718	2029	6966	1725	717	1255	2196	587	1166	3496	589	737	859	614	434	174	582	691	588	2404	1393	481	165	413	280	186	191	350	783	1657	971	1473	6521	258	1769	575	323	224	1775	321	167	3255	221	2023	11024	1286	569	4550	17400	11662	718	1234	4560	3160	642	257	2328	529	894	1211	579	256	506	909	688	2805	882	12678	27229	9905	8194	690	1257	786	734	852	2316	1227	1305	203	1235	585	1289	6637	6275	7344	596	2993	1093	199	81	784	866	959	1940	527	2090	452	362	7523	6256	18337	9647	5141	8828	3798	17697	2009	2458	9177	2905	5062	4758	1977	2374	922	306	215	1332	239	332	783	875	5373	16505	153966	10369	17786	5145	3987	2840	388	2542	1062	2393	3988	10780	46495	35443	5441	2750	3089	7490	44543	4522	7389	30017	41341	6083	16256	11272	14499	17752	12640	4905	12457	10533	8046	11038	3131	1047	9235	2518	7924	2114	8155	786504	20595	4724	18877	16816	3257	20972	174536	10915	10591	53044	9521	3903	5021	2460	3040	4609	4420	5187	966	207182	10038	4869	7684	1525	3982	2569	2485	342	1094	2782	1929	8190	6125	3783	3835	3938	1472	2345	1122	3299	13563	7847	15191	53606	151932	10494	12925	6127	1369	14734	2286	1409	4612	2395	20399	21833	37032	17626	2744	15445	6995	5652	15687	23622	24690	300234	38628	20789	7096	26987	63959	6745	13800	4071	5326	10434	3218	2338	5241	24342	17104	31725	24079	54301	80045	16097	14430	19838	3836	1915	20476	5640	2057	19218	17512	9583	19429	14930	4053	2368	36692	28478	17960	12763	3211	15723	17455	4262	15836	5574	17075	2971	1549	11262	1816	2481	3031	1711	2245	3302	2239	5581	5436	898	3189	6402	7369	19431	10181	13982	19518	19378	6052	3397	7060	48792	49466	166394	16294	11481	7588	2631	9634	818	7222	8071	5098	50033	3363	2907	3316	2831	28201	23752	15257	6539	31273	20417	8330	18882	2784	7312	11264	5719	37305	11156	34369	28532	7521	2088	5106	136216	6760	3184	8826	4505	17420	89725	5786	9835	47563	42284	228449	23151	10905	9629	2291	852	539	21600	1595	1643	83308	3168	9230	1691	5252	3309	1515	5225	4626	1267	7645	10913	3289	11718	160149	96128	20051	4231	10627	21149	6156	9864	8341	10069	2123	20394	14350	9726	19497	27938	98863	14126	12365	11455	5934	8883	3699	2200	1856	2930	29028	20229	4265	13036	10997	123690	13292	23786	7293	26281	10459	4324	80443	74236	29597	4360	3106	7668	2936	50151	6032	8456	41215	30315	72582	22633	82098	56991	7444	11502	18815	3986	51306	4799	3007	3601	2699	32496	8227	8523	51338	3731	23833	383982	16734	54704	181869	15780	44891	8843	61934	8722	3511	9541	2014	2082	9791	12879	1256	1769	16492	23018	25711	3425	5757	7748	6637	8538	2421	1180	2306	3558	2511	6676	15736	2895	16995	12150	784	15694	19837	2235	2291	6787	14289	13577	33423	7455	104407	25193	11741	76444	149786	13133	19339	38730	9696	10093	11742	2843	2973	16682	8778	4261	3432	9341	2088	3519	5195	2142	3650	23502	21304	29334	11102	24475	3829	8448	25057	29207	4072	4295	15963	7557	13441	16457	6903	7517	18114	2888	15355	2912	9314	10223	7355	6996	23929	34758	32336	23582	18784	13062	4052	11500	5164	4390	4450	43219	15862	13078	12019	32352	11400	10789	7759	44295	10190	3755	43157	4945	3789	27000	728401	15353	25752	37886	6521	5833	10411	4997	13530	17532	19474	11376	13583	5615	59799	19137	5037	2415	10195	20867	7197	43957	40619	11990	3397	65413	14393	17403	45882	12444	17080	25725	6268	53375	26086	21210	13030	129383	28084	5386	30859	1007498	36810	9120	149119	20793	14276	9005	28255	24819	10532	6806	1929	2209	3994	923	4758	1557	5077	62586	3615	4418	25161	37477	29847	26458	4883	1416	16824	23999	7771	24194	18853	15112	7284	9706	25453	5458	1093	20049	5547	1700	13748	5212	7528	10561	2127	30562	9086	10290	22396	13044	7444	39588	38983	13299	10989	29106	3213	2719	7463	12171	1211	5657	907	946	25627	3807	2467	8638	3158	2323	1169	8655	20054	1144	2165	1022	473	515	318	9968	1982	1785	1586	645	932	1326	18572	6003	23624	24494	5382	4548	1073	2357	145	748	93	132	194	310	543	519	435	90	4330	484	165	904	623	1328	564	238	536	221	273	205	600	900	308	221	1905	591	606	861	459	142	100	18	42	102	37	51	143	25	28	49	15	80	85	30	219	395	310	209	208	2609	58	17	91	62	113	104	170	238	117	203	99	25	65	33	650	499	93	524	459	207	420	1906	39597	754	479	1113	1080	101	56	540	249	224	131	465	759	185	233	72	27	138	32	13	211	60	50	402	134	122	149	95	32	86	45	34	117	55	57	138	80	13	328	510	195	680	1400	373	2025	336	525	103	352	946	3106	48146	65443	4484	25973	1591	6249	333	394	949	267	1063	365	1543	2689	578	477	144	2523	847	129	3781	777	386	968	721	2034	314	9986	7600	6795	2312	2609	3265	3657	1206	1537	34719	81640	1937	1853	3224	4988	714	3826	2129	1135	1260	2243	2459	1314	1287	3252	1490	5798	1287	33839	828802	15071	6467	17694	11929	2470	5783	499	5132	4324	4576	4040	1232	2842	2115	1433	15255	2204	1353	4861	1205	444	2760	1524	838	8666	3804	902	55166	2046	981	760	1848	1086	590	13977	5962	3093	1474	4197	3879	1882	1310	1314	3970	1193	448	1349	1551	886	2579	855	2295	13815	6410	5875	1631	2855	2952	549	8320	6165	4995	9738	15798	9726	13766	3409	3604	1852	4391	4035	19978	1370	11897	15640	4216	4196	5271	98189	3141	6442	2689	1344	10728	1082	1077	9202	4433	4742	3403	2571	684	4671	4971	2838	4010	8424	12091	3648	2359	5308	6442	1811	1627	19424	12480	4202	2763	1678	1400	6800	7776	10122	9578	190337	91025	34402	23174	2379	8401	3013	1489	10760	1976	1679	3867	13143	2621	11394	3139	1164	4008	23586	6376	9367	8775	6496	5845	9468	6204	465	3811	43823	12209	3920	20046	8528	2284	1178	3011	1706	18792	25150	38254	9642	7318	9454	4337	5776	1202	7027	18078	11395	1937	29155	13898	14404	135641	161207	7066	4404	11155	8655	6772	18892	24799	128909	26431	30188	46143	3328	87384	25884	8823	8085	3989	4756	7137	3970	8207	14751	3275	1486	3042	5599	2671	4629	21374	10866	7013	34532	9214	2570	12047	5339	2723	5135	3375	1212	1891	2006	9614	2371	3466	30358	5952	3412	2603	3365	2028	5615	444	6723	21353	4983	25946	6977	8179	2315	24559	2797	6644	7684	13108	9082	26909	3560	15175	27961	3236	5753	15358	9662	43960	13939	28670	208831	16478	275147	37432	3074	4436	1782	536	352	1036	1415	2556	21366	5609	8805	32111	1025	830	1367	477	2793	3119	8611	10826	3384	28549	21014	6481	9057	11687	5277	9019	15543	10283	27900	7132	4644	16608	2018	7261	6962	979	1551	2580	1025	9650	6228	1202	1888	2288	2266	8281	11051	5152	776	6184	6588	1243	11157	2088	1143	1834	3611	10885	7167	16069	1712	2014	709	563	509	343	1480	626	1128	3365	329	5016	2783	345	220	1965	14235	4296	5956	2167	887	1004	456	74	810	994	254	825	255	394	125	31	151	35	868	519	2423	435	80	919	675	18	1111	56	52	59	14	411	133	337	198	19	27	240	9	53	543	15	33	6	10	23	46	36	22	205	72	34	175	166	274	120	228	251	173	562	24	821	202	140	46	30	2102	39	16	40	22	24	0	172	191	512	370	1253	727	423	874	10347	3877	3532	3094	1517	4942	848	334	965	910	546	1048	774	276	104	112	559	997	136	190	61	66	85	20	35	6	489	2961	58	128	29	98	51	3	13	389	51	11	5	12	9	0	68	45	88	29	110	14	72	44	1	3	3	1	0	4	2	1	101	11	0	4	0	59	10	275	38	7	29	272	47	20	0	17	13	8	10	0	122	799	32	17	25	3	10	35	2	149	21	81	19	5	0	31	167	22	4	114	64	12	24	0	44	61	38	37	19	61	19	164	673	51	6	203	88	44	8	0	6	2	4	0	7	12	0	2	5	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverage:14437.7997788
--- a/reactivity_cal/parse_dis_react.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-
-def parse_dist(in_file):
-    result = []
-    distribution = {}
-    name = []
-    f = open(in_file)
-    flag = 0
-    for aline in f.readlines():
-        line = aline.strip()
-        dis = line.strip()
-        dist = dis.split('\t')
-        if len(dist) > 0:
-            if len(dist) == 1:
-                if dist[0].strip().find('coverage')==-1:
-                    if flag == 0:
-                        name.append(line)
-                        flag = 1
-                        t_name = line
-                    else:
-                        distribution[t_name] = 'null'
-                        name.append(line)
-                        flag = 1
-                        t_name = line
-            else:
-                distri = []
-                for i in range(0, len(dist)):
-                    distri.append(dist[i].strip())
-                distribution[t_name] = distri
-                flag = 0
-    result.append(name)
-    result.append(distribution)
-    f.close()
-    return result
-                
-                
-
-
-
-
-
-
-
-        
-
-
-
-
-
--- a/reactivity_cal/rRNA.txt	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->25s rRNA 3375nts
-GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACTAACAAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAGAGCCCAGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGGAAAGGGGCGCCAGAGAGGGTGAGAGCCCGTCGTGCCCGGACCCTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGCAGCCCCAATCGGGCGGTAAATTCCGTCCAAGGCTAAATACGGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGTAAAGATGAAAAGGACTTTGAAAAGAGAGTCAAAGAGTGCTTGAAATTGTCGGGAGGGAAGCGGATGGGGGCCGGCGATGCGTCCTGGTCGGATGCGGAACGGAGCAATCCGGTCCGCCGATCGATTCGGGGCGTGGACCGACGCGGATTACGGTGGCGGCCTAAGCCCGGGCTTTTGATACGCTTGTGGAGACGTCGCTGCCGTGATCGTGGTCTGCAGCACGCGCCTAACGGCGTGCCTCGGCATCAGCGTGCTCCGGGCGTCGGCCTGTGGGCTCCCCATTCGACCCGTCTTGAAACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTGGCGGGATCCTCGCGGGTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGTGAGCATGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGTAAAGCCAGAGGAAACTCTGGTGGAAGCCCGCAGCGATACTGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGGACGCGAGTTCTATCGGGTAAAGCCAATGATTAGAGGCATTGGGGGCGCAACGCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACGTGTCGGCTGCTTTGTTGAGCCGTCACACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGGAAGCCGGGTTACGGTGCCCAACTGCGCGCTAACCTAGAACCCACAAAGGGTGTTGGTCGATTAAGACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATGGCGCTTAAGCGCGACCTATACCCGGCCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGGGCGCGGCGGTCGCTGCAAAACCTAGGGCGCGAGGCGCGGAGCGGCCGTCGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGGCGCCCTTGAAAATCCGGAGGACCGAGTGCCGCTCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTTCCGAACCCGTCGGCTGTCAGCGGACTGCTCGAGCTGCTTCCGCGGCGAGAGCGGGTCGCCGGCTGCCGGCCGGGGGACGACTGGGAACGGCTCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGCAAGTGAAATACCACTACTTTTAACGTTATTTTACTTACTCCGTGAATCGGAGGCCGGGGTACAACCCCTGTTTTTGGTCCCAAGGCTCGCTTCGGCGGGTCGATCCGGGCGGAGGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGTGTTGGATTGTTCACCCACCAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGCCCGCGTCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGAAGCGACGCATGCGCCCGCCGCCCGATTGCCGACCCTCAGTAGGAGCTTAGGCTCCAAAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAACGGTCGTTCGGACCGCCTTGAATTATAATTACCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAAGTGGCAGAGTGGCCTTGCTGCCACGATCCACTGAGATTCAGCCCTTTGTCGCTAAGATTCGA
->gi|20197903:2706-4513 Arabidopsis thaliana chromosome 2 BAC F23H14 genomic sequence, complete sequence
-TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACGAATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTAACTACTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGGCCTACCATGGTGGTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATAAATAACAATACTGGGCTCTTTCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCCCTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTATAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAATGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAGGCATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTTTAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAGTGTTCGGATCGCGGCGACGTGGGTGGTTCGCCGCCCGCGACGTCGCGAGAAGTCCACTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTG
->Arabidopsis thaliana 1
-GGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCATCCCTC
->gi|186498419|ref|NR_022453.1| Arabidopsis thaliana (AT2G01020) rRNA
-AAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAA
\ No newline at end of file
--- a/reactivity_cal/react_cal.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-from Bio import SeqIO
-import math
-from parse_dis_react import *
-from react_norm_function import *
-import os
-import random
-import string
-
-
-dist_file1 = sys.argv[1] #plus library
-dist_file2 = sys.argv[2] #minus library
-seq_file = sys.argv[3] #Reference library(genome/cDNA)
-nt_spec = sys.argv[4] #only show reactivity for AC or ATCG
-flag_in = sys.argv[5] # perform 2-8% normalization (1) or not (0)
-threshold = sys.argv[6] #Threshold to cap the reactivities
-output_file = sys.argv[7]
-
-
-distri_p = parse_dist(dist_file1)
-distri_m = parse_dist(dist_file2)
-threshold = float(threshold)
-
-
-syspathrs = os.getcwd()
-
-h = file(syspathrs+"react.txt",'w')
-flag_in = int(flag_in)
-
-seqs = SeqIO.parse(open(seq_file),'fasta');
-nt_s = set()
-for i in range(len(nt_spec)):
-    nt_s.add(nt_spec[i])
-
-flag = 0
-trans = []
-distri_p = distri_p[1]
-distri_m = distri_m[1]
-
-#thres = int(threshold)
-
-
-transcripts = {}
-for seq in seqs:
-    n = seq.id
-    trans.append(n)
-    transcripts[n] = seq.seq.tostring()
-    
-
-#print(distri_p)
-        
-
-for i in range(0, len(trans)):
-    h.write(trans[i])
-    h.write('\n')       
-    for j in range(len(distri_p[trans[i]])):
-        distri_p[trans[i]][j] = math.log((int(distri_p[trans[i]][j])+1),math.e)
-    for j in range(len(distri_m[trans[i]])):
-        distri_m[trans[i]][j] = math.log((int(distri_m[trans[i]][j])+1),math.e)       
-    s_p = sum(distri_p[trans[i]])
-    s_m = sum(distri_m[trans[i]])
-    length = len(distri_p[trans[i]])
-    if s_p!= 0 and s_m!= 0:
-        r = []
-        for j in range(0, len(distri_p[trans[i]])):
-            f_p = (float(distri_p[trans[i]][j]))/float(s_p)*length
-            f_m = (float(distri_m[trans[i]][j]))/float(s_m)*length
-            raw_react = f_p-f_m
-            r.append(max(0, raw_react))
-                
-    if s_p!= 0 and s_m!= 0:    
-        for k in range(1,(len(r)-1)):
-            if transcripts[trans[i]][k-1] in nt_s:
-                h.write(str(r[k]))
-                h.write('\t')
-            else:
-                h.write('NA')
-                h.write('\t')
-        k = k+1
-        if transcripts[trans[i]][k-1] in nt_s:
-            h.write(str(r[k]))
-            h.write('\n')
-        else:
-            h.write('NA')
-            h.write('\n')
-            
-
-h.close()
-
-if flag_in:
-    react_norm((syspathrs+"react.txt"),output_file, threshold)
-else:
-    h_o = file(output_file, 'w')
-    f_i = open(syspathrs+"react.txt")
-    for aline in f_i.readlines():
-        h_o.write(aline.strip())
-        h_o.write('\n')
-os.system("rm -f "+syspathrs+"react.txt")
-
-#os.system("rm -r "+syspathrs)
-    
-     
-            
-    
-    
-        
-
-
-
-
-
-
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-
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-
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-
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-        
-
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-
-
--- a/reactivity_cal/react_norm_function.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-from Bio import SeqIO
-import math
-from parse_dis_react import *
-
-def cap(a,value):
-    if a>=value:
-        return value
-    else:
-        return a
-
-def react_norm(react_file, result_file, capped_value):
-    print("Normalizing.....")
-    react1 = parse_dist(react_file)
-    react = react1[1]
-    h = file(result_file, 'w')
-
-    capped = int(capped_value)
-
-    all_react = []
-
-
-    for t in react:
-        if react[t]!='null':
-            for i in range(len(react[t])):
-                if react[t][i]!='NA':                   
-                    all_react.append(float(react[t][i]))
-
-
-    all_react.sort(reverse = True)
-
-
-    eight = all_react[int(len(all_react)*0.02):int(len(all_react)*0.1)]
-    meight = sum(eight)/len(eight)
-
-    for t in react:
-        h.write(t)
-        h.write('\n')
-        if react[t]!='null':
-            for i in range((len(react[t])-1)):
-                if react[t][i]!='NA':
-                    h.write(str(cap((float(react[t][i])/meight),capped)))
-                else:
-                    h.write('NA')
-                h.write('\t')
-            if react[t][i+1]!='NA':
-                h.write(str(cap((float(react[t][i+1])/meight),capped)))
-            else:
-                h.write('NA')
-            h.write('\n')
-
-    h.close()
-        
-
-
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-        
-
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-
--- a/reactivity_cal/reactivity_calculation.xml	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<tool id="react_cal_pipeline" name="Reactivity Calculation" version="1.0">
-	<description></description>
-	<command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-                <requirement type="package" version="1.7.1">numpy</requirement>
-        </requirements>
-	<inputs>
-                <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/>
-		        <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/>
-                <param name="seq_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
-                <param name="nt_spec" type="select" label="Nucleotide specificity">
-                    <option value="AC">AC</option>
-                    <option value="ATCG">AUCG</option>
-                </param>
-                <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/>
-                <param name="threshold" type="float" value = "7" optional = "true" label="Threshold to cap the reactivities"/>
-	</inputs>
-	<outputs>
-		<data name="output" format="txt"/>
-	</outputs>
-    <tests>
-        <test>
-            <param name="dist_file1" value="dis_f_N1Ap_rrna.txt" />
-	        <param name="dist_file2" value="dis_f_N1Am_rrna.txt" />
-            <param name="seq_file" value="rRNA.txt" />
-            <param name="nt_spec" value="AC" />
-            <param name="flag_in" value="1" />
-            <param name="threshold" value="7" />
-	        <output name="output" file="DMS_reactivities.out" />
- 
-          </test>
-    </tests>
-
-	<help>
-
-
-**TIPS**:
-
------
-
-**Input**:
-
-* 1. RTSC files (Output of Get RT Stop Counts) for (+) and (-) library
-* 2. Reference file (fasta) used to map the reads to
-* 3. Nucleotide Specificity (Type of nucleotides to have reactivity, e.g. AC for DMS and ACTG for SHAPE)
-* [Optional]:
-* 1. A threshold to cap the structural reactivities. {Default: 7}
-* 2. Flag that determines whether to perform 2%-8% normalization {Default: Yes}
-
------
-
-**Output**:
-
-A text file with structural reactivity for each nucleotide (Reactivity file)
-
-
-
-	</help>
-</tool>
--- a/reactivity_cal/read_file.py	Mon Nov 24 18:21:30 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_t_file(in_file):
-    f = open(in_file);
-    result = [];
-    for aline in f.readlines():
-        temp = [];
-        tline = aline.strip();
-        tl = tline.split('\t');
-        for i in range(0, len(tl)):
-            temp.append(tl[i].strip());
-        result.append(temp);
-    f.close();
-    return result;
-
-