# HG changeset patch
# User tyty
# Date 1418112191 18000
# Node ID 1c325ff557d93db7e9d2b18305ade522b1020038
# Parent 11f0f526dca9e707416af375d330b1e4bed6f68c
Uploaded
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/iterative_map.py
--- a/Iterative_mapping/iterative_map.py Tue Dec 09 03:02:49 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +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()
-syspathrs = syspathrs+'/'
-
-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 "+syspathrs+"combine.bam"+" "+ss)
-os.system("samtools sort "+syspathrs+"combine.bam sorted")
-os.system("samtools view -b -h sorted.bam > " + output_file)
-#print("samtools merge mapped_all.bam"+ss)
-os.system("rm "+syspathrs+"mapped*.bam")
-os.system("rm "+syspathrs+"combine.bam")
-os.system("rm "+syspathrs+"sorted.bam")
-os.system("rm "+syspathrs+"ref*")
-#os.system("rm -r "+syspathrs)
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/iterative_map.xml
--- a/Iterative_mapping/iterative_map.xml Tue Dec 09 03:02:49 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-
-
-
- #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
-
-
- biopython
- numpy
- samtools
- bowtie
-
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-
-
-**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
-
-
-
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/map_ex.py
--- a/Iterative_mapping/map_ex.py Tue Dec 09 03:02:49 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()
-
-
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/rRNA.txt
--- a/Iterative_mapping/rRNA.txt Tue Dec 09 03:02:49 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
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/read_file.py
--- a/Iterative_mapping/read_file.py Tue Dec 09 03:02:49 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;
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/read_file.pyc
Binary file Iterative_mapping/read_file.pyc has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/read_s_file.py
--- a/Iterative_mapping/read_s_file.py Tue Dec 09 03:02:49 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;
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/read_s_file.pyc
Binary file Iterative_mapping/read_s_file.pyc has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/remove_map.py
--- a/Iterative_mapping/remove_map.py Tue Dec 09 03:02:49 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()
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/sample.fasta
--- a/Iterative_mapping/sample.fasta Tue Dec 09 03:02:49 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
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/seq_track.py
--- a/Iterative_mapping/seq_track.py Tue Dec 09 03:02:49 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()
-
-
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/truncate.py
--- a/Iterative_mapping/truncate.py Tue Dec 09 03:02:49 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()
-
-
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 Iterative_mapping/unmap.py
--- a/Iterative_mapping/unmap.py Tue Dec 09 03:02:49 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()
-
-
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 get_reads/get_read.py
--- a/get_reads/get_read.py Tue Dec 09 03:02:49 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()
-
-
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 get_reads/get_read.xml
--- a/get_reads/get_read.xml Tue Dec 09 03:02:49 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-
-
- get_read.py $lib_file $map_file $output
-
- biopython
- numpy
- samtools
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**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)
-
-
-
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 get_reads/read_file.py
--- a/get_reads/read_file.py Tue Dec 09 03:02:49 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;
-
-
diff -r 11f0f526dca9 -r 1c325ff557d9 get_reads/read_file.pyc
Binary file get_reads/read_file.pyc has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 get_reads/test.bam
Binary file get_reads/test.bam has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/.DS_Store
Binary file reactivity_cal/.DS_Store has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/._.DS_Store
Binary file reactivity_cal/._.DS_Store has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/parse_dis_react.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/parse_dis_react.py Tue Dec 09 03:03:11 2014 -0500
@@ -0,0 +1,51 @@
+#!/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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/parse_dis_react.pyc
Binary file reactivity_cal/parse_dis_react.pyc has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/rRNA.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/rRNA.txt Tue Dec 09 03:03:11 2014 -0500
@@ -0,0 +1,8 @@
+>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
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/react_cal.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_cal.py Tue Dec 09 03:03:11 2014 -0500
@@ -0,0 +1,135 @@
+#!/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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diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/react_norm_function.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_norm_function.py Tue Dec 09 03:03:11 2014 -0500
@@ -0,0 +1,82 @@
+#!/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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diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/react_norm_function.pyc
Binary file reactivity_cal/react_norm_function.pyc has changed
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/reactivity_calculation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/reactivity_calculation.xml Tue Dec 09 03:03:11 2014 -0500
@@ -0,0 +1,60 @@
+
+
+ react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output
+
+ biopython
+ numpy
+
+
+
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+
+
+**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)
+
+
+
+
+
diff -r 11f0f526dca9 -r 1c325ff557d9 reactivity_cal/read_file.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/read_file.py Tue Dec 09 03:03:11 2014 -0500
@@ -0,0 +1,21 @@
+#!/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;
+
+
diff -r 11f0f526dca9 -r 1c325ff557d9 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Dec 09 03:02:49 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-
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