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changeset 5:7a8ddf1819b1 draft

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Uploaded
author tyty
date Mon, 15 Sep 2014 14:52:52 -0400
parents a292aaf51735
children 1a909794e94d
files predict/parse_dis_pac.py predict/predict_RNAs.py predict/predict_RNAs.xml predict/rRNA.txt predict/rRNA_react.txt predict/read_file.py predict/rtts_plot.py predict/tool_dependencies.xml reactivity_cal/.DS_Store reactivity_cal/parse_dis_react.py reactivity_cal/react_cal.py reactivity_cal/react_norm_function.py reactivity_cal/reactivity_calculation.xml reactivity_cal/read_file.py reactivity_cal/separate_rna.py reactivity_cal/tool_dependencies.xml
diffstat 16 files changed, 436 insertions(+), 301 deletions(-) [+]
line wrap: on
line diff
--- a/predict/parse_dis_pac.py	Mon Sep 15 14:52:43 2014 -0400
+++ /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 Sep 15 14:52:43 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-#RNA structure prediction & Output and illustrate reactivities
-
-import sys
-from parse_dis_pac import *
-from read_file import *
-from Bio import SeqIO
-import os
-from rtts_plot import *
-
-
-id_file = sys.argv[1]
-seq_file = sys.argv[2]
-output_file = sys.argv[4]
-
-
-flag = 0
-if sys.argv[3]!='None': #input reactivity file if provided
-    react_file = sys.argv[3]
-    react = parse_dist(react_file)
-    react = react[1]
-    flag = 1
-
-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+'/' 
-
-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)>10: #setup a limit of the number of sequence to be predicted
-    print("Number of sequences exceeds limitation!")
-    sys.exit(0)
-    
-
-#predict RNA structures
-os.system("mkdir "+syspath+"output_f")
-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:
-        f = file(syspath+"temp.txt", 'w')        
-        f.write('>'+id_s)
-        f.write('\n')
-        f.write(seqs[id_s])
-        f.close()
-        if flag == 0:
-            os.system("Fold "+syspath+"temp.txt"+" "+syspath+"output_f/"+id_s+".ct")
-        if flag == 1:
-            if id_s in react:
-                f = file(syspath+"constraint.txt",'w')
-                make_plot(react[id_s],id_s,(syspath+"output_f/")) #make a plot of the distribution of the reactivites of the input RNA
-                #h = file(syspath+"output_f/transcript_reactivities.txt", 'w')
-                #h.write(id_s)
-                #h.write('\n')
-                for j in range(0, (len(react[id_s]))):
-                    if react[id_s][j]!='NA':
-                        f.write(str(j+1))
-                        f.write('\t')
-                        f.write(str(react[id_s][j]))
-                        f.write('\n')
-                    #h.write(str(react[id_s][j])) #Output the reactivities
-                    #h.write('\t')
-                f.close()
-                #h.write('\n')
-                #h.write('\n')
-                os.system("Fold "+syspath+"temp.txt"+" -sh"+" "+syspath+"constraint.txt"+" "+syspath+"output_f/"+id_s+".ct")
-            else:
-                print(id_s+" not in the data of react!")
-        os.system("draw "+syspath+"output_f/"+id_s+".ct "+syspath+"output_f/"+id_s+".ps")
-    else:
-        print(id_s+" not in the data of sequences!")
-
-#Remove the unnecessary files
-os.system("tar -zcvPf "+output_file+" "+syspath+"output_f/"+"*.*")
-os.system("rm -f "+syspath+"temp.txt")
-os.system("rm -r "+syspath+"output_f")
-if flag == 1:
-    os.system("rm -f "+syspath+"constraint.txt")
- #   h.close()
-    
-    
-
-
-
--- a/predict/predict_RNAs.xml	Mon Sep 15 14:52:43 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +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">numpy</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"/>
-<!---
-        <conditional name="reactivity">
-            <param name="choose" type="select" label="Reactivity files exists?">
-                <option value="N">No</option>
-                <option value="Y">Yes</option>
-            </param>
-            <when value="Y">
-                <param name="reactivity_file" type="data" optional = "true" label="Reactivity"/>
-            </when>
-            <when value="N"/>
-        </conditional>  
-
--->		
-	</inputs>
-	<outputs>
-		<data name="output" format=".tgz"/>
-	</outputs>
-
-	<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
-* [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 Sep 15 14:52:43 2014 -0400
+++ /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/rRNA_react.txt	Mon Sep 15 14:52:43 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-gi|186498419|ref|NR_022453.1|
-0.0349942738544	0.219596062195	0.0958706408233	0.194395004716	0.165304592733	NA	0.649363521545	0.004703371147	NA	0.0	NA	0.0	NA	NA	0.226052814765	0.145104959196	0.235114323931	0.590973505942	NA	NA	0.671823965086	NA	0.600180467352	NA	0.0	NA	0.67204697444	NA	NA	0.0	NA	0.0	NA	0.0	NA	0.0	0.0905633447413	NA	0.0844580185128	NA	0.0	NA	NA	0.387056722073	0.063190678881	NA	0.302648296659	0.123623615737	0.0	NA	NA	0.288529445998	NA	0.0	NA	0.272682267617	1.18142319227	0.222698183429	NA	NA	0.0	NA	0.308507027145	NA	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	NA	1.09905990052	0.331081493258	NA	NA	NA	0.0	0.316741455	NA	0.152869347497	0.358830282006	NA	0.172524825658	0.0232297542077	0.397612802938	NA	NA	NA	0.591410529537	0.531312624449	0.0105725487651	0.0	0.544371401206	NA	0.764412925075	NA	1.31480559071	NA	NA	0.338476420086	NA	NA	NA	NA	0.315926121887	0.0	0.0	NA	0.0	0.708180867703	1.4961467391	NA	NA	NA	NA	0.664465128059	NA	0.0	0.0	0.562535200045	0.476678390556	2.19691885985	0.524311802546	NA	1.61857603596	0.0	NA	NA	0.0	NA	NA	NA	0.0	0.0	NA	1.46994373288	NA	NA	NA	0.0	0.0	0.0	NA	NA	0.0	NA	NA	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	0.0	0.0	0.0	0.0
-25s
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A	0.167954420125	0.0	0.0	NA	0.0	NA	1.25963308137	1.65490763074	0.349665039522	0.0	0.0	0.0	0.0	0.088135396391	NA	0.0	0.0	0.052063263328	1.10030351945	NA	NA	NA	0.0	0.0	0.0	NA	NA	NA	0.0	NA	NA	NA	NA	0.0	1.19282107102	NA	0.351500033721	0.0	NA	0.0	0.0	NA	0.0	NA	NA	NA	NA	0.639486692424	1.72246658214	1.27928669427	NA	1.79434484187	1.43487503629	NA	1.11459423067	1.28050635355	0.0	0.033808248598	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	0.037351845069	0.0	NA	0.0	NA	0.0	NA	NA	0.0	0.0	NA	0.0680509646718	0.0	NA	NA	NA	NA	NA	NA	0.216734779888	0.238453108898	0.0047777392186	NA	NA	0.0	0.0	NA	NA	NA	0.24091195962	NA	0.367136308324	NA	NA	NA	NA	NA	0.0364529921341	NA	NA	0.290430964122	NA	0.0292200666431	0.0	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	NA	0.376846428488	NA	NA	0.0538172630509	NA	0.478261010535	0.721287586992	0.582408590163	NA	NA	NA	0.41727516366	0.401127778986	0.723354419621	NA	0.095607199307	0.258806359595	0.0835986123205	0.0	0.0	NA	0.0	0.0	NA	NA	NA	NA	0.440304834094	0.265761431623	0.519660229692	NA	NA	NA	0.168302233778	NA	NA	NA	NA	0.157327271761	0.0	NA	NA	0.0	0.0	NA	0.0	0.0	NA	NA	NA	0.0924344002851	0.0	NA	0.0	NA	NA	0.375769028351	NA	NA	0.0446187487194	0.0	NA	NA	NA	NA	NA	0.516864204729	0.172416681072	0.0567192634098	0.0378721224169	0.00299445087817	0.0932354718163	0.0743292528517	0.0912629153496	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.992289703074	0.0	0.316404114911	0.107107875064	0.520226987768	NA	NA	0.0	NA	0.361658745396	NA	0.0	NA	NA	0.651767453937	NA	NA	0.373975972699	NA	NA	NA	NA	0.0	NA	1.38394570998	NA	0.0	1.00495180372	NA	NA	NA	0.284672456867	NA	NA	0.0	NA	NA	0.431826210178	0.0	0.0	NA	NA	NA	NA	0.0	0.0901844111313	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	1.33336901534	NA	NA	0.191191895748	1.4841175405	0.392189953008	1.45736007574	NA	0.311778885904	NA	NA	NA	NA	0.176831354715	0.673338414422	0.0443852672859	0.0929438936537	NA	0.0	NA	0.0	0.0	0.0	NA	0.0	0.0694646091221	NA	NA	NA	NA	NA	0.0	0.0	NA	0.192693932018	0.288541449812	NA	0.475655710856	NA	NA	0.388660038013	NA	0.00984462464751	NA	0.0	1.81119542895	1.58177307546	0.571881702456	NA	0.841799847816	NA	0.0	1.8803751819	1.55005205033	0.817218685186	NA	1.88597635494	1.3912539199	1.62016777444	NA	0.218813430261	NA	0.209125600132	NA	NA	NA	NA	NA	NA	0.00152129255625	0.0692149342689	0.482781374021	0.286646187881	0.116245486156	0.258681032169	0.0426374923982	NA	NA	NA	NA	1.19938393364	0.632277359129	0.551425712127	0.824991309934	NA	0.00546462277811	NA	0.0	NA	NA	NA	NA	NA	0.190663657047	NA	NA	0.0552614588428	NA	NA	0.340937408688	NA	NA	NA	NA	0.13847541988	0.20559094886	NA	NA	0.781555754406	0.0	NA	0.525171284317	0.436527075283	NA	0.0421028137972	0.0307349474561	NA	0.281933713892	0.0	0.629440274879	0.179786036677	NA	NA	NA	0.11835642342	0.198474100584	0.261444284574	NA	0.0	NA	NA	NA	NA	0.0	0.0	NA	0.26387724218	NA	0.0	NA	0.472854357389	NA	1.74976904497	0.87854869935	NA	NA	NA	0.0	NA	0.151450492281	0.0	NA	NA	0.0	NA	NA	0.351662153841	0.0	NA	NA	NA	NA	0.0701877141513	0.429452307682	NA	0.0	NA	0.0	NA	0.0	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.0	NA	NA	NA	0.0533163327192	0.0	0.0	0.0	0.0	0.0	NA	NA	NA	0.508254834906	NA	0.0	0.0	0.0	NA	NA	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.853405247499	NA	0.0	NA	NA	NA	0.0	0.0	NA	0.800049449505	NA	0.0	NA	0.0381971897849	0.0	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	NA	0.0	0.0	NA	NA	0.0	NA	0.653339817705	NA	NA	NA	0.0	NA	NA	0.0	NA	0.0	NA	NA	0.0	0.0	NA	0.0	NA	0.0	0.0	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	NA	0.678467855295	0.0	NA	NA	0.0	0.0	0.0	0.0	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	0.0	0.0	0.0	0.0	0.0	0.018664182086	0.0	0.0	0.0	0.0	NA	0.0	NA	NA	NA	0.0	0.121678706886	0.355299241427	NA	NA	NA	1.73293458871	NA	0.0493727138012	NA	NA	NA	NA	NA	NA	NA	0.0568785504168	NA	0.134312284659	0.0	0.0	NA	NA	0.0	NA	NA	NA	0.433579288967	NA	0.445397859363	0.0	0.975058935559	NA	NA	NA	NA	0.334019900058	NA	NA	NA	NA	NA	0.819899325822	0.0	0.0	0.0	NA	0.0	0.0	NA	NA	0.0	NA	NA	0.14790191642	0.355048973175	0.632457142469	NA	0.0885424973481	NA	NA	0.0	NA	0.245308306361	NA	1.45476259015	NA	0.461488242458	NA	NA	0.0403145742559	0.0669040008976	NA	NA	0.189059523364	0.223383021291	0.443345417968	0.302699986613	0.261935974538	NA	0.453463826854	NA	NA	0.281780796046	0.0	NA	0.222728714314	NA	0.496511941732	NA	NA	0.648092143251	0.867025205093	0.698984683105	0.342390556037	NA	NA	NA	NA	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	0.8816043907	0.0	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	NA	0.143927736109	NA	0.0	NA	NA	NA	NA	NA	NA	NA	0.0	0.643731475471	1.04357444649	0.662993815823	NA	0.0	0.0461426678103	0.0	NA	NA	NA	NA	0.0	NA	0.0	NA	0.0	0.033505630595	NA	0.0	NA	0.133469644664	0.0	0.234879130863	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	0.688130547851	NA	NA	0.732542656381	NA	NA	0.0	0.0	NA	NA	0.438119294374	0.558376720682	0.0	NA	0.918102306041	0.56240697358	NA	0.0	NA	0.237088351477	0.0	NA	NA	0.0	0.20233663462	NA	0.600412306412	0.183536339486	NA	0.0	0.0	NA	NA	NA	0.0	NA	0.0	NA	0.732387193297	0.63658249172	NA	0.010121757995	NA	0.0	0.0	NA	0.0	0.641739077143	NA	NA	0.0731629955416	NA	0.0	0.0	0.0	NA	0.0	0.0	NA	0.0	0.0	0.0	NA	0.0	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.0	NA	0.0	0.0	NA	NA	0.389549029322	NA	NA	0.0	NA	0.472854357389	NA	NA	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	0.0	0.37028839264	NA	NA	0.0	0.0481524671794	0.387465196563	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	0.0	NA	0.640486051737	0.354013107665	NA	NA	0.337971646441	0.0	NA	NA	NA	0.0	NA	NA	0.0	NA	NA	0.447020729153	0.309541139682	0.0	NA	NA	NA	0.686037910468	NA	NA	NA	0.3406752016	NA	NA	0.146691758883	0.0	0.0	NA	0.0	0.0	NA	NA	NA	0.913095760914	1.03984524992	NA	NA	0.868123808953	NA	0.273507880758	0.0	NA	NA	0.0	0.0562709433796	0.0	0.117755450683	1.09301118286	0.3406752016	NA	0.279937783278	NA	0.472854357389	NA	NA	0.0	NA	NA	NA	NA	1.1279640247	NA	2.021448478	0.0	NA	0.940786080429	1.03814311506	NA	NA	NA	NA	0.844770381547	0.661304456557	NA	0.741654233914	0.0	NA	0.0975430676565	0.0437438686722	NA	NA	0.594144441129	0.350319089768	1.93721008621	NA	1.22231078215	0.0	NA	0.0	NA	0.0	0.538436231703	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	0.0508327001275	0.279131420348	NA	NA	NA	NA	0.0	0.109423953351	NA	0.0	NA	NA	NA	NA	0.271679433027	0.0	NA	NA	NA	0.0	NA	NA	0.0	0.0	0.0	0.46793172304	NA	0.0	NA	0.0	0.0	0.0	0.0	NA	NA	0.749456424764	NA	0.0	NA	NA	0.472854357389	1.22231078215	NA	0.0	0.0	0.0	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	0.0	0.0	NA	0.0	NA	NA	0.0	NA
-Arabidopsis
-NA	NA	0.0	NA	NA	3.53700365182	NA	0.0	NA	0.0	0.0	NA	0.0	0.0	0.0	5.10017382764	NA	0.0	0.0	0.0	NA	0.0	0.0	NA	NA	0.0	0.0	0.0	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	1.04740785071	NA	0.751507319045	0.679065423588	NA	0.0	1.80093151001	0.0	NA	0.0	0.0	NA	0.0	0.0	NA	NA	NA	0.0	0.0	NA	2.35404575646	NA	NA	NA	4.93385220878	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	4.45571252703	NA	NA	0.0	NA	NA	0.0	0.0	NA	0.0	NA	NA	0.0	NA	NA	NA	NA	NA	NA	4.93385220878	0.0	0.0	NA	0.0	0.0	NA	NA	NA	NA	0.0	0.0	NA	NA	0.0	0.0	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	NA
-gi|20197903:2706-4513
-NA	0.012685795205	0.0	0.0	NA	NA	NA	NA	NA	NA	0.369865767367	NA	0.0	0.0	NA	NA	0.0	0.0	0.0	NA	NA	0.291074839291	NA	NA	0.0	0.0779489717102	NA	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0	NA	0.388739681544	0.607358801578	0.86505141743	0.419532419715	NA	0.775525397956	NA	NA	0.418634405395	0.310232647615	NA	0.0	0.0	0.51629506558	NA	NA	0.0	0.435316902631	NA	NA	NA	NA	NA	0.406071541412	0.102260948087	NA	NA	1.02827139604	NA	NA	0.555559168062	0.301220165622	0.0	NA	0.428351005927	0.0	NA	NA	0.0942381418988	0.340249958839	NA	0.402129377649	0.639234686516	NA	NA	NA	NA	0.935138133481	0.0592665799408	0.143289116981	0.0473507766862	NA	NA	0.0	NA	0.0266155577151	0.0982764742903	NA	NA	NA	0.0	NA	0.0	0.11309561083	NA	NA	0.628690973329	0.479906074642	0.102631619096	NA	0.0	0.434378189774	NA	NA	NA	0.0807132307206	NA	0.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.359209156119	NA	NA	NA	NA	0.648363725715	1.00111919062	1.04262692243	NA	0.755897037378	0.819932067068	NA	0.455162779021	1.20773264872	NA	0.0	NA	NA	0.296441851982	NA	0.37547834061	0.357493014857	0.0258046929258	0.0	NA	NA	0.505600332852	NA	NA	0.215493760216	0.137308939841	NA	NA	0.0	NA	0.327508086131	NA	0.0	NA	0.0	NA	0.110060629173	0.144925722316	NA	0.181195205113	0.198697622929	NA	NA	NA	0.430508890438	0.615380473507	0.413085955445	0.213399108191	0.970869271469	0.940875618616	0.816055880816	0.400666932367	0.0	0.0368366876912	0.0	NA	0.982940202181	0.0152093127598	NA	NA	0.772061687224	NA	NA	NA	0.524486960169	1.14258931334	NA	NA	NA	0.772909687503	0.350161317332	NA	0.0	0.339428903455	NA	NA	NA	0.289638535352	NA	NA	0.301380368516	NA	0.186709719344	NA	0.723493077315	0.549043071946	0.368933272512	0.346567668516	NA	NA	NA	0.0736517765796	NA	0.225216490874	0.0	NA	0.0	NA	NA	NA	0.282065581517	NA	0.0622206275738	NA	NA	0.0	0.0	0.0	NA	NA	NA	NA	0.0979798698289	NA	0.418716246672	NA	NA	0.127229218645	NA	NA	0.122048875919	NA	NA	0.0	0.459466284108	NA	NA	0.22611651355	NA	0.257988938793	0.242043547687	0.0445554892629	NA	0.0	NA	0.211377998276	0.0539458902463	NA	NA	0.705263055871	NA	0.122896017727	NA	0.0	0.364816537092	NA	NA	NA	0.0	0.0	NA	0.0	NA	NA	NA	NA	0.0	NA	NA	NA	0.134627940359	NA	0.384818842789	0.0	NA	0.0	0.298065186972	NA	0.0	0.148933065236	NA	NA	0.108571364914	0.245360133204	0.412047373188	0.0776738288945	NA	NA	NA	0.0	NA	NA	0.385371255467	0.0134780068585	0.186653352588	NA	0.670459919659	NA	0.0	0.163864042171	0.13720252139	0.0	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	NA	0.0	NA	NA	0.0478979106433	NA	0.0	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.215656364652	NA	NA	NA	NA	NA	NA	NA	0.676399501898	0.444238412823	0.0	NA	NA	NA	NA	NA	0.402502781349	0.324546337434	NA	NA	0.72428064676	NA	0.365349818072	0.282000801415	NA	NA	0.825136824379	NA	NA	NA	NA	NA	0.0	NA	0.285295564149	NA	NA	0.215476057191	0.182212745127	NA	NA	0.146330023967	NA	0.421564261825	NA	NA	NA	0.353084055047	NA	0.0	0.0	NA	NA	0.0	NA	0.236357075379	0.0	0.244357718994	0.128121995322	NA	NA	0.175198188965	NA	0.218494857155	0.0	0.0	0.00451933044375	0.0	0.927212739519	NA	0.132103213724	0.0	0.740927800969	0.957180040116	NA	NA	0.656796842311	0.580572417551	NA	NA	0.0	0.0	NA	0.0	0.0563230505075	NA	NA	0.120005485202	NA	0.226509753369	NA	0.0	0.471160925233	0.0877285693903	0.768176413935	NA	NA	0.235484190643	0.0	0.0	0.118062685793	0.419161295576	0.135347828419	NA	0.219059490441	0.426910429649	NA	NA	0.971233728998	0.0	0.0	0.48732449835	NA	NA	NA	NA	0.24138759394	NA	NA	NA	0.253899493465	NA	NA	NA	0.825841393383	0.82831906089	0.0	0.0717935208264	NA	0.279778367449	0.282811723237	0.229633772945	NA	0.0	0.0	0.0	0.509924844919	0.429039400771	NA	0.283392930386	0.0	NA	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	0.117058667345	NA	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0965635309754	0.092863243134	NA	NA	NA	NA	1.04941610567	1.19161444221	NA	NA	1.7376246406	NA	NA	0.391195828095	0.375473658421	0.433647125904	0.279359521091	NA	0.501405696729	NA	0.687660733308	0.864175250339	0.79158652207	NA	1.20320006049	0.56311253719	0.253888387685	NA	NA	1.83397160852	1.53706044242	0.961584043251	NA	0.784802938308	NA	NA	1.28330857645	NA	0.268894203299	0.314451464739	0.423300010695	NA	NA	NA	NA	0.259483681982	NA	NA	NA	1.26295217444	0.661502700034	0.652566369353	NA	NA	0.500429839944	NA	NA	NA	NA	NA	0.103898205626	0.255468262008	0.163276078797	NA	0.48540533193	0.395593446683	NA	0.2174452409	0.101616378857	NA	0.205131663835	NA	NA	NA	1.31997685379	0.753084647947	NA	NA	0.0519500996846	0.387428790866	0.34011021097	NA	0.0748065258161	NA	0.0580149462222	0.0768278927631	0.158589807897	0.25491474666	NA	0.347714135251	NA	0.11241524085	NA	NA	0.336941565822	NA	0.0887724160932	NA	NA	NA	0.916896362256	0.278780105213	NA	NA	NA	NA	NA	NA	NA	0.115173560016	0.31061772735	NA	NA	NA	0.486301566768	0.347179567168	0.617356828937	0.444803810174	0.408511448093	NA	0.0782866766856	NA	0.0	NA	NA	0.515740275652	NA	NA	NA	NA	0.61541889439	0.97298662914	0.462906210807	0.542827568418	NA	NA	NA	NA	NA	0.694038563065	NA	NA	NA	NA	NA	0.109092812624	NA	NA	0.0	0.117730829926	NA	NA	NA	0.134948233631	0.152419220299	NA	0.0511684766977	0.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.445995841454	0.47369948038	NA	NA	NA	NA	NA	0.040184020931	NA	NA	0.0	NA	NA	NA	NA	0.183024542293	0.464959665882	0.0240688858908	NA	NA	0.261038892925	NA	NA	NA	0.0905114061626	NA	NA	0.330123652207	NA	0.547654296191	NA	0.148523577717	0.0353180022104	NA	0.710181117619	NA	0.0	0.0498588966609	NA	NA	NA	NA	0.037765972332	NA	NA	0.293764451656	0.0	NA	NA	NA	NA	0.0	0.0	NA	NA	NA	NA	0.2319218601	NA	NA	NA	0.0	0.0007880491039	NA	0.0	0.0	NA	NA	0.484697941103	NA	0.48957925096	NA	NA	NA	NA	0.178775276637	0.0	NA	NA	NA	NA	0.204280518962	0.138427143763	NA	0.226834291993	0.582955027497	0.221502626079	NA	NA	0.172379156747	NA	0.00774474492492	NA	NA	NA	0.0	NA	0.0	0.0812527197534	0.139070064757	0.826428013686	NA	0.0	0.566373614269	0.297167065861	NA	0.0	0.43208771255	NA	0.585964397663	0.264915308651	NA	0.173247086337	NA	0.764112125968	NA	NA	NA	0.965842425791	NA	0.346877570077	0.0	0.400547148974	NA	NA	0.0400887452555	NA	0.0	0.0	NA	NA	NA	NA	0.233593147394	NA	0.238066822223	0.35044287177	0.0	1.22637073435	NA	0.588880241101	1.28674125846	NA	0.816194027366	NA	NA	0.21624168024	NA	NA	NA	0.0	NA	0.460702630062	NA	0.0844162750446	0.213999087673	NA	0.543841759443	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.0682752748169	0.0	NA	NA	0.0	NA	NA	NA	0.234279937188	NA	0.174056981406	NA	NA	0.085017264826	NA	NA	0.153333534594	0.0	NA	NA	0.703295059249	NA	NA	0.0	0.0	0.0	0.0216527294522	NA	NA	NA	0.0	0.0	0.0	NA	NA	0.0190758579281	NA	NA	NA	NA	NA	0.0	0.167793515723	NA	NA	0.0	NA	NA	0.0	NA	NA	NA	0.0	0.0	NA	0.0	NA	NA	0.0	0.0562847889823	NA	0.460573683496	NA	NA	NA	NA	0.223670417655	0.233256106881	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0	NA	NA	NA	0.0	NA	NA	0.084028304493	0.505561356557	0.0623049297976	NA	0.0	0.0	NA	0.833699137957	0.403279901024	0.0	0.0	0.0322768659755	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	NA	0.0	0.00045836350462	NA	NA	NA	NA	0.0	0.0	0.0	0.0	NA	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	NA	0.193128657755	0.0	NA	0.0	0.899536353647	0.363201566969	NA	0.0	0.0	0.0	NA	0.0	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	0.0	0.110477671057	NA	0.0	0.0	NA	0.0	NA	0.0	0.0	NA	0.182880927986	NA	0.108818565811	0.0	0.0	NA	NA	0.0	0.0	NA	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	0.0	0.0	0.0	NA	0.0	0.0	0.0	0.0	NA	0.0210625394541	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.0	NA	NA	NA	0.0	NA	0.0	0.0	NA	0.0	NA	NA	0.0	NA	NA	NA	NA	NA	0.0385781896847	NA	NA	0.0	NA	0.0	NA	NA	0.0	0.0	NA	0.0	0.0	NA	0.0	NA	NA	NA	0.0	0.0	0.0	0.0	NA	NA	0.0554462223962	NA	NA	0.0	NA	0.0	0.0	0.0	NA	0.0	0.0	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	NA	NA	NA	NA	NA	0.0	NA	NA	0.446085727425	NA	NA	NA	NA	0.0	NA	0.0	0.0	0.0	NA	NA	0.0	NA	NA	0.146663316857	0.0	0.0	0.0	NA	NA	0.0	0.285522876287	1.41360776485	NA	NA	0.188205541415	0.0	NA	NA	NA	0.0453327030088	0.0	NA	NA	0.0	0.0492143521014	NA	NA	NA	0.0	0.0	0.0291224196667	0.0	0.0	0.0	0.0	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0	NA	0.206914122658	0.0	NA	NA	0.0839474875882	NA	NA	0.0	NA	NA	0.134142893649	0.0	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.820586591704	0.0	0.0	0.0	0.386179006774	NA	NA	NA	NA	0.103032523431	0.0518166812743	0.0	0.120233931127	NA	NA	0.0	0.0	0.0	0.366525621541	NA	NA	NA	0.164870879261	0.0	1.38881890967	NA	0.404286868276	0.0	0.0	NA	0.178472663189	NA	NA	1.31563377475	1.30805369088	NA	NA	0.46978614339	NA	NA	NA	0.390001422112	0.333118860081	0.562108250761	NA	0.946892023632	0.448824683197	NA	NA	0.635745699413	NA	0.46622236075	NA	1.57309356534	NA	0.784800876851	NA	NA	NA	0.516184760729	NA	NA	NA	0.434129860905	NA	NA	0.0250374027677	NA	0.403626419597	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.374841885012	0.340220603837	NA	NA	NA	0.0	0.263065361814	NA	NA	NA	0.269610329411	NA	NA	0.317151321718	NA	NA	NA	NA	NA	NA	NA	NA	0.258599594016	NA	0.110617236497	NA	0.0	NA	NA	NA	NA	NA	0.324479568493	NA	NA	NA	NA	NA	0.325987512869	0.250209550258	NA	NA	0.0774563184444	0.112366803266	NA	NA	NA	0.102919447072	0.123330374332	NA	NA	0.348326050915	0.224773446775	0.0	NA	0.0808889707107	NA	0.214762378779	0.0287355857736	0.0	NA	0.252725257437	0.314236062616	NA	0.0554561654111	0.056815664406	NA	NA	0.345500702375	NA	0.0588579499196	0.0105952720591	0.0456298120613	NA	0.115106069305	NA	0.0199334602017	NA	0.577423401418	0.0462313906594	NA	NA	NA	NA	0.265048014067	NA	NA	0.419418099209	0.113243020283	NA	0.376066546077	0.208296306638	0.0	NA	NA	0.0	0.363219015946	0.198400194261	NA	NA	0.14356423081	0.379033229976	NA	NA	0.0	NA	NA	0.0	NA	NA	0.285411491071	NA	0.343270380421	NA	NA	NA	0.154003422396	0.0913176962236	NA	0.414093438881	NA	NA	NA	0.0	0.216108105084	NA	NA	NA	NA	0.405657537386	NA	NA	0.0	0.0	0.398647870694	0.466721779026	NA	NA	0.362549468307	0.0	NA	NA	NA	NA	NA	0.078297350411	NA	NA	0.0	0.52712134107	0.210547080514	NA	0.084029706675	0.0851834255013	0.0	0.546016042147	NA	NA	NA	0.0	NA	NA	NA	NA	0.210098470701	NA	NA	0.00513323027424	0.0	0.0	NA	NA	0.0872105330697	NA	0.173770776458	NA	NA	NA	NA	0.0	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0530451107643	0.0	NA	0.0	NA	0.0	NA	0.0	NA	0.0	0.0	0.0314542857359	0.0	NA	NA	0.0	NA	NA	NA	0.0	NA	NA	0.0	0.0	0.184888572061	0.0	NA	0.299087013424	NA	NA	NA	0.253824308291	0.476498867804	0.637367560491	0.557762304345	0.0424647165889	0.0227038975612	NA	NA	NA	NA	0.0	0.164048813678	NA	0.174332609454	0.0887971281539	0.517338202643	NA	NA	0.0	0.0	0.0356275913231	NA	NA	NA	NA	0.219870784412	0.16181267273	NA	0.0254540277981	NA	NA	NA	NA	0.0136899888528	0.0	0.0	NA	NA	NA	0.0	0.0	NA	0.0	NA	NA	NA	0.124832560383	NA	NA	NA	NA	NA	0.291168607862	NA	0.0	NA	0.0	NA	0.0	0.0	NA	NA	NA	0.0	0.0927979100847	0.300974630983	NA	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	0.0704858304923	0.0	0.0	0.0	NA	0.0	NA	NA	0.0835696851504	0.0518565943435	NA	NA	0.0	0.0335320265405	NA	0.0	NA	NA	0.12361132429	0.0692121040509	NA	0.0	NA	0.260064432493	NA	0.0959604666378	NA	NA	0.0	0.0904897461535	NA	0.096024873638	0.551806072603	NA	0.0	NA	0.0	NA	0.282845890039	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.206168383343	NA	NA	0.0337910137675	0.237818480755	0.0	NA	NA	0.0	0.0	0.0	NA	NA	NA	NA	NA	0.177374574	0.0	0.0	0.100596272282	0.340124774949	0.336749926715	0.0	NA	0.0	0.0	0.0	NA	NA	0.0	NA	0.0	NA	0.0	0.0	NA	0.0	0.0	0.0	NA	0.0	NA	NA	NA	0.0	0.0	NA	NA	0.0	NA	0.0	0.0	NA	NA	NA	NA	0.226897983481	0.0	NA	NA	NA	NA	NA	0.0	NA	NA	0.0734972121117	NA	0.0	NA	0.572649935308	NA	NA	0.383893601435	NA	0.0628733418693	0.296329616229	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.255561953725	NA	0.0	0.157858376637	NA	0.393736372309	0.0	0.119742668772	NA	0.393736372309	NA	1.01428769186	0.0	NA	NA	0.272044062708	NA	0.733760005611	NA	0.0660086032582	NA	0.900327296663	0.879392059123	NA	NA	0.0898683975317	0.0	0.0	0.0	NA	0.377579916714	1.12452142695	0.0	1.64185114287	0.029392400791	NA	NA	0.0	NA	0.490308287953	0.0	NA	NA	NA	0.0	NA	0.980828030569	NA	NA	0.746093235966	0.0	NA	NA	0.0	NA	0.54743287524	0.821826359884	NA	NA	0.720669950832	NA	NA	0.746435235532	0.0	0.0	0.852194994485	0.496018177117	NA	NA	NA	NA	NA	0.914227544844	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0	0.0	0.0	0.0	NA	NA	0.0	NA	NA	0.0	0.0	NA	NA	0.0	NA	0.0	0.0	NA	NA
--- a/predict/read_file.py	Mon Sep 15 14:52:43 2014 -0400
+++ /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 Sep 15 14:52:43 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-#Make a plot of reactivity distribution
-
-import sys
-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('DMS 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
-    ax.set_xticks(np.arange(0,N,intervel*tail))
-    print(np.arange(0,N,intervel*tail))
-    ax.set_xticklabels(np.arange(0,N,intervel*tail))
-
-    ax.set_title(id_s+" reactivity distribution")
-    savefig(path+id_s+'.tif')
-
-
-
-    
-    
-    
-
-
--- a/predict/tool_dependencies.xml	Mon Sep 15 14:52:43 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.61">
-        <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.7">
-        <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
Binary file reactivity_cal/.DS_Store has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/parse_dis_react.py	Mon Sep 15 14:52:52 2014 -0400
@@ -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
+                
+                
+
+
+
+
+
+
+
+        
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_cal.py	Mon Sep 15 14:52:52 2014 -0400
@@ -0,0 +1,151 @@
+#!/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
+
+
+dist_file1 = sys.argv[1] #plus library
+dist_file2 = sys.argv[2] #minus library
+seq_file = sys.argv[3]
+nt_spec = sys.argv[4]
+flag_in = sys.argv[5]
+threshold = sys.argv[6]
+output_file = sys.argv[7]
+
+
+distri_p = parse_dist(dist_file1)
+distri_m = parse_dist(dist_file2)
+threshold = float(threshold)
+
+print(flag_in)
+
+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+'/' 
+
+h = file(syspath+"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')
+    if (trans[i].find('AT1G29930')==-1) and (trans[i].find('At1g29930')==-1):        
+        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))
+    else:
+        for j in range(len(distri_p[trans[i]])):
+            distri_p[trans[i]][j] = int(distri_p[trans[i]][j])
+        for j in range(len(distri_m[trans[i]])):
+            distri_m[trans[i]][j] = int(distri_m[trans[i]][j])       
+        s_p = sum(distri_p[trans[i]])
+        s_m = sum(distri_m[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)
+                f_m = float(distri_m[trans[i]][j])/float(s_m)
+                r.append((max(0,(f_p-f_m)))*100)
+                
+    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((syspath+"react.txt"),output_file, threshold)
+else:
+    h_o = file(output_file, 'w')
+    f_i = open(syspath+"react.txt")
+    for aline in f_i.readlines():
+        h_o.write(aline.strip())
+        h_o.write('\n')
+os.system("rm -f "+syspath+"react.txt")
+    
+     
+            
+    
+    
+        
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+        
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_norm_function.py	Mon Sep 15 14:52:52 2014 -0400
@@ -0,0 +1,114 @@
+#!/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]))
+#                    except:
+#                        print(react[t][i])
+#                        print(t)
+#                        print(i)
+
+    all_react.sort(reverse = True)
+    #print((all_react))
+    #print(all_react[int(len(all_react)*0.02)])
+    #print(all_react[int(len(all_react)*0.03)])
+    #print(all_react[int(len(all_react)*0.025)])
+    #print(all_react[int(len(all_react)*0.04)])
+    #print(all_react[int(len(all_react)*0.05)])
+    '''
+    mean = sum(all_react)/len(all_react)
+    print(mean)
+    temp = 0
+
+    for i in range(len(all_react)):
+        temp = temp+all_react[i]*all_react[i]
+    temp = temp/len(all_react)
+    sd = math.sqrt(temp-mean*mean)
+    '''
+    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':
+            if (t.find('AT1G29930')==-1) and (t.find('At1g29930')==-1):
+                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')
+            else:
+                for i in range((len(react[t])-1)):
+                    if react[t][i]!='NA':
+                        h.write(str(float(react[t][i])*2.6))
+                    else:
+                        h.write('NA')
+                    h.write('\t')
+                if react[t][i+1]!='NA':
+                    h.write(str(float(react[t][i])*2.6))
+                else:
+                    h.write('NA')
+                h.write('\n')
+                
+                
+
+    h.close()
+        
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+        
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/reactivity_calculation.xml	Mon Sep 15 14:52:52 2014 -0400
@@ -0,0 +1,48 @@
+<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">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 library"/>
+                <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="Value to cap the reactivities"/>
+	</inputs>
+	<outputs>
+		<data name="output" format="txt"/>
+	</outputs>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**:
+
+* 1. RTSC files (Output of II) for (+) and (-) library
+* 2. Reference file (fasta) used to map the reads
+* 3. Nucleotide Specificity (Type of nucleotide 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/read_file.py	Mon Sep 15 14:52:52 2014 -0400
@@ -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;
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/separate_rna.py	Mon Sep 15 14:52:52 2014 -0400
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from parse_dis_pac import *
+
+
+dist_file = sys.argv[1]
+cdna_file = sys.argv[2]
+rrna_file = sys.argv[3]
+
+dist = parse_dist(dist_file)
+dist = dist[1]
+hc = file(cdna_file, 'w')
+hr = file(rrna_file, 'w')
+
+for t in dist:
+    if t.find('AT') != -1:
+        hc.write(t)
+        hc.write('\n')
+        for i in range(len(dist[t])-1):
+            hc.write(dist[t][i])
+            hc.write('\t')
+        i = i+1
+        hc.write(dist[t][i])
+        hc.write('\n')
+    else:
+        hr.write(t)
+        hr.write('\n')
+        for i in range(len(dist[t])-1):
+            hr.write(dist[t][i])
+            hr.write('\t')
+        i = i+1
+        hr.write(dist[t][i])
+        hr.write('\n')
+
+hc.close()
+hr.close()
+
+    
+        
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/tool_dependencies.xml	Mon Sep 15 14:52:52 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="biopython" version="1.61">
+        <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.7">
+        <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>