| Previous changeset 2:82770f07a036 (2018-07-10) Next changeset 4:8f6469ffef85 (2018-07-19) |
|
Commit message:
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy |
|
modified:
Tryp_G.py Tryp_V.py VAP.xml data/congodata.csv data/congodata_deviationfromthemean.csv |
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removed:
data/ogeoTv.csv |
| b |
| diff -r 82770f07a036 -r 4432e4183ebd Tryp_G.py --- a/Tryp_G.py Tue Jul 10 09:22:53 2018 -0400 +++ b/Tryp_G.py Wed Jul 11 08:58:14 2018 -0400 |
| [ |
| @@ -56,11 +56,6 @@ argString = "transeq " + name + ".fa " + name + "_6frame.fas -frame=6 " #+quietString print(argString) returncode = subprocess.call(argString, shell=True) - #subprocess.call('ls -l *.fa', shell = True) - #sys.exit(1) - #if returncode != 0: - # return "Error in Transeq" - #return 'ok' def HMMerMotifSearch(name): @@ -123,60 +118,6 @@ #print("--------") return countList -""" -def HMMerMotifSearch(name): - motifs = ['1', '2a', '2b', '3', '4a', '4b', '4c', '5', '6', '7', '8a', '8b', '9a', '9b', - '9c', '10a', '10b', '11a', '11b', '12', '13a', '13b', '13c', '13d', '14', '15a', '15b', '15c'] - lineCounts = [] - compoundList = [] - dir_path = os.path.dirname(os.path.realpath(__file__)) - phylopath = dir_path+"/data/Motifs/Phylotype" - for m in motifs: - argString = "hmmsearch "+phylopath + m + ".hmm " + name + "_6frame.fas > Phy" + m + ".out" #+quietString - #argString = "hmmsearch "+phylopath + m + ".hmm " + dir_path+"/data/Test_6frame.fas > Phy" + m + ".out" - print(argString) - subprocess.call(argString, shell=True) - - hmmResult = open("Phy" + m + ".out", 'r') - tempout = open(dir_path+"/data/"+"Phy" + m + ".txt", 'w') - regex = r"NODE_[0-9]{1,7}_length_[0-9]{1,7}_cov_[0-9]{1,10}.[0-9]{1,7}_[0-9]{1,2}" - n = 0 - outList = [] - for line in hmmResult: - m = re.search(regex, line) - if m: - tempout.write(m.group() + "\n") - outList.append(""+m.group()+"\n") - n += 1 - if re.search(r"inclusion", line): - print("inclusion threshold reached") - break - compoundList.append(outList) - lineCounts.append(n) - hmmResult.close() - #tempout.close() - print(lineCounts) - motifGroups = [['1'], ['2a', '2b'], ['3'], ['4a', '4b', '4c'], ['5'], ['6'], ['7'], ['8a', '8b'], ['9a', '9b', - '9c'], - ['10a', '10b'], ['11a', '11b'], ['12'], ['13a', '13b', '13c', '13d'], ['14'], ['15a', '15b', '15c']] - concatGroups = [1, 2, 1, 3, 1, 1, 1, 2, 3, 2, 2, 1, 4, 1, 3] - countList = [] - countIndex = 0 - totalCount = 0 - - for c in concatGroups: - a = [] - for n in range(0, c): - a = a + compoundList.pop(0) - t = set(a) - countList.append(len(t)) - totalCount += len(t) - countList.append(totalCount) - print(countList) - print("--------") - return countList -""" - def relativeFrequencyTable(countList, name, htmlresource): @@ -223,9 +164,11 @@ congo_df = pd.read_csv(j_fname) congo_df.drop('Colour', axis=1, inplace=True) congo_df.loc[congo_df.index.max() + 1] = localFreqList + ysize = len(congo_df) * 20 / 97.0 # make vertical size equivlanet 20' is ok for 97. + congo_df.set_index('Strain', inplace=True) - cg = sns.clustermap(congo_df, method='ward', cmap = "RdBu_r", col_cluster=False, yticklabels = congo_df.index.values) + cg = sns.clustermap(congo_df, method='ward', cmap = "RdBu_r", col_cluster=False, yticklabels = congo_df.index.values,figsize = (10,ysize)) plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0, fontsize=8) # get y labels printed horizontally ax=cg.ax_heatmap title = "Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ estimated as the phylotype proportion across the\nsample cohort. " @@ -259,8 +202,9 @@ congo_df = pd.read_csv(j_fname) congo_df.drop('Colour', axis=1, inplace=True) congo_df.loc[congo_df.index.max() + 1] = localDevList + ysize = len(congo_df) * 20 / 97.0 # make vertical size equivlanet 20' is ok for 97. congo_df.set_index('Strain', inplace=True) - cg = sns.clustermap(congo_df, method='ward',cmap = "RdBu_r", col_cluster=False, yticklabels = congo_df.index.values) + cg = sns.clustermap(congo_df, method='ward',cmap = "RdBu_r", col_cluster=False, yticklabels = congo_df.index.values,figsize = (10,ysize)) plt.setp(cg.ax_heatmap.yaxis.get_majorticklabels(), rotation=0, fontsize=8) # get y labels printed horizontally ax = cg.ax_heatmap title = "Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ expressed as the deviation from the mean phylotypes " @@ -306,8 +250,8 @@ compoundList[col].append(-item[0]) compoundList[col].append(item[1]) i = i + 1 - cols = ['r', 'g', 'b', 'c', 'm', 'y', 'grey', 'k'] - + colormap = plt.cm.tab20 # nipy_spectral, Set1,Paired + cols = [colormap(i) for i in np.linspace(0, 1, 20)] fig, ax = plt.subplots(figsize=(9, 6)) #plt.figure(num=1,figsize=(12, 6)) i = 0 |
| b |
| diff -r 82770f07a036 -r 4432e4183ebd Tryp_V.py --- a/Tryp_V.py Tue Jul 10 09:22:53 2018 -0400 +++ b/Tryp_V.py Wed Jul 11 08:58:14 2018 -0400 |
| [ |
| @@ -183,17 +183,16 @@ col = cg.ax_col_dendrogram.get_position() cg.ax_col_dendrogram.set_position([col.x0, col.y0*1.08, col.width, col.height*1.1]) - + countryList = pd.unique(geo_df['Location']) + colourList = pd.unique(geo_df['colour']) legend_elements = [Patch(facecolor='orangered', label='COG Present'), - Patch (facecolor='skyblue', label='COG Absent'), - Patch(facecolor='w', label=''), - Patch (facecolor='b', label='Nigeria'), - Patch(facecolor = 'g', label='Uganda'), - Patch (facecolor='c', label='Gambia'), - Patch (facecolor='r', label='Ivory Coast'), - Patch(facecolor='m', label='Brazil'), - Patch(facecolor='k', label=name)] - #legend_test = [[Patch(facecolor='orangered'),Patch(facecolor='r')],["test","test2"]] + Patch(facecolor='skyblue', label='COG Absent')] + + for i in range(0, len(colourList)): + print("country = %s, colour = %s" % (countryList[i], colourList[i])) + p = Patch(facecolor=str(colourList[i]), label=countryList[i]) + legend_elements.append(p) + ax.legend(handles = legend_elements, bbox_to_anchor=(-0.3,1.2),loc = 'upper left') |
| b |
| diff -r 82770f07a036 -r 4432e4183ebd VAP.xml --- a/VAP.xml Tue Jul 10 09:22:53 2018 -0400 +++ b/VAP.xml Wed Jul 11 08:58:14 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="VAPPER" name="VAPPER" version="1.0.0"> +<tool id="VAP" name="VAPPER" version="1.0.0"> <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description> <requirements> <requirement type="package" version="1.2.10">velvet</requirement> @@ -7,6 +7,8 @@ <requirement type="package" version="1.6">samtools</requirement> <requirement type="package" version="2.2.1">cufflinks</requirement> <requirement type="package" version="2.7.1">blast</requirement> + <requirement type="package" version="6.6.0.0">EMBOSS</requirement> + <requirement type="package" version="0.8.0">seaborn</requirement> </requirements> |
| b |
| diff -r 82770f07a036 -r 4432e4183ebd data/congodata.csv --- a/data/congodata.csv Tue Jul 10 09:22:53 2018 -0400 +++ b/data/congodata.csv Wed Jul 11 08:58:14 2018 -0400 |
| b |
| b'@@ -1,1 +1,1 @@\n-Strain,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15,Colour\rIL3578,0.06920904,0.050847458,0.039548023,0.012711864,0.066384181,0.13700565,0.103107345,0.005649718,0.019774011,0.035310734,0.107344633,0.076271186,0.080508475,0.049435028,0.146892655,Burkina Faso\rIL2995,0.126126126,0.207207207,0.09009009,0.018018018,0.027027027,0.018018018,0.027027027,0,0.036036036,0.027027027,0.162162162,0.063063063,0.117117117,0.018018018,0.063063063,Burkina Faso\rIL3897,0.120798319,0.108193277,0.085084034,0.011554622,0.050420168,0.053571429,0.06512605,0.015756303,0.013655462,0.028361345,0.125,0.05987395,0.066176471,0.037815126,0.158613445,Burkina Faso\rBANAN CL2,0.153939394,0.164848485,0.128484848,0.019393939,0.029090909,0.042424242,0.015757576,0.012121212,0.020606061,0.03030303,0.155151515,0.043636364,0.073939394,0.032727273,0.077575758,Burkina Faso\rDIND,0.158184319,0.132049519,0.104539202,0.020632737,0.081155433,0.022008253,0.041265475,0.011004127,0.011004127,0.041265475,0.166437414,0.04264099,0.072902338,0.031636864,0.063273728,Burkina Faso\rKARAN,0.144676979,0.148316652,0.103730664,0.012738854,0.083712466,0.08189263,0.03366697,0.010009099,0.013648772,0.034576888,0.104640582,0.042766151,0.055505005,0.020018198,0.110100091,Burkina Faso\rSA267,0.138941399,0.155954631,0.119092628,0.02173913,0.052930057,0.06710775,0.018903592,0.008506616,0.013232514,0.050094518,0.140831758,0.029300567,0.055765595,0.032136106,0.095463138,Burkina Faso\rSA268,0.144965278,0.144097222,0.113715278,0.025173611,0.058159722,0.071180556,0.019097222,0.010416667,0.010416667,0.048611111,0.139756944,0.027777778,0.0625,0.030381944,0.09375,Burkina Faso\rSA95-3308,0.171717172,0.161616162,0.123737374,0.016414141,0.035353535,0.039141414,0.012626263,0.01010101,0.017676768,0.037878788,0.148989899,0.034090909,0.070707071,0.021464646,0.098484848,Burkina Faso\rALME,0.105034722,0.1015625,0.085069444,0.010416667,0.084201389,0.092881944,0.053819444,0.015625,0.014756944,0.026041667,0.131076389,0.045138889,0.055555556,0.019965278,0.158854167,Cameroon\rBEKA,0.135538954,0.141942369,0.108858058,0.013874066,0.059765208,0.069370331,0.022411953,0.016008538,0.01814301,0.037353255,0.140875133,0.037353255,0.060832444,0.023479189,0.114194237,Cameroon\rKONT1/129,0.147275405,0.151693667,0.12371134,0.013254786,0.051546392,0.057437408,0.026509573,0.020618557,0.011782032,0.033873343,0.122238586,0.038291605,0.051546392,0.023564065,0.126656848,Cameroon\rKONT2/133,0.13660619,0.132337247,0.102454642,0.011739594,0.065101387,0.075773746,0.032017076,0.005336179,0.013874066,0.048025614,0.134471718,0.037353255,0.057630736,0.024546425,0.122732124,Cameroon\rKONT2/151,0.123529412,0.147058824,0.108235294,0.010588235,0.052941176,0.077647059,0.032941176,0.005882353,0.015294118,0.04,0.132941176,0.037647059,0.054117647,0.023529412,0.137647059,Cameroon\rPOUSS,0.108728943,0.113323124,0.105666156,0.018376723,0.061255743,0.079632466,0.045941807,0.009188361,0.007656968,0.026033691,0.127105666,0.062787136,0.055130168,0.018376723,0.160796325,Cameroon\rDJUMA,0.101867572,0.118845501,0.071307301,0.010186757,0.032258065,0.03565365,0.100169779,0.008488964,0.01188455,0.0237691,0.130730051,0.071307301,0.049235993,0.030560272,0.203735144,Congo\rMATADI,0.15625,0.151041667,0.090277778,0.017361111,0.105902778,0.027777778,0.017361111,0.008680556,0.015625,0.026041667,0.170138889,0.045138889,0.102430556,0.026041667,0.039930556,Congo\rZRE/AGRIUMBE G143 90,0.160377358,0.139622642,0.098113208,0.00754717,0.120754717,0.030188679,0.00754717,0.011320755,0.024528302,0.022641509,0.156603774,0.035849057,0.10754717,0.030188679,0.047169811,Congo\rZRE/NKUIYI G291 90,0.178509532,0.142114385,0.081455806,0.013864818,0.117850953,0.022530329,0.008665511,0.017331023,0.017331023,0.022530329,0.169844021,0.039861352,0.095320624,0.017331023,0.055459272,Congo\rPAUWE73,0.119205298,0.138126774,0.090823084,0.006622517,0.063386944,0.071901608,0.028382214,0.008514664,0.010406812,0.028382214,0.141911069,0.041627247,0.071901608,0.017975402,0.160832545,Ethiopia\rWETEJA F'..b'059060403,0.056375839,0.026845638,0.010738255,0.020134228,0.037583893,0.190604027,0.053691275,0.069798658,0.028187919,0.080536913,Zambia\rMPHITA 4028 C1,0.12173913,0.130434783,0.092173913,0.012173913,0.04,0.046956522,0.026086957,0.006956522,0.012173913,0.027826087,0.166956522,0.050434783,0.074782609,0.029565217,0.16173913,Zambia\rMSORO M19 C1,0.130580357,0.146205357,0.103794643,0.013392857,0.041294643,0.042410714,0.056919643,0.015625,0.018973214,0.017857143,0.131696429,0.0390625,0.060267857,0.033482143,0.1484375,Zambia\rMSOSORO M7 C1,0.117091596,0.118035883,0.090651558,0.023607177,0.039660057,0.044381492,0.065155807,0.007554297,0.017941454,0.033994334,0.153918791,0.043437205,0.079320113,0.031161473,0.134088763,Zambia\rTRT1,0.136406397,0.127939793,0.096895579,0.013170273,0.068673565,0.075258702,0.021636877,0.008466604,0.016933208,0.030103481,0.139228598,0.043273754,0.0724365,0.022577611,0.126999059,Zambia\rTRT12,0.158751696,0.160108548,0.101763908,0.018995929,0.016282225,0.021709634,0.024423338,0.008141113,0.020352782,0.023066486,0.162822252,0.036635007,0.090909091,0.03256445,0.123473541,Zambia\rTRT15,0.145992366,0.131679389,0.10019084,0.013358779,0.063931298,0.06870229,0.020038168,0.008587786,0.017175573,0.033396947,0.140267176,0.041984733,0.078244275,0.022900763,0.113549618,Zambia\rTRT17C1,0.118181818,0.100909091,0.079090909,0.02,0.072727273,0.082727273,0.034545455,0.01,0.018181818,0.024545455,0.181818182,0.05,0.078181818,0.025454545,0.103636364,Zambia\rTRT21,0.177272727,0.152272727,0.109090909,0.029545455,0.040909091,0.047727273,0.045454545,0.020454545,0.013636364,0.025,0.125,0.040909091,0.056818182,0.011363636,0.104545455,Zambia\rTRT25,0.153846154,0.142389525,0.093289689,0.034369885,0.034369885,0.031096563,0.036006547,0.024549918,0.016366612,0.037643208,0.166939444,0.049099836,0.065466448,0.026186579,0.088379705,Zambia\rTRT37,0.136701337,0.138187221,0.111441308,0.013372957,0.059435364,0.059435364,0.016344725,0.010401189,0.020802377,0.019316493,0.151560178,0.043090639,0.08320951,0.017830609,0.118870728,Zambia\rTRT38,0.128583129,0.108927109,0.09009009,0.012285012,0.058968059,0.063882064,0.058149058,0.006552007,0.016380016,0.026208026,0.162162162,0.053235053,0.074529075,0.022932023,0.117117117,Zambia\rTRT42,0.089041096,0.095890411,0.089041096,0.022260274,0.068493151,0.061643836,0.058219178,0.008561644,0.008561644,0.02739726,0.131849315,0.066780822,0.070205479,0.015410959,0.186643836,Zambia\rTRT44,0.157681941,0.144204852,0.106469003,0.010781671,0.032345013,0.035040431,0.022911051,0.008086253,0.016172507,0.030997305,0.148247978,0.04851752,0.082210243,0.014824798,0.141509434,Zambia\rTRT46,0.133779264,0.132664437,0.105908584,0.013377926,0.046822742,0.053511706,0.045707915,0.00780379,0.015607581,0.022296544,0.151616499,0.04793757,0.086956522,0.028985507,0.107023411,Zambia\rTRT54,0.141007194,0.142446043,0.110791367,0.018705036,0.024460432,0.031654676,0.017266187,0.008633094,0.020143885,0.023021583,0.168345324,0.041726619,0.089208633,0.041726619,0.120863309,Zambia\rTRT573R,0.135185185,0.155555556,0.111111111,0.011111111,0.022222222,0.02037037,0.012962963,0.011111111,0.016666667,0.022222222,0.161111111,0.042592593,0.096296296,0.033333333,0.148148148,Zambia\rTRT59,0.117391304,0.156521739,0.104347826,0.013043478,0.004347826,0.013043478,0.02173913,0.013043478,0.004347826,0.008695652,0.147826087,0.047826087,0.117391304,0.013043478,0.217391304,Zambia\rTRT61,0.151855047,0.134598792,0.104400345,0.012942192,0.059534081,0.055220017,0.030198447,0.011216566,0.017256255,0.028472821,0.146678171,0.038826575,0.062122519,0.028472821,0.118205349,Zambia\rYOBO 2007 C2,0.10994152,0.123976608,0.092397661,0.01871345,0.045614035,0.045614035,0.045614035,0.007017544,0.01754386,0.031578947,0.18245614,0.057309942,0.085380117,0.031578947,0.105263158,Zambia\rYOBO 2038 C2,0.132764921,0.118148599,0.09500609,0.013398295,0.063337393,0.054811206,0.029232643,0.009744214,0.018270402,0.037758831,0.180267966,0.040194884,0.071863581,0.020706456,0.114494519,Zambia\n\\ No newline at end of file\n' |
| b |
| diff -r 82770f07a036 -r 4432e4183ebd data/congodata_deviationfromthemean.csv --- a/data/congodata_deviationfromthemean.csv Tue Jul 10 09:22:53 2018 -0400 +++ b/data/congodata_deviationfromthemean.csv Wed Jul 11 08:58:14 2018 -0400 |
| b |
| b'@@ -1,1 +1,1 @@\n-Strain,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15,Colour\rIL2995,-0.019637186,-0.108350357,-0.01512639,-0.002392738,0.041261003,0.052742362,0.030150623,0.00831415,-0.019757856,0.006440593,-0.020610832,-0.010139913,-0.046085817,0.014763942,0.088528327,Burkina Faso\rIL3578,0.0372799,0.048009392,0.035415677,0.002913416,0.001903849,-0.06624527,-0.045929695,0.002664432,-0.003495831,-0.001843114,0.034206697,-0.023348036,-0.009477175,-0.016653068,0.004698735,Burkina Faso\rIL3897,-0.014309379,-0.009336427,-0.010120334,0.004070658,0.017867862,0.017188951,-0.0079484,-0.007442153,0.002622718,0.005106275,0.01655133,-0.0069508,0.004854829,-0.005033166,-0.007022055,Burkina Faso\rIL3900,-0.041337147,-0.036795324,-0.041558039,-0.006983416,-0.008233709,0.034238641,0.027612433,0.003096759,-0.011547907,-0.013488902,-0.032361713,0.002488367,-0.005490439,-0.002000649,0.132460955,Forest sub-type\rIL3926,-0.043745802,-0.027903713,-0.043972137,-0.007848898,0.000995385,0.03789653,0.018054019,-0.002640467,-0.000936217,-0.011915792,-0.041547262,0.004409848,-0.002521126,0.006177891,0.11559765,Forest sub-type\rIL3932,0.041882198,0.03144112,0.001929992,0.001580336,-0.027217588,-0.005082317,-0.024283024,-0.005730794,-0.00619373,0.013804699,0.017955824,-0.020110558,0.031705457,-0.000925905,-0.050655801,Kenya\rIL274,0.003817821,-0.017169861,-0.00767403,0.001434963,-0.01268025,-0.011042625,0.006259453,0.004975252,-0.000416311,0.00592171,0.015507924,0.012021647,0.007592235,0.004401326,-0.012849345,Kenya\rIL374,-0.029005657,-0.020843898,-0.012318096,0.002325197,-0.006524938,-0.008208864,0.012289869,0.001664108,0.000484331,0.008529964,0.012706775,0.016347921,0.013674692,0.009506815,-0.000528311,Kenya\rIL396,-0.023019257,-0.013438232,-0.014380562,0.003330198,-0.012859511,-0.008747817,0.008816994,0.004215789,0.003163426,0.011336472,0.021879199,0.012759216,0.012834579,0.010650812,-0.016441397,Kenya\rIL399,-0.021825859,-0.009783013,-0.019989251,0.004504664,-0.007845417,-0.007939363,0.009273458,0.002326126,0.000880404,0.006949228,0.019224555,0.01442871,0.006018469,0.012251592,-0.008374393,Kenya\rIL409,-0.015774808,-0.015932258,-0.014198073,0.005481126,-0.00539056,0.002420818,0.001651756,0.002441219,0.002396706,0.005704673,0.020355388,0.008609215,0.009098572,0.007688527,-0.01445239,Kenya\rIL410,0.002932455,-0.014113861,-0.019178559,0.003072979,-0.005979752,-0.004553428,0.004876395,0.003084024,0.002679854,0.012547118,0.021258443,0.014220221,-0.003236482,0.013953508,-0.031463003,Kenya\rIL438,0.01351169,0.006868719,0.024518596,0.000788485,-0.030623938,-0.027162469,0.001786948,0.00831415,0.001441385,0.00280491,0.002085455,0.009401884,0.000803802,0.003108369,-0.017548076,Kenya\rIL439,-0.011589236,-0.018406994,-0.012984183,0.002595964,-0.012330863,-0.00904418,0.009132047,0.004242489,0.0016202,0.005780324,0.019401493,0.014649534,0.012399378,0.005908996,-0.01127506,Kenya\rILC66,-0.022971641,-0.022304976,-0.022131736,0.003177147,-0.007230642,-0.00143879,0.010704621,1.53948E-05,0.004659923,0.00940123,0.019559629,0.015578752,0.005471134,0.012864948,-0.005255083,Kenya\rIL3035,-0.01535014,-0.014553112,-0.006262354,-0.002765525,0.001621363,0.00332743,0.015032056,-0.000114969,-0.005177759,0.002049995,-0.010939091,0.010777556,-0.00712962,0.010559738,0.01902434,Kenya\rILC55,0.084654879,0.05955554,0.048762827,0.006891656,-0.053982712,-0.055877175,-0.038892219,0.00831415,0.007544556,0.011633559,-0.011287098,0.004888216,-0.00757132,0.002214274,-0.066749221,Kenya\rIL3779,0.016833768,0.036787884,0.040480941,-0.018857479,0.016563892,0.01213969,-0.049718902,-0.008927229,0.002485077,-0.014808242,0.007068571,-0.016042367,0.015858886,-0.00859735,-0.031167231,Kenya\rIL3949,-0.02155984,-0.031224451,-0.024629796,-0.001651143,0.028653884,0.027061193,0.006364642,-0.003880972,0.005099318,-0.004134006,-0.008855174,0.011256483,-0.002139432,0.004326675,0.015412528,Kenya\rIL2992,-0.006201415,0.002410149,-0.003208889,0.004457767,0.017526609,0.01289236,-0.012873111,-0.007929505,0.004095439,0.001995539'..b'14223,-0.003337127,-0.02193366,-0.015375482,-0.019292612,-0.00247681,-0.003259702,-0.004017559,0.022085325,0.001195771,0.003103077,0.000214531,0.025976017,Zambia\rMSORO M19 C1,0.008828771,0.028787038,0.015734953,-0.002118183,-0.020639017,-0.01992129,0.011540074,0.006191668,0.003539599,-0.013986503,-0.013174768,-0.010176512,-0.011411675,0.004131457,0.012674387,Zambia\rMSOSORO M7 C1,-0.00465999,0.000617564,0.002591868,0.008096137,-0.022273603,-0.017950512,0.019776238,-0.001879035,0.002507839,0.002150688,0.009047594,-0.005801807,0.007640581,0.001810787,-0.00167435,Zambia\rTRT1,0.014654811,0.010521474,0.008835889,-0.002340767,0.006739905,0.012926698,-0.023742692,-0.000966728,0.001499593,-0.001740165,-0.005642599,-0.005965258,0.000756968,-0.006773075,-0.008764054,Zambia\rTRT12,0.03700011,0.042690229,0.013704218,0.003484889,-0.045651435,-0.04062237,-0.020956231,-0.001292219,0.004919167,-0.00877716,0.017951055,-0.012604005,0.019229559,0.003213764,-0.012289572,Zambia\rTRT15,0.02424078,0.01426107,0.01213115,-0.002152261,0.001997638,0.006370286,-0.025341401,-0.000845546,0.001741958,0.001553301,-0.004604021,-0.007254279,0.006564743,-0.006449923,-0.022213495,Zambia\rTRT17C1,-0.003569768,-0.016509228,-0.008968781,0.00448896,0.010793613,0.020395269,-0.010834114,0.000566668,0.002748203,-0.007298191,0.036946985,0.000760988,0.006502286,-0.003896141,-0.032126749,Zambia\rTRT21,0.055521141,0.034854408,0.021031219,0.014034415,-0.021024569,-0.014604731,7.49764E-05,0.011021213,-0.001797251,-0.006843646,-0.019871197,-0.008329921,-0.01486135,-0.01798705,-0.031217658,Zambia\rTRT25,0.032094568,0.024971206,0.005229999,0.018858845,-0.027563775,-0.031235441,-0.009373022,0.015116586,0.000932997,0.005799562,0.022068247,-0.000139176,-0.006213084,-0.003164107,-0.047383408,Zambia\rTRT37,0.014949751,0.020768902,0.023381618,-0.002138083,-0.002498296,-0.00289664,-0.029034844,0.000967857,0.005368762,-0.012527153,0.006688981,-0.006148373,0.011529978,-0.011520077,-0.016892385,Zambia\rTRT38,0.006831543,-0.00849121,0.0020304,-0.003226028,-0.002965601,0.00155006,0.012769489,-0.002881325,0.000946401,-0.00563562,0.017290965,0.003996041,0.002849543,-0.006418663,-0.018645996,Zambia\rTRT42,-0.03271049,-0.021527908,0.000981406,0.006749234,0.006559491,-0.000688168,0.012839609,-0.000871688,-0.006871971,-0.004446386,-0.013021882,0.01754181,-0.001474053,-0.013939727,0.050880723,Zambia\rTRT44,0.035930355,0.026786533,0.018409313,-0.004729369,-0.029588647,-0.027291573,-0.022468518,-0.001347079,0.000738892,-0.000846341,0.003376781,-0.000721492,0.010530711,-0.014525888,0.005746321,Zambia\rTRT46,0.012027678,0.015246118,0.017848894,-0.002133114,-0.015110918,-0.008820298,0.000328346,-0.001629542,0.000173966,-0.009547102,0.006745302,-0.001301442,0.01527699,-0.000365179,-0.028739702,Zambia\rTRT54,0.019255608,0.025027724,0.022731677,0.003193996,-0.037473228,-0.030677328,-0.028113382,-0.000800238,0.00471027,-0.008822063,0.023474127,-0.007512393,0.017529101,0.012375933,-0.014899804,Zambia\rTRT573R,0.013433599,0.038137237,0.023051421,-0.004399929,-0.039711438,-0.041961634,-0.032416606,0.001677779,0.001233052,-0.009621424,0.016239914,-0.006646419,0.024616764,0.003982647,0.012385035,Zambia\rTRT59,-0.004360282,0.03910342,0.016288136,-0.002467562,-0.057585834,-0.049288526,-0.023640439,0.003610146,-0.011085789,-0.023147994,0.00295489,-0.001412925,0.045711772,-0.016307208,0.081628191,Zambia\rTRT61,0.030103461,0.017180473,0.016340655,-0.002568848,-0.002399579,-0.007111987,-0.015181122,0.001783234,0.00182264,-0.003370825,0.001806974,-0.010412437,-0.009557013,-0.000877865,-0.017557764,Zambia\rYOBO 2007 C2,-0.011810066,0.006558289,0.004337971,0.00320241,-0.016319625,-0.016717969,0.000234466,-0.002415788,0.002110245,-0.000264699,0.037584943,0.00807093,0.013700585,0.002228261,-0.030499955,Zambia\rYOBO 2038 C2,0.011013335,0.00073028,0.0069464,-0.002112745,0.001403733,-0.007520798,-0.016146926,0.000310882,0.002836787,0.005915185,0.035396769,-0.009044128,0.000184049,-0.00864423,-0.021268594,Zambia\n\\ No newline at end of file\n' |
| b |
| diff -r 82770f07a036 -r 4432e4183ebd data/ogeoTv.csv --- a/data/ogeoTv.csv Tue Jul 10 09:22:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -Strain,Location,colour -TvY486,Nigeria,b -Tv11,Nigeria,b -Tv306,Nigeria,b -Tv319,Nigeria,b -Tv338,Nigeria,b -Tv340,Nigeria,b -Tv462,Nigeria,b -Tv465,Nigeria,b -Tv493,Nigeria,b -Tv596,Nigeria,b -Tv684,Nigeria,b -Tv1392,Nigeria,b -Tv2005,Uganda,g -Tv2323,Uganda,g -Tv2714,Uganda,g -TvILV-21,Uganda,g -Tv3171,Gambia,c -Tv3638,Ivory Coast,r -Tv3651,Ivory Coast,r -Tv3658,Ivory Coast,r -TvLins,Brazil,m |