| Previous changeset 10:68ee7c84d498 (2020-01-07) Next changeset 12:aa5e2c64dff8 (2022-10-22) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370" |
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modified:
overlapping_reads.py overlapping_reads.xml signature.py signature.r signature.xml test-data/global.pdf test-data/h.tab test-data/lattice.pdf test-data/z.tab |
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| diff -r 68ee7c84d498 -r 8d3ca9652a5b overlapping_reads.py --- a/overlapping_reads.py Tue Jan 07 06:59:56 2020 -0500 +++ b/overlapping_reads.py Sat Oct 23 22:55:19 2021 +0000 |
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| @@ -74,7 +74,7 @@ def query_positions(self, bam_object, overlap): all_query_positions = defaultdict(list) - for genomicKey in self.alignement_dic.keys(): + for genomicKey in list(self.alignement_dic): chrom, coord, pol = genomicKey if pol == 'F' and len(self.alignement_dic[(chrom, coord+overlap-1, |
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| diff -r 68ee7c84d498 -r 8d3ca9652a5b overlapping_reads.xml --- a/overlapping_reads.xml Tue Jan 07 06:59:56 2020 -0500 +++ b/overlapping_reads.xml Sat Oct 23 22:55:19 2021 +0000 |
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| @@ -1,7 +1,8 @@ -<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.6"> +<tool id="overlapping_reads" name="Get overlapping reads" version="3.3"> <description /> <requirements> - <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> + <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement> + <requirement type="package" version="1.13=h8c37831_0">samtools</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> |
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| diff -r 68ee7c84d498 -r 8d3ca9652a5b signature.py --- a/signature.py Tue Jan 07 06:59:56 2020 -0500 +++ b/signature.py Sat Oct 23 22:55:19 2021 +0000 |
| [ |
| @@ -82,7 +82,7 @@ ''' this method does not filter on read size, just forward reads that overlap reverse reads in the overlap range''' all_query_positions = defaultdict(list) - for genomicKey in self.map_dict.keys(): + for genomicKey in list(self.map_dict): chrom, coord, pol = genomicKey for i in self.scope: if pol == 'F' and len(self.map_dict[chrom, |
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| diff -r 68ee7c84d498 -r 8d3ca9652a5b signature.r --- a/signature.r Tue Jan 07 06:59:56 2020 -0500 +++ b/signature.r Sat Oct 23 22:55:19 2021 +0000 |
| [ |
| @@ -1,6 +1,10 @@ ## Setup R error handling to go to stderr -#options(show.error.messages=F, - #error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(show.error.messages = F, + error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, F) + } +) warnings() library(RColorBrewer) @@ -11,89 +15,90 @@ library(optparse) option_list <- list( - make_option("--h_dataframe", type="character", help="path to h-signature dataframe"), - make_option("--z_dataframe", type="character", help="path to z-signature dataframe"), - make_option("--plot_method", type = "character", help="How data should be plotted (global or lattice)"), - make_option("--pdf", type = "character", help="path to the pdf file with plots"), - make_option("--title", type = "character", help="Graph Title") + make_option("--h_dataframe", type = "character", + help = "path to h-signature dataframe"), + make_option("--z_dataframe", type = "character", + help = "path to z-signature dataframe"), + make_option("--plot_method", type = "character", + help = "How data should be plotted (global or lattice)"), + make_option("--pdf", type = "character", help = "path to the pdf file with plots"), + make_option("--title", type = "character", help = "Graph Title") ) - parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) -args = parse_args(parser) - - - +args <- parse_args(parser) # data frames implementation -h_dataframe = read.delim(args$h_dataframe, header=F) -colnames(h_dataframe) = c("chrom", "overlap", "sig", "z-score") -h_dataframe$sig = h_dataframe$sig * 100 # to get probs in % -z_dataframe = read.delim(args$z_dataframe, header=F) -colnames(z_dataframe) = c("chrom", "overlap", "sig", "z-score") +h_dataframe <- read.delim(args$h_dataframe, header = F) +colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score") +h_dataframe$sig <- h_dataframe$sig * 100 # to get probs in % +z_dataframe <- read.delim(args$z_dataframe, header = F) +colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score") # functions - globalgraph = function () { + globalgraph <- function() { pdf(args$pdf) - par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) - - plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,3)], - type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", - ylab="Numbers of pairs", col="darkslateblue", lwd=4) + par(mfrow = c(2, 2), oma = c(0, 0, 3, 0)) + plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 3)], + type = "h", main = "Numbers of pairs", cex.main = 1, xlab = "overlap (nt)", + ylab = "Numbers of pairs", col = "darkslateblue", lwd = 4) - plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,4)], - type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", - ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) + plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 4)], + type = "l", main = "Number of pairs Z-scores", cex.main = 1, xlab = "overlap (nt)", + ylab = "z-score", pch = 19, cex = 0.2, col = "darkslateblue", lwd = 2) - plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,3)], - type = "l", main="Overlap probabilities", cex.main=1, xlab="overlap (nt)", - ylab="Probability [%]", ylim=c(0,50), pch=19, col="darkslateblue", lwd=2) + plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 3)], + type = "l", main = "Overlap probabilities", cex.main = 1, + xlab = "overlap (nt)", + ylab = "Probability [%]", ylim = c(0, 50), pch = 19, + col = "darkslateblue", lwd = 2) - plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,4)], - type = "l", main="Overlap Probability Z-scores", cex.main=1, - xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, - col="darkslateblue", lwd=2) - - mtext(args$title, outer = TRUE, cex=1) + plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 4)], + type = "l", main = "Overlap Probability Z-scores", cex.main = 1, + xlab = "overlap (nt)", ylab = "z-score", pch = 19, cex = 0.2, + col = "darkslateblue", lwd = 2) + mtext(args$title, outer = TRUE, cex = 1) dev.off() - } + } - treillisgraph = function (df, ...) { - pdf(args$pdf, paper="special", height=11.69, width=6 ) # 8.2677 - p = xyplot(sig ~ overlap|factor(method, levels=unique(method))+chrom, data = df, + treillisgraph <- function(df, ...) { + pdf(args$pdf, paper = "special", height = 11.69, width = 6) + p <- xyplot(sig ~ overlap | factor(method, levels = unique(method)) + chrom, + data = df, type = "l", - col='darkblue', - cex=0.5, - scales=list(y=list(tick.number=4, relation="free", cex=0.6, rot=0), x=list(cex=0.6, alternating=FALSE)), + col = "darkblue", + cex = 0.5, + scales = list(y = list(tick.number = 4, relation = "free", cex = 0.6, + rot = 0), + x = list(cex = 0.6, alternating = FALSE)), xlab = "Overlap", ylab = "signature (Nbr of pairs / Overlap prob.)", main = args$title, - par.strip.text=list(cex=.5), - pch=19, lwd =2, - as.table=TRUE, - layout=c(2,12), + par.strip.text = list(cex = .5), + pch = 19, lwd = 2, + as.table = TRUE, + layout = c(2, 12), newpage = T, ...) - plot(p) + plot(p) dev.off() - } + } # main -if (args$plot_method=="global") { +if (args$plot_method == "global") { globalgraph() - } +} -if(args$plot_method=="lattice") { +if (args$plot_method == "lattice") { # rearrange dataframes - h_sig = h_dataframe[,c(1,2,3)] - h_sig = cbind(rep("Overlap Prob (%)", length(h_sig[,1])), h_sig) - colnames(h_sig) = c("method", "chrom", "overlap", "sig") - z_pairs = z_dataframe[,c(1,2,3)] - z_pairs = cbind(rep("Nbr of pairs", length(z_pairs[,1])), z_pairs) - colnames(z_pairs) = c("method", "chrom", "overlap", "sig") - lattice_df = rbind(z_pairs, h_sig) - par.settings.treillis=list(strip.background = list( + h_sig <- h_dataframe[, c(1, 2, 3)] + h_sig <- cbind(rep("Overlap Prob (%)", length(h_sig[, 1])), h_sig) + colnames(h_sig) <- c("method", "chrom", "overlap", "sig") + z_pairs <- z_dataframe[, c(1, 2, 3)] + z_pairs <- cbind(rep("Nbr of pairs", length(z_pairs[, 1])), z_pairs) + colnames(z_pairs) <- c("method", "chrom", "overlap", "sig") + lattice_df <- rbind(z_pairs, h_sig) + par_settings_treillis <- list(strip.background = list( col = c("lightblue", "lightgreen"))) - - treillisgraph(lattice_df, par.settings=par.settings.treillis) + treillisgraph(lattice_df, par.settings = par_settings_treillis) } |
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| diff -r 68ee7c84d498 -r 8d3ca9652a5b signature.xml --- a/signature.xml Tue Jan 07 06:59:56 2020 -0500 +++ b/signature.xml Sat Oct 23 22:55:19 2021 +0000 |
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| @@ -1,11 +1,12 @@ -<tool id="signature" name="Small RNA Signatures" version="3.2.1"> +<tool id="signature" name="Small RNA Signatures" version="3.3>"> <description /> <requirements> - <requirement type="package" version="1.11.2=py27_0">numpy</requirement> - <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> - <requirement type="package" version="1.6.1=r351h6115d3f_0">r-optparse</requirement> - <requirement type="package" version="0.6_28=r351h6115d3f_0">r-latticeextra</requirement> - <requirement type="package" version="2.3=r351h6115d3f_0">r-gridextra</requirement> + <requirement type="package" version="1.13=h8c37831_0">samtools</requirement> + <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement> + <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement> + <requirement type="package" version="1.7.1=r40hc72bb7e_0">r-optparse</requirement> + <requirement type="package" version="0.6_29=r40hc72bb7e_1">r-latticeextra</requirement> + <requirement type="package" version="2.3=r40hc72bb7e_1003">r-gridextra</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> |
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| diff -r 68ee7c84d498 -r 8d3ca9652a5b test-data/global.pdf |
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| Binary file test-data/global.pdf has changed |
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| diff -r 68ee7c84d498 -r 8d3ca9652a5b test-data/h.tab --- a/test-data/h.tab Tue Jan 07 06:59:56 2020 -0500 +++ b/test-data/h.tab Sat Oct 23 22:55:19 2021 +0000 |
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| b'@@ -1,14 +1,14 @@\n-FBgn0000004_17.6\t5\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t6\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t7\t0.00369003690037\t0.989949493661\n-FBgn0000004_17.6\t8\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t9\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t10\t0.00369003690037\t0.989949493661\n-FBgn0000004_17.6\t11\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t12\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t13\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t14\t0.0\t-0.565685424949\n-FBgn0000004_17.6\t15\t0.00738007380074\t2.54558441227\n+FBgn0000004_17.6\t5\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t6\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t7\t0.0036900369003690036\t0.9899494936611665\n+FBgn0000004_17.6\t8\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t9\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t10\t0.0036900369003690036\t0.9899494936611665\n+FBgn0000004_17.6\t11\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t12\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t13\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t14\t0.0\t-0.565685424949238\n+FBgn0000004_17.6\t15\t0.007380073800738007\t2.545584412271571\n FBgn0000005_297\t5\t0\t0\n FBgn0000005_297\t6\t0\t0\n FBgn0000005_297\t7\t0\t0\n@@ -20,83 +20,83 @@\n FBgn0000005_297\t13\t0\t0\n FBgn0000005_297\t14\t0\t0\n FBgn0000005_297\t15\t0\t0\n-FBgn0000006_412\t5\t0.0\t-0.876714007519\n-FBgn0000006_412\t6\t0.00186046511628\t-0.187867287326\n-FBgn0000006_412\t7\t0.00279069767442\t0.156556072771\n-FBgn0000006_412\t8\t0.0\t-0.876714007519\n-FBgn0000006_412\t9\t0.0046511627907\t0.845402792965\n-FBgn0000006_412\t10\t0.00837209302326\t2.22309623335\n-FBgn0000006_412\t11\t0.00279069767442\t0.156556072771\n-FBgn0000006_412\t12\t0.0\t-0.876714007519\n-FBgn0000006_412\t13\t0.00558139534884\t1.18982615306\n-FBgn0000006_412\t14\t0.0\t-0.876714007519\n-FBgn0000006_412\t15\t0.0\t-0.876714007519\n-FBgn0000007_1731\t5\t0.0\t-0.383239046572\n-FBgn0000007_1731\t6\t0.0\t-0.383239046572\n-FBgn0000007_1731\t7\t0.0\t-0.383239046572\n-FBgn0000007_1731\t8\t0.0\t-0.383239046572\n-FBgn0000007_1731\t9\t0.0\t-0.383239046572\n-FBgn0000007_1731\t10\t0.0017667844523\t-0.149037407\n-FBgn0000007_1731\t11\t0.0265017667845\t3.12978554701\n-FBgn0000007_1731\t12\t0.0\t-0.383239046572\n-FBgn0000007_1731\t13\t0.0\t-0.383239046572\n-FBgn0000007_1731\t14\t0.00353356890459\t0.0851642325717\n-FBgn0000007_1731\t15\t0.0\t-0.383239046572\n-FBgn0000155_roo\t5\t0.0\t-0.849506616033\n-FBgn0000155_roo\t6\t0.00292153589316\t-0.39207997663\n-FBgn0000155_roo\t7\t0.000834724540902\t-0.718813290489\n-FBgn0000155_roo\t8\t0.00333889816361\t-0.326733313859\n-FBgn0000155_roo\t9\t0.0016694490818\t-0.588119964946\n-FBgn0000155_roo\t10\t0.0200333889816\t2.28713319701\n-FBgn0000155_roo\t11\t0.00667779632721\t0.196039988315\n-FBgn0000155_roo\t12\t0.00125208681135\t-0.653466627717\n-FBgn0000155_roo\t13\t0.0\t-0.849506616033\n-FBgn0000155_roo\t14\t0.00709515859766\t0.261386651087\n-FBgn0000155_roo\t15\t0.0158597662771\t1.63366656929\n-FBgn0000199_blood\t5\t0.0\t-0.661855797999\n-FBgn0000199_blood\t6\t0.0\t-0.661855797999\n-FBgn0000199_blood\t7\t0.000625782227785\t1.14670161951e-16\n-FBgn0000199_blood\t8\t0.0\t-0.661855797999\n-FBgn0000199_blood\t9\t0.0\t-0.661855797999\n-FBgn0000199_blood\t10\t0.0\t-0.661855797999\n-FBgn0000199_blood\t11\t0.000417188151856\t-0.220618599333\n-FBgn0000199_blood\t12\t0.000834376303713\t0.220618599333\n-FBgn0000199_blood\t13\t0.00333750521485\t2.86804179133\n-FBgn0000199_blood\t14\t0.000417188151856\t-0.220618599333\n-FBgn0000199_blood\t15\t0.00125156445557\t0.661855797999\n-FBgn0000224_BS\t5\t0.0\t-0.316227766017\n-FBgn0000224_BS\t6\t0.0\t-0.316227766017\n-FBgn0000224_BS\t7\t0.0\t-0.316227766017\n-FBgn0000224_BS\t8\t0.0\t-0.316227766017\n-FBgn0000224_BS\t9\t0.0\t-0.316227766017\n-FBgn0000224_BS\t10\t0.0\t-0.316227766017\n-FBgn0000224_BS\t11\t0.0\t-0.316227766017\n-FBgn0000224_BS\t12\t0.0\t-0.316227766017\n-FBgn0000224_BS\t13\t0.00772200772201\t3.16227766017\n-FBgn0000224_BS\t14\t0.0\t-0.316227766017\n-FBgn0000224_BS\t15\t0.0\t-0.316227766017\n-FBgn0000349_copia\t5\t0.0\t-0.586301969978\n-FBgn0000349_copia\t6\t0.0\t-0.586301969978\n-FBgn0000349_copia\t7\t0.0\t-0.586301969978\n-FBgn0000349_copia\t8\t0.0\t-0.586301969978\n-FBgn0000349_copia\t9\t0.00392156862745\t0.0\n-FBgn0000349_copia\t10\t0.0196078431373\t2.34520787991\n-FBgn0000349_copia\t11\t0.00392156862745\t0.0\n-FBgn0000'..b'7385_invader6\t11\t0.020179372197309416\t1.0979432827130893\n+FBgn0067385_invader6\t12\t0.0033632286995515697\t-0.27448582067827226\n+FBgn0067385_invader6\t13\t0.01008968609865471\t0.2744858206782725\n+FBgn0067385_invader6\t14\t0.0\t-0.5489716413565445\n+FBgn0067385_invader6\t15\t0.0\t-0.5489716413565445\n FBgn0067386_gypsy11\t5\t0\t0\n FBgn0067386_gypsy11\t6\t0\t0\n FBgn0067386_gypsy11\t7\t0\t0\n@@ -1263,17 +1263,17 @@\n FBgn0067421_Fw2\t13\t0\t0\n FBgn0067421_Fw2\t14\t0\t0\n FBgn0067421_Fw2\t15\t0\t0\n-FBgn0067624_BS3\t5\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t6\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t7\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t8\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t9\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t10\t0.346153846154\t3.16227766017\n-FBgn0067624_BS3\t11\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t12\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t13\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t14\t0.0\t-0.316227766017\n-FBgn0067624_BS3\t15\t0.0\t-0.316227766017\n+FBgn0067624_BS3\t5\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t6\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t7\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t8\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t9\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t10\t0.34615384615384615\t3.1622776601683795\n+FBgn0067624_BS3\t11\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t12\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t13\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t14\t0.0\t-0.31622776601683794\n+FBgn0067624_BS3\t15\t0.0\t-0.31622776601683794\n FBgn0067624_BS4\t5\t0\t0\n FBgn0067624_BS4\t6\t0\t0\n FBgn0067624_BS4\t7\t0\t0\n@@ -1285,17 +1285,17 @@\n FBgn0067624_BS4\t13\t0\t0\n FBgn0067624_BS4\t14\t0\t0\n FBgn0067624_BS4\t15\t0\t0\n-FBgn0069340_Tc1-2\t5\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t6\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t7\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t8\t0.103448275862\t3.16227766017\n-FBgn0069340_Tc1-2\t9\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t10\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t11\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t12\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t13\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t14\t0.0\t-0.316227766017\n-FBgn0069340_Tc1-2\t15\t0.0\t-0.316227766017\n+FBgn0069340_Tc1-2\t5\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t6\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t7\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t8\t0.10344827586206896\t3.1622776601683795\n+FBgn0069340_Tc1-2\t9\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t10\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t11\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t12\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t13\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t14\t0.0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t15\t0.0\t-0.316227766016838\n FBgn0069433_G5A\t5\t0\t0\n FBgn0069433_G5A\t6\t0\t0\n FBgn0069433_G5A\t7\t0\t0\n@@ -1318,14 +1318,14 @@\n FBgn0069587_Doc4-element\t13\t0\t0\n FBgn0069587_Doc4-element\t14\t0\t0\n FBgn0069587_Doc4-element\t15\t0\t0\n-all_chromosomes\t5\t4.26865796963e-06\t-1.02078731734\n-all_chromosomes\t6\t0.000272508714058\t-0.505836219906\n-all_chromosomes\t7\t0.000314189173203\t-0.425820585808\n-all_chromosomes\t8\t0.000481492106257\t-0.104642495418\n-all_chromosomes\t9\t0.000402138333192\t-0.256981087653\n-all_chromosomes\t10\t0.00205870585512\t2.92319742793\n-all_chromosomes\t11\t0.000380479180279\t-0.298561024389\n-all_chromosomes\t12\t0.000209011312505\t-0.627734705504\n-all_chromosomes\t13\t0.000334785271578\t-0.386281437121\n-all_chromosomes\t14\t0.000668570428043\t0.254499194734\n-all_chromosomes\t15\t0.000769859707507\t0.448948250475\n+all_chromosomes\t5\t4.597016274988517e-06\t-1.0469141525331194\n+all_chromosomes\t6\t0.0002824030976458536\t-0.52144365445537\n+all_chromosomes\t7\t0.000340456835038392\t-0.4116349484961661\n+all_chromosomes\t8\t0.0005109744379707215\t-0.08910072137729177\n+all_chromosomes\t9\t0.0004259214471628285\t-0.2499785438579372\n+all_chromosomes\t10\t0.0020996847468840105\t2.9159465159128586\n+all_chromosomes\t11\t0.0004052560308455948\t-0.2890672007786769\n+all_chromosomes\t12\t0.00022552377211365463\t-0.6290309591329472\n+all_chromosomes\t13\t0.00035575730465490775\t-0.3826940939600091\n+all_chromosomes\t14\t0.0006968571672892477\t0.26249665862628785\n+all_chromosomes\t15\t0.0007914510562247529\t0.4414211000523717\n' |
| b |
| diff -r 68ee7c84d498 -r 8d3ca9652a5b test-data/lattice.pdf |
| b |
| Binary file test-data/lattice.pdf has changed |
| b |
| diff -r 68ee7c84d498 -r 8d3ca9652a5b test-data/z.tab --- a/test-data/z.tab Tue Jan 07 06:59:56 2020 -0500 +++ b/test-data/z.tab Sat Oct 23 22:55:19 2021 +0000 |
| b |
| b'@@ -1,14 +1,14 @@\n-FBgn0000004_17.6\t5\t0\t-0.612372435696\n-FBgn0000004_17.6\t6\t0\t-0.612372435696\n-FBgn0000004_17.6\t7\t1\t1.63299316186\n-FBgn0000004_17.6\t8\t0\t-0.612372435696\n-FBgn0000004_17.6\t9\t0\t-0.612372435696\n-FBgn0000004_17.6\t10\t1\t1.63299316186\n-FBgn0000004_17.6\t11\t0\t-0.612372435696\n-FBgn0000004_17.6\t12\t0\t-0.612372435696\n-FBgn0000004_17.6\t13\t0\t-0.612372435696\n-FBgn0000004_17.6\t14\t0\t-0.612372435696\n-FBgn0000004_17.6\t15\t1\t1.63299316186\n+FBgn0000004_17.6\t5\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t6\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t7\t1\t1.632993161855452\n+FBgn0000004_17.6\t8\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t9\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t10\t1\t1.632993161855452\n+FBgn0000004_17.6\t11\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t12\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t13\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t14\t0\t-0.6123724356957945\n+FBgn0000004_17.6\t15\t1\t1.632993161855452\n FBgn0000005_297\t5\t0\t0\n FBgn0000005_297\t6\t0\t0\n FBgn0000005_297\t7\t0\t0\n@@ -20,83 +20,83 @@\n FBgn0000005_297\t13\t0\t0\n FBgn0000005_297\t14\t0\t0\n FBgn0000005_297\t15\t0\t0\n-FBgn0000006_412\t5\t0\t-0.733235575107\n-FBgn0000006_412\t6\t2\t0.0733235575107\n-FBgn0000006_412\t7\t1\t-0.329956008798\n-FBgn0000006_412\t8\t0\t-0.733235575107\n-FBgn0000006_412\t9\t5\t1.28316225644\n-FBgn0000006_412\t10\t8\t2.49300095536\n-FBgn0000006_412\t11\t3\t0.476603123819\n-FBgn0000006_412\t12\t0\t-0.733235575107\n-FBgn0000006_412\t13\t1\t-0.329956008798\n-FBgn0000006_412\t14\t0\t-0.733235575107\n-FBgn0000006_412\t15\t0\t-0.733235575107\n-FBgn0000007_1731\t5\t0\t-0.565685424949\n-FBgn0000007_1731\t6\t0\t-0.565685424949\n-FBgn0000007_1731\t7\t0\t-0.565685424949\n-FBgn0000007_1731\t8\t0\t-0.565685424949\n-FBgn0000007_1731\t9\t0\t-0.565685424949\n-FBgn0000007_1731\t10\t1\t0.989949493661\n-FBgn0000007_1731\t11\t2\t2.54558441227\n-FBgn0000007_1731\t12\t0\t-0.565685424949\n-FBgn0000007_1731\t13\t0\t-0.565685424949\n-FBgn0000007_1731\t14\t1\t0.989949493661\n-FBgn0000007_1731\t15\t0\t-0.565685424949\n-FBgn0000155_roo\t5\t0\t-1.25325662732\n-FBgn0000155_roo\t6\t2\t-0.442325868465\n-FBgn0000155_roo\t7\t1\t-0.847791247891\n-FBgn0000155_roo\t8\t3\t-0.0368604890387\n-FBgn0000155_roo\t9\t2\t-0.442325868465\n-FBgn0000155_roo\t10\t8\t1.99046640809\n-FBgn0000155_roo\t11\t7\t1.58500102867\n-FBgn0000155_roo\t12\t3\t-0.0368604890387\n-FBgn0000155_roo\t13\t0\t-1.25325662732\n-FBgn0000155_roo\t14\t4\t0.368604890387\n-FBgn0000155_roo\t15\t4\t0.368604890387\n-FBgn0000199_blood\t5\t0\t-0.886405260428\n-FBgn0000199_blood\t6\t0\t-0.886405260428\n+FBgn0000006_412\t5\t0\t-0.7332355751067665\n+FBgn0000006_412\t6\t2\t0.07332355751067668\n+FBgn0000006_412\t7\t1\t-0.3299560087980449\n+FBgn0000006_412\t8\t0\t-0.7332355751067665\n+FBgn0000006_412\t9\t5\t1.2831622564368412\n+FBgn0000006_412\t10\t8\t2.493000955363006\n+FBgn0000006_412\t11\t3\t0.47660312381939823\n+FBgn0000006_412\t12\t0\t-0.7332355751067665\n+FBgn0000006_412\t13\t1\t-0.3299560087980449\n+FBgn0000006_412\t14\t0\t-0.7332355751067665\n+FBgn0000006_412\t15\t0\t-0.7332355751067665\n+FBgn0000007_1731\t5\t0\t-0.5656854249492381\n+FBgn0000007_1731\t6\t0\t-0.5656854249492381\n+FBgn0000007_1731\t7\t0\t-0.5656854249492381\n+FBgn0000007_1731\t8\t0\t-0.5656854249492381\n+FBgn0000007_1731\t9\t0\t-0.5656854249492381\n+FBgn0000007_1731\t10\t1\t0.9899494936611666\n+FBgn0000007_1731\t11\t2\t2.545584412271571\n+FBgn0000007_1731\t12\t0\t-0.5656854249492381\n+FBgn0000007_1731\t13\t0\t-0.5656854249492381\n+FBgn0000007_1731\t14\t1\t0.9899494936611666\n+FBgn0000007_1731\t15\t0\t-0.5656854249492381\n+FBgn0000155_roo\t5\t0\t-1.2532566273166255\n+FBgn0000155_roo\t6\t2\t-0.44232586846469135\n+FBgn0000155_roo\t7\t1\t-0.8477912478906584\n+FBgn0000155_roo\t8\t3\t-0.03686048903872425\n+FBgn0000155_roo\t9\t2\t-0.44232586846469135\n+FBgn0000155_roo\t10\t8\t1.9904664080911112\n+FBgn0000155_roo\t11\t7\t1.5850010286651441\n+FBgn0000155_roo\t12\t3\t-0.03686048903872425\n+FBgn0000155_roo\t13\t0\t-1.2532566273166255\n+FBgn0000155_roo\t14\t4\t0.36860489038724287\n+FBgn0000155_roo\t15\t4\t0.36860489038724287\n+FBgn0000199_blood\t5\t0\t-0.8864052604279183\n+FBgn0000199_blood\t6\t0\t-0.8864052604279183\n FBgn0000199_blood\t7\t1\t0.0\n-FBgn0000199_blood\t8\t0\t-0.886405260428\n-FBgn0000199_blood\t9\t0\t-0.886405260428\n-FBgn0000199_blood\t10\t0\t-0.886405260428\n+FBgn0000199_blood\t'..b'0.2834733547569204\n+FBgn0067385_gypsy12\t10\t0\t-0.7559289460184545\n+FBgn0067385_gypsy12\t11\t1\t0.2834733547569204\n+FBgn0067385_gypsy12\t12\t0\t-0.7559289460184545\n+FBgn0067385_gypsy12\t13\t0\t-0.7559289460184545\n+FBgn0067385_gypsy12\t14\t0\t-0.7559289460184545\n+FBgn0067385_gypsy12\t15\t1\t0.2834733547569204\n+FBgn0067385_invader6\t5\t0\t-0.6933752452815365\n+FBgn0067385_invader6\t6\t0\t-0.6933752452815365\n+FBgn0067385_invader6\t7\t0\t-0.6933752452815365\n+FBgn0067385_invader6\t8\t0\t-0.6933752452815365\n+FBgn0067385_invader6\t9\t0\t-0.6933752452815365\n+FBgn0067385_invader6\t10\t1\t0.8320502943378437\n+FBgn0067385_invader6\t11\t1\t0.8320502943378437\n+FBgn0067385_invader6\t12\t1\t0.8320502943378437\n+FBgn0067385_invader6\t13\t2\t2.357475833957224\n+FBgn0067385_invader6\t14\t0\t-0.6933752452815365\n+FBgn0067385_invader6\t15\t0\t-0.6933752452815365\n FBgn0067386_gypsy11\t5\t0\t0\n FBgn0067386_gypsy11\t6\t0\t0\n FBgn0067386_gypsy11\t7\t0\t0\n@@ -1263,17 +1263,17 @@\n FBgn0067421_Fw2\t13\t0\t0\n FBgn0067421_Fw2\t14\t0\t0\n FBgn0067421_Fw2\t15\t0\t0\n-FBgn0067624_BS3\t5\t0\t-0.316227766017\n-FBgn0067624_BS3\t6\t0\t-0.316227766017\n-FBgn0067624_BS3\t7\t0\t-0.316227766017\n-FBgn0067624_BS3\t8\t0\t-0.316227766017\n-FBgn0067624_BS3\t9\t0\t-0.316227766017\n-FBgn0067624_BS3\t10\t3\t3.16227766017\n-FBgn0067624_BS3\t11\t0\t-0.316227766017\n-FBgn0067624_BS3\t12\t0\t-0.316227766017\n-FBgn0067624_BS3\t13\t0\t-0.316227766017\n-FBgn0067624_BS3\t14\t0\t-0.316227766017\n-FBgn0067624_BS3\t15\t0\t-0.316227766017\n+FBgn0067624_BS3\t5\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t6\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t7\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t8\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t9\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t10\t3\t3.16227766016838\n+FBgn0067624_BS3\t11\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t12\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t13\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t14\t0\t-0.31622776601683794\n+FBgn0067624_BS3\t15\t0\t-0.31622776601683794\n FBgn0067624_BS4\t5\t0\t0\n FBgn0067624_BS4\t6\t0\t0\n FBgn0067624_BS4\t7\t0\t0\n@@ -1285,17 +1285,17 @@\n FBgn0067624_BS4\t13\t0\t0\n FBgn0067624_BS4\t14\t0\t0\n FBgn0067624_BS4\t15\t0\t0\n-FBgn0069340_Tc1-2\t5\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t6\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t7\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t8\t1\t3.16227766017\n-FBgn0069340_Tc1-2\t9\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t10\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t11\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t12\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t13\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t14\t0\t-0.316227766017\n-FBgn0069340_Tc1-2\t15\t0\t-0.316227766017\n+FBgn0069340_Tc1-2\t5\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t6\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t7\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t8\t1\t3.16227766016838\n+FBgn0069340_Tc1-2\t9\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t10\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t11\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t12\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t13\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t14\t0\t-0.316227766016838\n+FBgn0069340_Tc1-2\t15\t0\t-0.316227766016838\n FBgn0069433_G5A\t5\t0\t0\n FBgn0069433_G5A\t6\t0\t0\n FBgn0069433_G5A\t7\t0\t0\n@@ -1318,14 +1318,14 @@\n FBgn0069587_Doc4-element\t13\t0\t0\n FBgn0069587_Doc4-element\t14\t0\t0\n FBgn0069587_Doc4-element\t15\t0\t0\n-all_chromosomes\t5\t2\t-1.08978129104\n-all_chromosomes\t6\t43\t-0.422900202493\n-all_chromosomes\t7\t44\t-0.40663481009\n-all_chromosomes\t8\t60\t-0.146388531632\n-all_chromosomes\t9\t71\t0.0325307848072\n-all_chromosomes\t10\t254\t3.00909759466\n-all_chromosomes\t11\t70\t0.0162653924036\n-all_chromosomes\t12\t43\t-0.422900202493\n-all_chromosomes\t13\t43\t-0.422900202493\n-all_chromosomes\t14\t58\t-0.17891931644\n-all_chromosomes\t15\t71\t0.0325307848072\n+all_chromosomes\t5\t2\t-1.0897812910406286\n+all_chromosomes\t6\t43\t-0.42290020249337823\n+all_chromosomes\t7\t44\t-0.40663481008978675\n+all_chromosomes\t8\t60\t-0.14638853163232324\n+all_chromosomes\t9\t71\t0.03253078480718294\n+all_chromosomes\t10\t254\t3.009097594664422\n+all_chromosomes\t11\t70\t0.01626539240359147\n+all_chromosomes\t12\t43\t-0.42290020249337823\n+all_chromosomes\t13\t43\t-0.42290020249337823\n+all_chromosomes\t14\t58\t-0.17891931643950618\n+all_chromosomes\t15\t71\t0.03253078480718294\n' |