Mercurial > repos > artbio > small_rna_signatures
changeset 11:8d3ca9652a5b draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
| author | artbio |
|---|---|
| date | Sat, 23 Oct 2021 22:55:19 +0000 |
| parents | 68ee7c84d498 |
| children | aa5e2c64dff8 |
| files | 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 |
| diffstat | 9 files changed, 1632 insertions(+), 1625 deletions(-) [+] |
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--- a/overlapping_reads.py Tue Jan 07 06:59:56 2020 -0500 +++ b/overlapping_reads.py Sat Oct 23 22:55:19 2021 +0000 @@ -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,
--- a/overlapping_reads.xml Tue Jan 07 06:59:56 2020 -0500 +++ b/overlapping_reads.xml Sat Oct 23 22:55:19 2021 +0000 @@ -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" />
--- 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,
--- 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) }
--- a/signature.xml Tue Jan 07 06:59:56 2020 -0500 +++ b/signature.xml Sat Oct 23 22:55:19 2021 +0000 @@ -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" />
--- 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 @@ -1,14 +1,14 @@ -FBgn0000004_17.6 5 0.0 -0.565685424949 -FBgn0000004_17.6 6 0.0 -0.565685424949 -FBgn0000004_17.6 7 0.00369003690037 0.989949493661 -FBgn0000004_17.6 8 0.0 -0.565685424949 -FBgn0000004_17.6 9 0.0 -0.565685424949 -FBgn0000004_17.6 10 0.00369003690037 0.989949493661 -FBgn0000004_17.6 11 0.0 -0.565685424949 -FBgn0000004_17.6 12 0.0 -0.565685424949 -FBgn0000004_17.6 13 0.0 -0.565685424949 -FBgn0000004_17.6 14 0.0 -0.565685424949 -FBgn0000004_17.6 15 0.00738007380074 2.54558441227 +FBgn0000004_17.6 5 0.0 -0.565685424949238 +FBgn0000004_17.6 6 0.0 -0.565685424949238 +FBgn0000004_17.6 7 0.0036900369003690036 0.9899494936611665 +FBgn0000004_17.6 8 0.0 -0.565685424949238 +FBgn0000004_17.6 9 0.0 -0.565685424949238 +FBgn0000004_17.6 10 0.0036900369003690036 0.9899494936611665 +FBgn0000004_17.6 11 0.0 -0.565685424949238 +FBgn0000004_17.6 12 0.0 -0.565685424949238 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+FBgn0042682_Rt1b 6 0.0 -0.5005327397833322 +FBgn0042682_Rt1b 7 0.009708509637987776 0.029518597474401557 +FBgn0042682_Rt1b 8 0.004513399153737659 -0.2541166217361533 +FBgn0042682_Rt1b 9 0.007052186177715091 -0.11550755533461522 +FBgn0042682_Rt1b 10 0.06580636601561941 3.0922692048290936 +FBgn0042682_Rt1b 11 0.0022973280967685463 -0.37510650288212255 +FBgn0042682_Rt1b 12 0.010682327915096303 0.08268573633242932 +FBgn0042682_Rt1b 13 0.0007861453444010266 -0.45761189954970477 +FBgn0042682_Rt1b 14 0.0 -0.5005327397833322 +FBgn0042682_Rt1b 15 0.0 -0.5005327397833322 +FBgn0043055_Ivk 5 0.0 -0.4714045207910317 +FBgn0043055_Ivk 6 0.0 -0.4714045207910317 +FBgn0043055_Ivk 7 0.0 -0.4714045207910317 +FBgn0043055_Ivk 8 0.0 -0.4714045207910317 +FBgn0043055_Ivk 9 0.008 2.1213203435596424 +FBgn0043055_Ivk 10 0.0 -0.4714045207910317 +FBgn0043055_Ivk 11 0.0 -0.4714045207910317 +FBgn0043055_Ivk 12 0.0 -0.4714045207910317 +FBgn0043055_Ivk 13 0.008 2.1213203435596424 +FBgn0043055_Ivk 14 0.0 -0.4714045207910317 +FBgn0043055_Ivk 15 0.0 -0.4714045207910317 +FBgn0043969_diver 5 0.0 -0.31622776601683794 +FBgn0043969_diver 6 0.0 -0.31622776601683794 +FBgn0043969_diver 7 0.0 -0.31622776601683794 +FBgn0043969_diver 8 0.0 -0.31622776601683794 +FBgn0043969_diver 9 0.0 -0.31622776601683794 +FBgn0043969_diver 10 0.0 -0.31622776601683794 +FBgn0043969_diver 11 0.0 -0.31622776601683794 +FBgn0043969_diver 12 0.0 -0.31622776601683794 +FBgn0043969_diver 13 0.0 -0.31622776601683794 +FBgn0043969_diver 14 0.0 -0.31622776601683794 +FBgn0043969_diver 15 0.02247191011235955 3.1622776601683795 +FBgn0044355_Quasimodo 5 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 6 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 7 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 8 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 9 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 10 0.015463917525773196 3.1622776601683795 +FBgn0044355_Quasimodo 11 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 12 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 13 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 14 0.0 -0.31622776601683794 +FBgn0044355_Quasimodo 15 0.0 -0.31622776601683794 FBgn0045970_Tabor 5 0 0 FBgn0045970_Tabor 6 0 0 FBgn0045970_Tabor 7 0 0 @@ -625,17 +625,17 @@ FBgn0045970_Tabor 13 0 0 FBgn0045970_Tabor 14 0 0 FBgn0045970_Tabor 15 0 0 -FBgn0046110_Juan 5 0.0 -0.398682912646 -FBgn0046110_Juan 6 0.121359223301 3.1380203447 -FBgn0046110_Juan 7 0.00970873786408 -0.115746652059 -FBgn0046110_Juan 8 0.0 -0.398682912646 -FBgn0046110_Juan 9 0.0 -0.398682912646 -FBgn0046110_Juan 10 0.0 -0.398682912646 -FBgn0046110_Juan 11 0.00970873786408 -0.115746652059 -FBgn0046110_Juan 12 0.0 -0.398682912646 -FBgn0046110_Juan 13 0.0 -0.398682912646 -FBgn0046110_Juan 14 0.0 -0.398682912646 -FBgn0046110_Juan 15 0.00970873786408 -0.115746652059 +FBgn0046110_Juan 5 0.0 -0.40362686334960024 +FBgn0046110_Juan 6 0.12378640776699029 3.13441486069924 +FBgn0046110_Juan 7 0.009708737864077669 -0.1261333947967501 +FBgn0046110_Juan 8 0.0 -0.40362686334960024 +FBgn0046110_Juan 9 0.0 -0.40362686334960024 +FBgn0046110_Juan 10 0.0 -0.40362686334960024 +FBgn0046110_Juan 11 0.012135922330097087 -0.056760027658537514 +FBgn0046110_Juan 12 0.0 -0.40362686334960024 +FBgn0046110_Juan 13 0.0 -0.40362686334960024 +FBgn0046110_Juan 14 0.0 -0.40362686334960024 +FBgn0046110_Juan 15 0.009708737864077669 -0.1261333947967501 FBgn0046701_Penelope 5 0 0 FBgn0046701_Penelope 6 0 0 FBgn0046701_Penelope 7 0 0 @@ -647,17 +647,17 @@ FBgn0046701_Penelope 13 0 0 FBgn0046701_Penelope 14 0 0 FBgn0046701_Penelope 15 0 0 -FBgn0061485_rover 5 0.0 -0.316227766017 -FBgn0061485_rover 6 0.0 -0.316227766017 -FBgn0061485_rover 7 0.0 -0.316227766017 -FBgn0061485_rover 8 0.0 -0.316227766017 -FBgn0061485_rover 9 0.0192307692308 3.16227766017 -FBgn0061485_rover 10 0.0 -0.316227766017 -FBgn0061485_rover 11 0.0 -0.316227766017 -FBgn0061485_rover 12 0.0 -0.316227766017 -FBgn0061485_rover 13 0.0 -0.316227766017 -FBgn0061485_rover 14 0.0 -0.316227766017 -FBgn0061485_rover 15 0.0 -0.316227766017 +FBgn0061485_rover 5 0.0 -0.3162277660168379 +FBgn0061485_rover 6 0.0 -0.3162277660168379 +FBgn0061485_rover 7 0.0 -0.3162277660168379 +FBgn0061485_rover 8 0.0 -0.3162277660168379 +FBgn0061485_rover 9 0.019230769230769232 3.1622776601683795 +FBgn0061485_rover 10 0.0 -0.3162277660168379 +FBgn0061485_rover 11 0.0 -0.3162277660168379 +FBgn0061485_rover 12 0.0 -0.3162277660168379 +FBgn0061485_rover 13 0.0 -0.3162277660168379 +FBgn0061485_rover 14 0.0 -0.3162277660168379 +FBgn0061485_rover 15 0.0 -0.3162277660168379 FBgn0061513_frogger 5 0 0 FBgn0061513_frogger 6 0 0 FBgn0061513_frogger 7 0 0 @@ -669,17 +669,17 @@ FBgn0061513_frogger 13 0 0 FBgn0061513_frogger 14 0 0 FBgn0061513_frogger 15 0 0 -FBgn0062343_Dm88 5 0.0 -0.471404520791 -FBgn0062343_Dm88 6 0.0 -0.471404520791 -FBgn0062343_Dm88 7 0.0 -0.471404520791 -FBgn0062343_Dm88 8 0.0 -0.471404520791 -FBgn0062343_Dm88 9 0.0 -0.471404520791 -FBgn0062343_Dm88 10 0.0 -0.471404520791 -FBgn0062343_Dm88 11 0.0107913669065 2.12132034356 -FBgn0062343_Dm88 12 0.0 -0.471404520791 -FBgn0062343_Dm88 13 0.0107913669065 2.12132034356 -FBgn0062343_Dm88 14 0.0 -0.471404520791 -FBgn0062343_Dm88 15 0.0 -0.471404520791 +FBgn0062343_Dm88 5 0.0 -0.47140452079103173 +FBgn0062343_Dm88 6 0.0 -0.47140452079103173 +FBgn0062343_Dm88 7 0.0 -0.47140452079103173 +FBgn0062343_Dm88 8 0.0 -0.47140452079103173 +FBgn0062343_Dm88 9 0.0 -0.47140452079103173 +FBgn0062343_Dm88 10 0.0 -0.47140452079103173 +FBgn0062343_Dm88 11 0.01079136690647482 2.121320343559643 +FBgn0062343_Dm88 12 0.0 -0.47140452079103173 +FBgn0062343_Dm88 13 0.01079136690647482 2.121320343559643 +FBgn0062343_Dm88 14 0.0 -0.47140452079103173 +FBgn0062343_Dm88 15 0.0 -0.47140452079103173 FBgn0063369_transib4 5 0 0 FBgn0063369_transib4 6 0 0 FBgn0063369_transib4 7 0 0 @@ -702,17 +702,17 @@ FBgn0063370_transib3 13 0 0 FBgn0063370_transib3 14 0 0 FBgn0063370_transib3 15 0 0 -FBgn0063371_transib2 5 0.0 -0.316227766017 -FBgn0063371_transib2 6 0.0 -0.316227766017 -FBgn0063371_transib2 7 0.0 -0.316227766017 -FBgn0063371_transib2 8 0.0 -0.316227766017 -FBgn0063371_transib2 9 0.0 -0.316227766017 -FBgn0063371_transib2 10 0.0 -0.316227766017 -FBgn0063371_transib2 11 0.0 -0.316227766017 -FBgn0063371_transib2 12 0.136363636364 3.16227766017 -FBgn0063371_transib2 13 0.0 -0.316227766017 -FBgn0063371_transib2 14 0.0 -0.316227766017 -FBgn0063371_transib2 15 0.0 -0.316227766017 +FBgn0063371_transib2 5 0.0 -0.3162277660168379 +FBgn0063371_transib2 6 0.0 -0.3162277660168379 +FBgn0063371_transib2 7 0.0 -0.3162277660168379 +FBgn0063371_transib2 8 0.0 -0.3162277660168379 +FBgn0063371_transib2 9 0.0 -0.3162277660168379 +FBgn0063371_transib2 10 0.0 -0.3162277660168379 +FBgn0063371_transib2 11 0.0 -0.3162277660168379 +FBgn0063371_transib2 12 0.13636363636363635 3.162277660168379 +FBgn0063371_transib2 13 0.0 -0.3162277660168379 +FBgn0063371_transib2 14 0.0 -0.3162277660168379 +FBgn0063371_transib2 15 0.0 -0.3162277660168379 FBgn0063372_transib1 5 0 0 FBgn0063372_transib1 6 0 0 FBgn0063372_transib1 7 0 0 @@ -724,17 +724,17 @@ FBgn0063372_transib1 13 0 0 FBgn0063372_transib1 14 0 0 FBgn0063372_transib1 15 0 0 -FBgn0063394_rooA 5 0.0 -0.842664840618 -FBgn0063394_rooA 6 0.00945179584121 2.72245563892 -FBgn0063394_rooA 7 0.0 -0.842664840618 -FBgn0063394_rooA 8 0.00189035916824 -0.12964074471 -FBgn0063394_rooA 9 0.00189035916824 -0.12964074471 -FBgn0063394_rooA 10 0.0 -0.842664840618 -FBgn0063394_rooA 11 0.00189035916824 -0.12964074471 -FBgn0063394_rooA 12 0.00189035916824 -0.12964074471 -FBgn0063394_rooA 13 0.00378071833648 0.583383351197 -FBgn0063394_rooA 14 0.0 -0.842664840618 -FBgn0063394_rooA 15 0.00378071833648 0.583383351197 +FBgn0063394_rooA 5 0.0 -0.9743547036924465 +FBgn0063394_rooA 6 0.00945179584120983 2.598279209846523 +FBgn0063394_rooA 7 0.0 -0.9743547036924465 +FBgn0063394_rooA 8 0.002835538752362949 0.09743547036924449 +FBgn0063394_rooA 9 0.002835538752362949 0.09743547036924449 +FBgn0063394_rooA 10 0.0 -0.9743547036924465 +FBgn0063394_rooA 11 0.002835538752362949 0.09743547036924449 +FBgn0063394_rooA 12 0.002835538752362949 0.09743547036924449 +FBgn0063394_rooA 13 0.003780718336483932 0.45469886172314145 +FBgn0063394_rooA 14 0.0 -0.9743547036924465 +FBgn0063394_rooA 15 0.003780718336483932 0.45469886172314145 FBgn0063401_mariner2 5 0 0 FBgn0063401_mariner2 6 0 0 FBgn0063401_mariner2 7 0 0 @@ -746,17 +746,17 @@ FBgn0063401_mariner2 13 0 0 FBgn0063401_mariner2 14 0 0 FBgn0063401_mariner2 15 0 0 -FBgn0063402_looper1 5 0.0 -0.316227766017 -FBgn0063402_looper1 6 0.0 -0.316227766017 -FBgn0063402_looper1 7 0.0 -0.316227766017 -FBgn0063402_looper1 8 0.0 -0.316227766017 -FBgn0063402_looper1 9 0.0 -0.316227766017 -FBgn0063402_looper1 10 0.0 -0.316227766017 -FBgn0063402_looper1 11 0.0 -0.316227766017 -FBgn0063402_looper1 12 0.0 -0.316227766017 -FBgn0063402_looper1 13 0.0 -0.316227766017 -FBgn0063402_looper1 14 0.0666666666667 3.16227766017 -FBgn0063402_looper1 15 0.0 -0.316227766017 +FBgn0063402_looper1 5 0.0 -0.3162277660168379 +FBgn0063402_looper1 6 0.0 -0.3162277660168379 +FBgn0063402_looper1 7 0.0 -0.3162277660168379 +FBgn0063402_looper1 8 0.0 -0.3162277660168379 +FBgn0063402_looper1 9 0.0 -0.3162277660168379 +FBgn0063402_looper1 10 0.0 -0.3162277660168379 +FBgn0063402_looper1 11 0.0 -0.3162277660168379 +FBgn0063402_looper1 12 0.0 -0.3162277660168379 +FBgn0063402_looper1 13 0.0 -0.3162277660168379 +FBgn0063402_looper1 14 0.06666666666666667 3.162277660168379 +FBgn0063402_looper1 15 0.0 -0.3162277660168379 FBgn0063425_jockey2 5 0 0 FBgn0063425_jockey2 6 0 0 FBgn0063425_jockey2 7 0 0 @@ -779,61 +779,61 @@ FBgn0063426_invader5 13 0 0 FBgn0063426_invader5 14 0 0 FBgn0063426_invader5 15 0 0 -FBgn0063427_invader4 5 0.0 -0.427361209838 -FBgn0063427_invader4 6 0.0 -0.427361209838 -FBgn0063427_invader4 7 0.0 -0.427361209838 -FBgn0063427_invader4 8 0.229437229437 2.98567420572 -FBgn0063427_invader4 9 0.00865800865801 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8 0.0 -0.316227766017 -FBgn0063429_invader2 9 0.0 -0.316227766017 -FBgn0063429_invader2 10 0.015625 3.16227766017 -FBgn0063429_invader2 11 0.0 -0.316227766017 -FBgn0063429_invader2 12 0.0 -0.316227766017 -FBgn0063429_invader2 13 0.0 -0.316227766017 -FBgn0063429_invader2 14 0.0 -0.316227766017 -FBgn0063429_invader2 15 0.0 -0.316227766017 -FBgn0063430_invader1 5 0.0 -0.660597289685 -FBgn0063430_invader1 6 0.00814332247557 0.112442091861 -FBgn0063430_invader1 7 0.00651465798046 -0.042165784448 -FBgn0063430_invader1 8 0.00488599348534 -0.196773660757 -FBgn0063430_invader1 9 0.0 -0.660597289685 -FBgn0063430_invader1 10 0.0342019543974 2.58616811281 -FBgn0063430_invader1 11 0.0 -0.660597289685 -FBgn0063430_invader1 12 0.0 -0.660597289685 -FBgn0063430_invader1 13 0.0 -0.660597289685 -FBgn0063430_invader1 14 0.00162866449511 -0.505989413375 -FBgn0063430_invader1 15 0.0211726384365 1.34930510233 -FBgn0063431_gypsy6 5 0.0 -0.771099600956 -FBgn0063431_gypsy6 6 0.00625 0.385549800478 -FBgn0063431_gypsy6 7 0.0 -0.771099600956 -FBgn0063431_gypsy6 8 0.0 -0.771099600956 -FBgn0063431_gypsy6 9 0.00416666666667 0.0 -FBgn0063431_gypsy6 10 0.00416666666667 0.0 -FBgn0063431_gypsy6 11 0.00833333333333 0.771099600956 -FBgn0063431_gypsy6 12 0.0 -0.771099600956 -FBgn0063431_gypsy6 13 0.0 -0.771099600956 -FBgn0063431_gypsy6 14 0.00416666666667 0.0 -FBgn0063431_gypsy6 15 0.01875 2.69884860335 +FBgn0063427_invader4 5 0.0 -0.42736120983776815 +FBgn0063427_invader4 6 0.0 -0.42736120983776815 +FBgn0063427_invader4 7 0.0 -0.42736120983776815 +FBgn0063427_invader4 8 0.22943722943722944 2.9856742057159145 +FBgn0063427_invader4 9 0.008658008658008658 -0.2985674205715915 +FBgn0063427_invader4 10 0.07792207792207792 0.7317828935578221 +FBgn0063427_invader4 11 0.0 -0.42736120983776815 +FBgn0063427_invader4 12 0.0 -0.42736120983776815 +FBgn0063427_invader4 13 0.0 -0.42736120983776815 +FBgn0063427_invader4 14 0.0 -0.42736120983776815 +FBgn0063427_invader4 15 0.0 -0.42736120983776815 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-0.7710996009560598 +FBgn0063431_gypsy6 9 0.004166666666666667 0.0 +FBgn0063431_gypsy6 10 0.004166666666666667 0.0 +FBgn0063431_gypsy6 11 0.008333333333333333 0.7710996009560598 +FBgn0063431_gypsy6 12 0.0 -0.7710996009560598 +FBgn0063431_gypsy6 13 0.0 -0.7710996009560598 +FBgn0063431_gypsy6 14 0.004166666666666667 0.0 +FBgn0063431_gypsy6 15 0.01875 2.6988486033462094 FBgn0063432_gypsy5 5 0 0 FBgn0063432_gypsy5 6 0 0 FBgn0063432_gypsy5 7 0 0 @@ -845,17 +845,17 @@ FBgn0063432_gypsy5 13 0 0 FBgn0063432_gypsy5 14 0 0 FBgn0063432_gypsy5 15 0 0 -FBgn0063433_gypsy4 5 0.0 -0.441249367724 -FBgn0063433_gypsy4 6 0.0 -0.441249367724 -FBgn0063433_gypsy4 7 0.00497512437811 -0.313519287593 -FBgn0063433_gypsy4 8 0.00497512437811 -0.313519287593 -FBgn0063433_gypsy4 9 0.00995024875622 -0.185789207463 -FBgn0063433_gypsy4 10 0.139303482587 3.13519287593 -FBgn0063433_gypsy4 11 0.0174129353234 0.00580591273321 -FBgn0063433_gypsy4 12 0.00746268656716 -0.249654247528 -FBgn0063433_gypsy4 13 0.0 -0.441249367724 -FBgn0063433_gypsy4 14 0.0 -0.441249367724 -FBgn0063433_gypsy4 15 0.00497512437811 -0.313519287593 +FBgn0063433_gypsy4 5 0.0 -0.44948178289472457 +FBgn0063433_gypsy4 6 0.0 -0.44948178289472457 +FBgn0063433_gypsy4 7 0.006633499170812603 -0.2846717958333256 +FBgn0063433_gypsy4 8 0.006633499170812603 -0.2846717958333256 +FBgn0063433_gypsy4 9 0.011194029850746266 -0.17136492972861384 +FBgn0063433_gypsy4 10 0.14424899312959014 3.1343996768198936 +FBgn0063433_gypsy4 11 0.017857142857142856 -0.005819183796404964 +FBgn0063433_gypsy4 12 0.007462686567164179 -0.2640705474506507 +FBgn0063433_gypsy4 13 0.0 -0.44948178289472457 +FBgn0063433_gypsy4 14 0.0 -0.44948178289472457 +FBgn0063433_gypsy4 15 0.004975124378109453 -0.32587429259867534 FBgn0063434_gypsy3 5 0 0 FBgn0063434_gypsy3 6 0 0 FBgn0063434_gypsy3 7 0 0 @@ -878,50 +878,50 @@ FBgn0063435_gypsy2 13 0 0 FBgn0063435_gypsy2 14 0 0 FBgn0063435_gypsy2 15 0 0 -FBgn0063436_gtwin 5 0.0 -0.66966391361 -FBgn0063436_gtwin 6 0.0068306010929 0.081999662891 -FBgn0063436_gtwin 7 0.0327868852459 2.93832125359 -FBgn0063436_gtwin 8 0.0068306010929 0.081999662891 -FBgn0063436_gtwin 9 0.00956284153005 0.382665093491 -FBgn0063436_gtwin 10 0.00136612021858 -0.519331198309 -FBgn0063436_gtwin 11 0.00273224043716 -0.368998483009 -FBgn0063436_gtwin 12 0.0 -0.66966391361 -FBgn0063436_gtwin 13 0.0 -0.66966391361 -FBgn0063436_gtwin 14 0.0068306010929 0.081999662891 -FBgn0063436_gtwin 15 0.0 -0.66966391361 -FBgn0063439_diver2 5 0.0 -0.471404520791 -FBgn0063439_diver2 6 0.0 -0.471404520791 -FBgn0063439_diver2 7 0.0 -0.471404520791 -FBgn0063439_diver2 8 0.0155440414508 2.12132034356 -FBgn0063439_diver2 9 0.0 -0.471404520791 -FBgn0063439_diver2 10 0.0 -0.471404520791 -FBgn0063439_diver2 11 0.0 -0.471404520791 -FBgn0063439_diver2 12 0.0 -0.471404520791 -FBgn0063439_diver2 13 0.0 -0.471404520791 -FBgn0063439_diver2 14 0.0155440414508 2.12132034356 -FBgn0063439_diver2 15 0.0 -0.471404520791 -FBgn0063440_baggins 5 0.0 -0.879882690128 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FBgn0067624_BS4 13 0 0 FBgn0067624_BS4 14 0 0 FBgn0067624_BS4 15 0 0 -FBgn0069340_Tc1-2 5 0.0 -0.316227766017 -FBgn0069340_Tc1-2 6 0.0 -0.316227766017 -FBgn0069340_Tc1-2 7 0.0 -0.316227766017 -FBgn0069340_Tc1-2 8 0.103448275862 3.16227766017 -FBgn0069340_Tc1-2 9 0.0 -0.316227766017 -FBgn0069340_Tc1-2 10 0.0 -0.316227766017 -FBgn0069340_Tc1-2 11 0.0 -0.316227766017 -FBgn0069340_Tc1-2 12 0.0 -0.316227766017 -FBgn0069340_Tc1-2 13 0.0 -0.316227766017 -FBgn0069340_Tc1-2 14 0.0 -0.316227766017 -FBgn0069340_Tc1-2 15 0.0 -0.316227766017 +FBgn0069340_Tc1-2 5 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 6 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 7 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 8 0.10344827586206896 3.1622776601683795 +FBgn0069340_Tc1-2 9 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 10 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 11 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 12 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 13 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 14 0.0 -0.316227766016838 +FBgn0069340_Tc1-2 15 0.0 -0.316227766016838 FBgn0069433_G5A 5 0 0 FBgn0069433_G5A 6 0 0 FBgn0069433_G5A 7 0 0 @@ -1318,14 +1318,14 @@ FBgn0069587_Doc4-element 13 0 0 FBgn0069587_Doc4-element 14 0 0 FBgn0069587_Doc4-element 15 0 0 -all_chromosomes 5 4.26865796963e-06 -1.02078731734 -all_chromosomes 6 0.000272508714058 -0.505836219906 -all_chromosomes 7 0.000314189173203 -0.425820585808 -all_chromosomes 8 0.000481492106257 -0.104642495418 -all_chromosomes 9 0.000402138333192 -0.256981087653 -all_chromosomes 10 0.00205870585512 2.92319742793 -all_chromosomes 11 0.000380479180279 -0.298561024389 -all_chromosomes 12 0.000209011312505 -0.627734705504 -all_chromosomes 13 0.000334785271578 -0.386281437121 -all_chromosomes 14 0.000668570428043 0.254499194734 -all_chromosomes 15 0.000769859707507 0.448948250475 +all_chromosomes 5 4.597016274988517e-06 -1.0469141525331194 +all_chromosomes 6 0.0002824030976458536 -0.52144365445537 +all_chromosomes 7 0.000340456835038392 -0.4116349484961661 +all_chromosomes 8 0.0005109744379707215 -0.08910072137729177 +all_chromosomes 9 0.0004259214471628285 -0.2499785438579372 +all_chromosomes 10 0.0020996847468840105 2.9159465159128586 +all_chromosomes 11 0.0004052560308455948 -0.2890672007786769 +all_chromosomes 12 0.00022552377211365463 -0.6290309591329472 +all_chromosomes 13 0.00035575730465490775 -0.3826940939600091 +all_chromosomes 14 0.0006968571672892477 0.26249665862628785 +all_chromosomes 15 0.0007914510562247529 0.4414211000523717
--- 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 @@ -1,14 +1,14 @@ -FBgn0000004_17.6 5 0 -0.612372435696 -FBgn0000004_17.6 6 0 -0.612372435696 -FBgn0000004_17.6 7 1 1.63299316186 -FBgn0000004_17.6 8 0 -0.612372435696 -FBgn0000004_17.6 9 0 -0.612372435696 -FBgn0000004_17.6 10 1 1.63299316186 -FBgn0000004_17.6 11 0 -0.612372435696 -FBgn0000004_17.6 12 0 -0.612372435696 -FBgn0000004_17.6 13 0 -0.612372435696 -FBgn0000004_17.6 14 0 -0.612372435696 -FBgn0000004_17.6 15 1 1.63299316186 +FBgn0000004_17.6 5 0 -0.6123724356957945 +FBgn0000004_17.6 6 0 -0.6123724356957945 +FBgn0000004_17.6 7 1 1.632993161855452 +FBgn0000004_17.6 8 0 -0.6123724356957945 +FBgn0000004_17.6 9 0 -0.6123724356957945 +FBgn0000004_17.6 10 1 1.632993161855452 +FBgn0000004_17.6 11 0 -0.6123724356957945 +FBgn0000004_17.6 12 0 -0.6123724356957945 +FBgn0000004_17.6 13 0 -0.6123724356957945 +FBgn0000004_17.6 14 0 -0.6123724356957945 +FBgn0000004_17.6 15 1 1.632993161855452 FBgn0000005_297 5 0 0 FBgn0000005_297 6 0 0 FBgn0000005_297 7 0 0 @@ -20,83 +20,83 @@ FBgn0000005_297 13 0 0 FBgn0000005_297 14 0 0 FBgn0000005_297 15 0 0 -FBgn0000006_412 5 0 -0.733235575107 -FBgn0000006_412 6 2 0.0733235575107 -FBgn0000006_412 7 1 -0.329956008798 -FBgn0000006_412 8 0 -0.733235575107 -FBgn0000006_412 9 5 1.28316225644 -FBgn0000006_412 10 8 2.49300095536 -FBgn0000006_412 11 3 0.476603123819 -FBgn0000006_412 12 0 -0.733235575107 -FBgn0000006_412 13 1 -0.329956008798 -FBgn0000006_412 14 0 -0.733235575107 -FBgn0000006_412 15 0 -0.733235575107 -FBgn0000007_1731 5 0 -0.565685424949 -FBgn0000007_1731 6 0 -0.565685424949 -FBgn0000007_1731 7 0 -0.565685424949 -FBgn0000007_1731 8 0 -0.565685424949 -FBgn0000007_1731 9 0 -0.565685424949 -FBgn0000007_1731 10 1 0.989949493661 -FBgn0000007_1731 11 2 2.54558441227 -FBgn0000007_1731 12 0 -0.565685424949 -FBgn0000007_1731 13 0 -0.565685424949 -FBgn0000007_1731 14 1 0.989949493661 -FBgn0000007_1731 15 0 -0.565685424949 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-0.316227766016838 FBgn0069433_G5A 5 0 0 FBgn0069433_G5A 6 0 0 FBgn0069433_G5A 7 0 0 @@ -1318,14 +1318,14 @@ FBgn0069587_Doc4-element 13 0 0 FBgn0069587_Doc4-element 14 0 0 FBgn0069587_Doc4-element 15 0 0 -all_chromosomes 5 2 -1.08978129104 -all_chromosomes 6 43 -0.422900202493 -all_chromosomes 7 44 -0.40663481009 -all_chromosomes 8 60 -0.146388531632 -all_chromosomes 9 71 0.0325307848072 -all_chromosomes 10 254 3.00909759466 -all_chromosomes 11 70 0.0162653924036 -all_chromosomes 12 43 -0.422900202493 -all_chromosomes 13 43 -0.422900202493 -all_chromosomes 14 58 -0.17891931644 -all_chromosomes 15 71 0.0325307848072 +all_chromosomes 5 2 -1.0897812910406286 +all_chromosomes 6 43 -0.42290020249337823 +all_chromosomes 7 44 -0.40663481008978675 +all_chromosomes 8 60 -0.14638853163232324 +all_chromosomes 9 71 0.03253078480718294 +all_chromosomes 10 254 3.009097594664422 +all_chromosomes 11 70 0.01626539240359147 +all_chromosomes 12 43 -0.42290020249337823 +all_chromosomes 13 43 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