miga-base 0.2.0.6

data/utils/adapters.fa

@@ -0,0 +1,302 @@
+>Illumina_Single_End_Apapter_1
+ACACTCTTTCCCTACACGACGCTGTTCCATCT
+>Illumina_Single_End_Apapter_2
+CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+>Illumina_Single_End_PCR_Primer_1
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>Illumina_Single_End_PCR_Primer_2
+CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+>Illumina_Single_End_Sequencing_Primer
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+>Illumina_Paired_End_Adapter_1
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>Illumina_Paired_End_Adapter_2
+CTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>Illumina_Paried_End_PCR_Primer_1
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>Illumina_Paired_End_PCR_Primer_2
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>Illumina_Paried_End_Sequencing_Primer_1
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>Illumina_Paired_End_Sequencing_Primer_2
+CGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT
+
+>Illumina_DpnII_expression_Adapter_1
+ACAGGTTCAGAGTTCTACAGTCCGAC
+>Illumina_DpnII_expression_Adapter_2
+CAAGCAGAAGACGGCATACGA
+>Illumina_DpnII_expression_PCR_Primer_1
+CAAGCAGAAGACGGCATACGA
+>Illumina_DpnII_expression_PCR_Primer_2
+AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+>Illumina_DpnII_expression_Sequencing_Primer
+CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+>Illumina_NlaIII_expression_Adapter_1
+ACAGGTTCAGAGTTCTACAGTCCGACATG
+>Illumina_NlaIII_expression_Adapter_2
+CAAGCAGAAGACGGCATACGA
+>Illumina_NlaIII_expression_PCR_Primer_1
+CAAGCAGAAGACGGCATACGA
+>Illumina_NlaIII_expression_PCR_Primer_2
+AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+>Illumina_NlaIII_expression_Sequencing_Primer
+CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+>Illumina_Small_RNA_Adapter_1
+GTTCAGAGTTCTACAGTCCGACGATC
+>Illumina_Small_RNA_Adapter_2
+TCGTATGCCGTCTTCTGCTTGT
+>Illumina_Small_RNA_RT_Primer
+CAAGCAGAAGACGGCATACGA
+>Illumina_Small_RNA_PCR_Primer_1
+CAAGCAGAAGACGGCATACGA
+>Illumina_Small_RNA_PCR_Primer_2
+AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+>Illumina_Small_RNA_Sequencing_Primer
+CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+>Illumina_Multiplexing_Adapter_1
+GATCGGAAGAGCACACGTCT
+>Illumina_Multiplexing_Adapter_2
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>Illumina_Multiplexing_PCR_Primer_1.01
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>Illumina_Multiplexing_PCR_Primer_2.01
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>Illumina_Multiplexing_Read1_Sequencing_Primer
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>Illumina_Multiplexing_Index_Sequencing_Primer
+GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>Illumina_Multiplexing_Read2_Sequencing_Primer
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+
+>Illumina_PCR_Primer_Index_1
+CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_2
+CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_3
+CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_4
+CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_5
+CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_6
+CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_7
+CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_8
+CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_9
+CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_10
+CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_11
+CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC
+>Illumina_PCR_Primer_Index_12
+CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC
+
+>Illumina_DpnII_Gex_Adapter_1
+GATCGTCGGACTGTAGAACTCTGAAC
+>Illumina_DpnII_Gex_Adapter_1.01
+ACAGGTTCAGAGTTCTACAGTCCGAC
+>Illumina_DpnII_Gex_Adapter_2
+CAAGCAGAAGACGGCATACGA
+>Illumina_DpnII_Gex_Adapter_2.01
+TCGTATGCCGTCTTCTGCTTG
+>Illumina_DpnII_Gex_PCR_Primer_1
+CAAGCAGAAGACGGCATACGA
+>Illumina_DpnII_Gex_PCR_Primer_2
+AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+>Illumina_DpnII_Gex_Sequencing_Primer
+CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+>Illumina_NlaIII_Gex_Adapter_1.01
+TCGGACTGTAGAACTCTGAAC
+>Illumina_NlaIII_Gex_Adapter_1.02
+ACAGGTTCAGAGTTCTACAGTCCGACATG
+>Illumina_NlaIII_Gex_Adapter_2.01
+CAAGCAGAAGACGGCATACGA
+>Illumina_NlaIII_Gex_Adapter_2.02
+TCGTATGCCGTCTTCTGCTTG
+>Illumina_NlaIII_Gex_PCR_Primer_1
+CAAGCAGAAGACGGCATACGA
+>Illumina_NlaIII_Gex_PCR_Primer_2
+AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+>Illumina_NlaIII_Gex_Sequencing_Primer
+CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+>Illumina_Small_RNA_RT_Primer
+CAAGCAGAAGACGGCATACGA
+>Illumina_5p_RNA_Adapter
+GTTCAGAGTTCTACAGTCCGACGATC
+>Illumina_RNA_Adapter1
+TCGTATGCCGTCTTCTGCTTGT
+
+>Illumina_Small_RNA_3p_Adapter_1
+ATCTCGTATGCCGTCTTCTGCTTG
+>Illumina_Small_RNA_PCR_Primer_1
+CAAGCAGAAGACGGCATACGA
+>Illumina_Small_RNA_PCR_Primer_2
+AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+>Illumina_Small_RNA_Sequencing_Primer
+CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+>TruSeq_Universal_Adapter
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>TruSeq_Adapter_Index_1
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_2
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_3
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_4
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_5
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_6
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_7
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_8
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_9
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_10
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_11
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
+>TruSeq_Adapter_Index_12
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
+
+>Illumina_RNA_RT_Primer
+GCCTTGGCACCCGAGAATTCCA
+>Illumina_RNA_PCR_Primer
+AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
+
+>RNA_PCR_Primer_Index_1
+CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_2
+CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_3
+CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_4
+CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_5
+CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_6
+CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_7
+CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_8
+CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_9
+CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_10
+CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_11
+CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_12
+CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_13
+CAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_14
+CAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_15
+CAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_16
+CAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_17
+CAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_18
+CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_19
+CAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_20
+CAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_21
+CAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_22
+CAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_23
+CAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_24
+CAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_25
+CAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_26
+CAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_27
+CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_28
+CAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_29
+CAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_30
+CAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_31
+CAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_32
+CAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_33
+CAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_34
+CAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_35
+CAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_36
+CAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_37
+CAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_38
+CAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_39
+CAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_40
+CAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_41
+CAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_42
+CAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_43
+CAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_44
+CAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_45
+CAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_46
+CAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_47
+CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+>RNA_PCR_Primer_Index_48
+CAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+
+>ABI_Dynabead_EcoP_Oligo
+CTGATCTAGAGGTACCGGATCCCAGCAGT
+>ABI_Solid3_Adapter_A
+CTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG
+>ABI_Solid3_Adapter_B
+CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
+>ABI_Solid3_5_AMP_Primer
+CCACTACGCCTCCGCTTTCCTCTCTATG
+>ABI_Solid3_3_AMP_Primer
+CTGCCCCGGGTTCCTCATTCT
+>ABI_Solid3_EF1_alpha_Sense_Primer
+CATGTGTGTTGAGAGCTTC
+>ABI_Solid3_EF1_alpha_Antisense_Primer
+GAAAACCAAAGTGGTCCAC
+>ABI_Solid3_GAPDH_Forward_Primer
+TTAGCACCCCTGGCCAAGG
+>ABI_Solid3_GAPDH_Reverse_Primer
+CTTACTCCTTGGAGGCCATG
+>TruSeq2_SE
+AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>TruSeq2_PE_f
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>TruSeq2_PE_r
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+>TruSeq3_IndexedAdapter
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>TruSeq3_UniversalAdapter
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA

data/utils/mytaxa_scan.R

@@ -0,0 +1,89 @@
+
+mytaxa.scan <- function(
+      wintax,
+      col=c('#4dbeee','#7e2f8e','#0072bd','#d95319',
+	 '#edb120','#77ac30','#a2142f'),
+      main='MyTaxa scan'){
+   a <- read.table(wintax, sep='\t', h=F, row.names=1, na.strings='', quote='');
+   if(! "NA" %in% rownames(a)) a["NA", ] <- 0
+   b <- as.matrix(a[-which(rownames(a)=="NA"),-1]);
+   if(ncol(b) <= 1){
+      plot(1,t='n',bty='n',axes=FALSE);
+      legend('center',legend='Insufficient data');
+      return(c());
+   }
+
+   layout(matrix(c(6,6,1,4,2,3,5,5),byrow=T,ncol=2),
+      widths=c(7,1), heights=c(1/4,1,2,3));
+   
+   #::: DISTANCES
+   par(mar=c(1,5,2,0)+0.1);
+   d <- apply( a[,-1], 2,
+      function(x,y) sqrt(sum((sqrt(x)-sqrt(y))^2)/2), y=a[,1] );
+   d.thr <- quantile(d, probs=0.95, names=F, na.rm=TRUE)
+   plot(1, xlim=c(0, length(d)+1), ylim=c(0,1), xlab='', xaxs='i', xaxt='n',
+      t='n', pch=19, cex=1/2, col=grey(0.3), bty='n', ylab='Signal', las=1);
+   rect((1:length(d))-1, 0, 1:length(d), d, col=ifelse(d>d.thr, grey(0.3),
+      grey(0.5)), border='NA');
+
+   #::: WINDOWS BARPLOT
+   par(mar=c(0,5,0,0)+0.1);
+   plot(1, t='n', xlim=c(0,ncol(b)+1), xaxs='i', ylim=c(0,1.2),
+      yaxs='i', xlab='', ylab='Frequency', bty='n', xaxt='n', yaxt='n');
+   axis(2, at=seq(0,1,by=0.2), las=1);
+   # Regions (outliers)
+   regs <- c();
+   for(j in 1:ncol(b))  if(d[j] > d.thr) regs <- c(regs, j);
+   if(length(regs)>0){
+      x <- regs-0.5;
+      y <- rep(1.05,length(regs)) + ((1:length(regs)) %% 2)/10;
+      points(x, y, pch=19, cex=3, col='darkred');
+      arrows(x0=x, y0=0.01, y1=y, col='darkred', length=0);
+      text(x, y, 1:length(regs), col='white', font=2, cex=3/4);
+      write.table(regs, paste(wintax,".regions",sep=""), col.names=F,
+	 row.names=F, quote=F)
+   }
+   # Bars
+   h <- rep(0, ncol(b));
+   all_cols <- c();
+   for(i in 1:nrow(b)){
+      i.col = 1+((i-1) %% (length(col)-1));
+      hn <- h + as.numeric(b[i, ]);
+      for(j in 1:ncol(b))
+	 if(b[i,j]>0)
+	    rect(j-1, h[j], j, hn[j], col=col[i.col], border=NA);
+      all_cols <- c(all_cols, col[i.col]);
+      if(i.col+1 == length(col))
+	 for(j in 1:length(col)){
+	    k = col2rgb(col[j]);
+	    col[j] = rgb(k[1], k[2], k[3], maxColorValue=256*1.3)
+	 }
+      h <- hn;
+   }
+
+   #::: GENOME PROFILE
+   par(mar=c(0,0,0,2)+0.1);
+   plot(1, t='n', xlim=c(0,1), xaxs='i', ylim=c(0,1.2), yaxs='i',
+      xlab='', ylab='', bty='n', xaxt='n', yaxt='n');
+   rect(0, cumsum(c(0,a[-nrow(a),1])), 1, cumsum(a[, 1]),
+      col=all_cols, border=NA);
+   text(0.5, 1.1, 'Genome', font=2, cex=1.5, col='darkred');
+
+   #::: DISTANCES BOXPLOT
+   par(mar=c(1,0,2,2)+0.1);
+   boxplot(d, ylim=c(0,1), yaxs='i', axes=F, col=grey(0.3), pch=19);
+   
+   #::: LEGEND
+   par(mar=c(0,2,0,2)+0.1);
+   plot(1, t='n', bty='n', xlim=c(0,1),
+      ylim=c(0,1), xaxs='i', yaxs='i', axes=F);
+   legend('top', pt.bg=all_cols, col=grey(0.3), pch=22,
+      legend=gsub('.*::','',rownames(b)), ncol=5, cex=3/4, bty='n');
+
+   #::: MAIN
+   plot(1, t='n', bty='n', xlim=c(0,1), ylim=c(0,1), axes=F);
+   text(.5,.5,main);
+   
+   return(regs);
+}
+

data/utils/mytaxa_scan.rb

@@ -0,0 +1,58 @@
+#!/usr/bin/env ruby
+
+abort "
+Usage:
+#{$0} {FastA file} {MyTaxa file} {Data output}
+
+" if ARGV[2].nil?
+
+begin
+   # Get arguments
+   faa, mytaxa, outdata = ARGV
+   winsize = 10
+
+   # Extract gene IDs
+   ids = File.open(faa).grep(/^>/).map{|dl| dl.chomp.sub(/^>/,"").sub(/\s.*/,"")}
+   tax = Hash[ids.map{|k| [k, "NA"]}]
+
+   # Get MyTaxa distributions
+   k, l = nil
+   File.open(mytaxa).each do |ln|
+      ln.chomp!
+      if $.%2 == 1
+	 k, l = ln.split /\t/
+      else
+	 tax[k] = ln.gsub(/<[^>]+>/,"").gsub(/;/,"::")
+      end
+   end
+   all_tax = tax.values.uniq.sort{|x,y| tax.values.count(y) <=> tax.values.count(x) }
+
+   # Estimate Windows and save gene IDs
+   fh = File.open(outdata + ".genes", "w")
+   c = []
+   c << all_tax.map{|t| tax.values.count(t) }
+   n_wins = (ids.size/winsize).ceil
+   (0 .. (n_wins-1)).each do |win|
+      k = ids[win*winsize, winsize]
+      win_t = tax.values_at(*k)
+      fh.puts k.join("\t")
+      c << all_tax.map{|t| win_t.count(t)}
+   end
+   p = c.map{|col| col.map{|cell| cell.to_f/col.inject(:+)}}
+   fh.close
+
+   # Save window profiles
+   fh = File.open(outdata, "w")
+   fh.puts "# Data derived from #{mytaxa}, with #{winsize}-genes windows"
+   fh.puts "# " + (["Tax-label", "Genome"] + (1 .. n_wins).map{|i| "Win_#{i}"}).join("\t")
+   (0 .. (all_tax.size - 1)).each do |row|
+      fh.puts ([all_tax[row]] + p.map{|col| col[row]}).join "\t"
+   end
+   fh.close
+rescue => err
+   $stderr.puts "Exception: #{err}\n\n"
+   err.backtrace.each { |l| $stderr.puts l + "\n" }
+   err
+end
+
+

data/utils/requirements.txt

@@ -0,0 +1,19 @@
+Software		Test executable		Website								Notes
+--------		---------------		-------								-----
+Enve-omics scripts	FastQ.tag.rb		http://github.com/lmrodriguezr/enveomics			All the collection must be present
+SolexaQA++		SolexaQA++		http://solexaqa.sourceforge.net					Required version: v3.1.3+
+Scythe			scythe			https://github.com/vsbuffalo/scythe				Required version: 0.991+
+FastQC			fastqc			http://www.bioinformatics.babraham.ac.uk/projects/fastqc
+IDBA			idba_ud			http://i.cs.hku.hk/~alse/hkubrg/projects/idba
+MetaGeneMark		gmhmmp			http://exon.gatech.edu/genemark/license_download.cgi		The folder must contain the key and the scripts
+HMMer 3.0+		hmmsearch		http://hmmer.janelia.org/software
+NCBI BLAST+		blastp			ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
+R			R			http://www.r-project.org/
+SQLite3			sqlite3			https://www.sqlite.org/
+RAxML (pthreads)	raxmlHPC-PTHREADS	http://sco.h-its.org/exelixis/web/software/raxml/index.html
+MCL			mcl			http://micans.org/mcl/
+DIAMOND			diamond			http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.7.9+
+MyTaxa			MyTaxa			http://enve-omics.ce.gatech.edu/mytaxa				The folder must contain the db and utils dirs, and the AllGenomes.faa BLAST database
+Krona			ktImportText		https://github.com/marbl/Krona/wiki
+Barrnap			barrnap			http://www.vicbioinformatics.com/software.barrnap.shtml
+bedtools		bedtools		http://bedtools.readthedocs.org/en/latest/

data/utils/subclades-compile.rb

@@ -0,0 +1,48 @@
+#!/usr/bin/env ruby
+#
+# @author  Luis M. Rodriguez-R
+# @update  Jan-15-2016
+# @license artistic license 2.0
+#
+
+$:.push File.expand_path(File.dirname(__FILE__) + "/lib")
+dir = ARGV.shift or abort "Usage: #{$0} <classif.dir>"
+
+def read_classif(dir, classif={})
+   fh = File.open(File.expand_path("miga-project.1.classif", dir), "r")
+   klass = []
+   while ln = fh.gets
+      r = ln.chomp.split("\t")
+      classif[r[0]] ||= []
+      classif[r[0]] << r[1]
+      klass[r[1].to_i] = r[1]
+   end
+   fh.close
+   klass.each do |i|
+      d = File.expand_path("miga-project.1.sc-#{i}", dir)
+      classif = read_classif(d, classif) if Dir.exist? d
+   end
+   classif
+end
+
+def print_tree(classif, col=0)
+   klass = classif.values.map{ |i| i[col] }.compact.uniq
+   if klass.size<=1
+      o = classif.keys
+   else
+      o = klass.map do |c|
+	 oo = print_tree(classif.select{ |k,v| v[col]==c }, col+1)
+	 "#{oo}[#{c}]" unless oo.nil?
+      end.compact
+   end
+   o.size==0 ? nil :
+      o.size==1 ? o[0] :
+      "(#{o.join(",")})"
+end
+
+c = read_classif(dir)
+max_depth = c.values.map{|i| i.count}.max
+c.each do |k,v|
+   puts ([k] + v + ["0"]*(max_depth-v.count)).join("\t")
+end
+$stderr.puts print_tree(c) + ";"

data/utils/subclades.R

@@ -0,0 +1,171 @@
+library(enveomics.R)
+library(ape)
+library(ggdendro)
+library(ggplot2)
+library(grid)
+library(gridExtra)
+library(cluster)
+library(dendextend)
+library(vegan)
+library(scatterplot3d)
+
+# Main function
+subclades <- function(ani_file, out_base, thr=1, ani=c()){
+   # Get ANI distances
+   cat("====", out_base, "\n")
+   if(missing(ani_file)){
+      a <- as.data.frame(ani)
+   } else {
+      a <- read.table(gzfile(ani_file), sep='\t', h=TRUE, as.is=T)
+   }
+   if(nrow(a)==0){
+      pdf(paste(out_base,'.pdf',sep=''), 7, 12)
+      plot(1,t='n',axes=F)
+      legend('center','No ANI data',bty='n')
+      dev.off()
+      file.create(paste(out_base,'.1.classif',sep=''))
+      file.create(paste(out_base,'.1.medoids',sep=''))
+      return(NULL)
+   }
+   ani.d <- enve.df2dist(cbind(a$a, a$b, 1-a$value/100), default.d=0.3)
+   ani.hc <- hclust(ani.d, method='ward.D2')
+   write.tree(as.phylo(ani.hc), 'miga-project.ani.nwk')
+   
+   # Silhouette
+   k <- 2:(length(labels(ani.d))-1)
+   s <- sapply(k, function(x) summary(silhouette(pam(ani.d, x)))$avg.width)
+   ds <- 10^(s[-c(1,length(s))]-(s[-length(s)+c(0,1)]+s[-c(1,2)])/2)
+   top.n <- head(k[order(c(-Inf,ds,-Inf), decreasing=T)],n=6)
+
+   # Save "ANI-types"
+   ani.types <- c()
+   ani.medoids <- list()
+   for(i in 1:length(top.n)){
+      k_i <- top.n[i]
+      ani.cl <- pam(ani.d, k_i)
+      ani.types <- cbind(ani.types, ani.cl$clustering)
+      ani.medoids[[ i ]]  <- ani.cl$medoids
+   }
+
+   # Generate graphic reports
+   pdf(paste(out_base,'.pdf',sep=''), 7, 12)
+   plotClusterAndMetadata(as.dendrogram(ani.hc), ani.types, main='ANI types')
+   ani.mds <- metaMDS(ani.d, k=3, autotransform=FALSE, parallel=thr, wascores=F)
+   layout(matrix(1:6, ncol=2))
+   for(i in 1:length(top.n)){
+      s <- scatterplot3d(ani.mds$points, pch=19, type='h',
+	 color=ggplotColours(top.n[i], alpha=1/2)[ani.types[,i]],
+	 cex.symbols=1/2, box=FALSE, lty.hplot=3,
+	 main=paste('NMDS of ANI distances with', top.n[i] ,'clusters'),
+	 angle=80, scale.y=3/2, las=2, xlab='', ylab='', zlab='')
+      for(cl in 1:top.n[i]){
+	 col <- ggplotColours(top.n[i])[cl]
+	 med <- s$xyz.convert(matrix(ani.mds$points[ ani.medoids[[i]][cl] , ],
+	    ncol=3))
+	 if(sum(ani.types[,i]==cl)>1){
+	    val <- s$xyz.convert(matrix(ani.mds$points[ ani.types[,i]==cl , ],
+	       ncol=3))
+	    arrows(x0=med$x, y0=med$y, x1=val$x, y1=val$y, length=0, col=col)
+	 }
+	 points(med, col=col, pch=19, cex=3/2)
+	 text(med, labels=cl, col='white', cex=2/3)
+      }
+   }
+   dev.off()
+
+   # Save results
+   for(i in 1:length(top.n)){
+      write.table(ani.medoids[[i]], paste(out_base,i,'medoids',sep='.'),
+	 quote=FALSE, col.names=FALSE, row.names=FALSE)
+      classif <- cbind(rownames(ani.types), ani.types[,i],
+	 ani.medoids[[i]][ ani.types[,i] ], NA)
+      for(j in 1:nrow(classif))
+	 classif[j,4] <- 100 - as.matrix(ani.d)[classif[j,1], classif[j,3]]
+      write.table(classif, paste(out_base,i,'classif',sep='.'),
+	 quote=FALSE, col.names=FALSE, row.names=FALSE, sep='\t')
+   }
+
+   # Explore subclades
+   for(i in 1:top.n[1]){
+      medoid <- ani.medoids[[1]][i]
+      ds_f <- rownames(ani.types)[ ani.types[,1]==i ]
+      cat("Analyzing subclade", i, "with medoid:", medoid, "\n")
+      cat("   ds_f: ", ds_f, "\n")
+      if(length(ds_f) > 5){
+	 a_f <- a[ (a$a %in% ds_f) & (a$b %in% ds_f), ]
+	 dir.create(paste(out_base,'.1.sc-',i,sep=''))
+	 write.table(ds_f,
+	    paste(out_base,'.1.sc-',i,'/miga-project.all',sep=''),
+	    quote=FALSE, col.names=FALSE, row.names=FALSE)
+	 cat("   looking for subclades within: ",
+	    out_base, ".1.sc-", i, "\n", sep="")
+	 subclades(
+	    out_base=paste(out_base,'.1.sc-',i,'/miga-project',sep=''),
+	    thr=thr, ani=a_f)
+      }
+   }
+}
+
+# Ancillary functions
+plotClusterAndMetadata <- function(c,m,addLabels=TRUE,main='',type='factor'){
+   ps <- list()
+   ps[[1]] <- rectGrob(gp=gpar(col="white"))
+   if(length(type)==1) type <- rep(type, ncol(m))
+   if(addLabels){
+      m <- cbind(m, NA)
+      m[labels(c),ncol(m)] <- labels(c)
+      type[ncol(m)] <- 'label'
+   }
+   for(i in 1:ncol(m)){
+      df <- data.frame(lab=factor(labels(c),levels=labels(c)),
+	 feat=m[labels(c),i])
+      if(type[i]=='factor'){
+	 ps[[i+1]] <- ggplotGrob(ggplot(df,  aes(1, lab, fill=factor(feat))) +
+	    geom_tile() + geom_text(size=3/4, label=df$feat, x=.8) +
+	    scale_x_continuous(expand=c(0,0)) +
+	    theme(axis.title=element_blank(), panel.margin=unit(1,'points'),
+	       plot.margin=unit(c(40,-12,20,-12),'points'),
+	       axis.ticks=element_blank(), axis.text=element_blank(),
+	       legend.position="none"))
+      }else if(type[i]=='numeric'){
+	 ps[[i+1]] <- ggplotGrob(ggplot(df, aes(1,lab,fill=as.numeric(feat))) +
+	    geom_tile() + geom_text(size=3/4, label=df$feat, x=.8) +
+	    scale_x_continuous(expand=c(0,0)) +
+	    theme(axis.title=element_blank(), panel.margin=unit(1,'points'),
+	       plot.margin=unit(c(40,-12,20,-12),'points'),
+	       axis.ticks=element_blank(), axis.text=element_blank(),
+	       legend.position="none"))
+      }else if(type[i]=='label'){
+	 ps[[i+1]] <- ggplotGrob(ggplot(df,  aes(1, lab)) +
+	    geom_tile(fill='white') + geom_text(size=3/4, label=df$feat, x=.8) +
+	    theme(axis.title=element_blank(), panel.margin=unit(1,'points'),
+	       plot.margin=unit(c(40,-12,20,-12),'points'),
+	       axis.ticks=element_blank(), axis.text=element_blank(),
+	       legend.position="none"))
+      }else{
+	 stop('Unsupported type: ', type[i])
+      }
+   }
+   ps[[i+2]] <- ggplotGrob(ggplot(segment(dendro_data(c, type="rectangle"))) +
+      geom_segment(aes(x = x, y = y, xend = xend, yend = yend)) +
+      scale_x_continuous(expand=c(0,.5)) +
+      coord_flip() + theme_dendro() +
+         theme(axis.title=element_blank(), axis.ticks=element_blank(),
+	    plot.margin=unit(c(40,20,20,ifelse(addLabels,-35,-30)),'points'),
+            panel.margin=unit(0,'points'), axis.text=element_blank(),
+	    legend.position="none"))
+   maxHeights = do.call(grid::unit.pmax, lapply(ps, function(x) x$heights[2:5]))
+   for(g in ps) g$heights[2:5] <- as.list(maxHeights)
+   ps$nrow <- 1
+   ps$widths <- c(0.1,rep(.07,ncol(m)),1)
+   ps$main <- main
+   do.call(grid.arrange, ps)
+   return(ps)
+}
+
+ggplotColours <- function(n=6, h=c(0, 360)+15, alpha=1){
+   if ((diff(h)%%360) < 1) h[2] <- h[2] - 360/n
+   hcl(h=seq(h[1], h[2], length=n), c=100, l=65, alpha=alpha)
+}
+
+