diff --git a/README.md b/README.md
index f68c1f43279c5ce55082ae5d97d39208fb57ec07..501693089e99b4a0e74a80e8ac5d48b252196a05 100644
--- a/README.md
+++ b/README.md
@@ -66,7 +66,9 @@ OPTIONS:
## Notes
-* First, _RepeatPlot_ determines the _x_ canonical _k_-mers that occur at least twice in the input sequence (_k_ = 15). Second, _RepeatPlot_ selects the _r_ sequence regions _R<sub>i</sub>_ composed by a set _K<sub>i</sub>_ of successive non-unique canonical _k_-mers such that | _K<sub>i</sub>_ | ≥ _l_ − _k_ + 1 (_l_ = 50 by default; option `-l`). Finally, _RepeatPlot_ compares the _k_-mer contents of each pair _R<sub>i</sub>_, _R<sub>j</sub>_ of selected regions. Two regions _R<sub>i</sub>_ and _R<sub>j</sub>_ are assessed as similar when | _K<sub>i</sub>_ ∩ _K<sub>j</sub>_ | ≥ _l_ − _k_ + 1 . Every pair of similar regions is plotted as a circle of radius proportional to | _K<sub>i</sub>_ ∩ _K<sub>j</sub>_ |. Given an input sequence of length _n_ nucleotide residues, the overall time complexity required by _RepeatPlot_ is _O_ ( _n_ + _x_ _r_<sup>2</sup> ), therefore enabling fast running times in many cases.
+* First, _RepeatPlot_ determines the _x_ canonical _k_-mers (_k_ = 15) that occur at least twice in the input sequence. Second, _RepeatPlot_ selects the _r_ sequence regions _R<sub>i</sub>_ composed by a set _K<sub>i</sub>_ of successive non-unique canonical _k_-mers such that | _K<sub>i</sub>_ | ≥ _l_ − _k_ + 1 (_l_ = 50 by default; option `-l`). Finally, _RepeatPlot_ compares the _k_-mer contents of each pair _R<sub>i</sub>_, _R<sub>j</sub>_ of selected regions. Two regions _R<sub>i</sub>_ and _R<sub>j</sub>_ are assessed as similar when | _K<sub>i</sub>_ ∩ _K<sub>j</sub>_ | ≥ _l_ − _k_ + 1 . Every pair of similar regions is plotted as a circle of radius proportional to | _K<sub>i</sub>_ ∩ _K<sub>j</sub>_ |. Given an input sequence of length _n_ nucleotide residues, the overall time complexity required by _RepeatPlot_ is _O_ ( _n_ + _x_ _r_<sup>2</sup> ), therefore enabling fast running times in many cases.
+
+* Denoting _F_<sub>1</sub>, _F_<sub>0</sub> and _f_<sub>1</sub>, the total number of _k_-mers, distinct _k_-mers, and unique (singleton) _k_-mers, respectively (e.g. Melsted and Halldórsson 2014), it is worth noting that _x_ = _F_<sub>0</sub> − _f_<sub>1</sub>. _RepeatPlot_ computes and displays the four values _F_<sub>1</sub>, _F_<sub>0</sub>, _f_<sub>1</sub> and _x_ (_k_ = 15), as well as the _k_-mer repeat index ( _F_<sub>1</sub> − _f_<sub>1</sub> ) / _F_<sub>0</sub>. The _k_-mer repeat index is as close to 0 (e.g. ≤ 0.05) as the specified chromosome sequence is mainly made up by unique _k_-mers; reciprocally, quite large _k_-mer repeat index values (e.g. ≥ 0.15) are indicative of the presence of highly-occurring repeated _k_-mers.
* The input file should be in FASTA format (UTF-8 character encoding) and may contain at least one nucleotide sequence. If the input file contains more than one sequence, they are concatenated to obtain a unique one. When compressed using _gzip_, the input file name should end with `.gz`.
@@ -135,5 +137,9 @@ This leads to the below figures:
## References
+
+Melsted P, Halldórsson PV (2014) _KmerStream: streaming algorithms for k-mer abundance estimation_. **Bioinformatics**, 30(24):3541-3547. [doi:10.1093/bioinformatics/btu71](https://doi.org/10.1093/bioinformatics/btu713).
+
+
Rocha EPC, Danchin A, Viari A (1999) _Analysis of Long Repeats in Bacterial Genomes Reveals Alternative Evolutionary Mechanisms in Bacillus subtilis and Other Competent Prokaryotes_. **Molecular Biology and Evolution**, 16(9):1219-1230. [doi:10.1093/oxfordjournals.molbev.a026212](https://doi.org/10.1093/oxfordjournals.molbev.a026212).
diff --git a/examples/Escherichia.coli.K-12.MG1655.svg b/examples/Escherichia.coli.K-12.MG1655.svg
index 07db2fbe7a6dfd046bc2f19e93fe138b8c00911f..3ee7dc7410ace76fe41e612f462b1caacf87feec 100644
--- a/examples/Escherichia.coli.K-12.MG1655.svg
+++ b/examples/Escherichia.coli.K-12.MG1655.svg
@@ -23,6 +23,8 @@
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diff --git a/examples/Klebsiella.pneumoniae.NTUH-K2044.svg b/examples/Klebsiella.pneumoniae.NTUH-K2044.svg
index 2fbe25f7c2d9f36c31f0197cd2042747869d8bd0..df49434685518986f20e22d599ee095e51f2f96f 100644
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index d696faaa3d2991f7784955c632d4211984d0eea6..4441e9afe90318455099188917bf888149c2fb76 100644
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diff --git a/examples/Mycoplasma.pneumoniae.NCTC10119.svg b/examples/Mycoplasma.pneumoniae.NCTC10119.svg
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diff --git a/examples/Salmonella.enterica.LT2.svg b/examples/Salmonella.enterica.LT2.svg
index 1b1b3c92c94a5852abe9215a1a2049b5379a28a6..1650b5163cb974a4a0002fdfa88b0f22be8254b5 100644
--- a/examples/Salmonella.enterica.LT2.svg
+++ b/examples/Salmonella.enterica.LT2.svg
@@ -23,6 +23,8 @@
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diff --git a/examples/Shigella.flexneri.2a.301.svg b/examples/Shigella.flexneri.2a.301.svg
index 20f1bf6db5c945b1667ce8e0eb6fa696caacbaef..1199f31efb30c409226427c86b643eb85d293965 100644
--- a/examples/Shigella.flexneri.2a.301.svg
+++ b/examples/Shigella.flexneri.2a.301.svg
@@ -23,6 +23,8 @@
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@@ -33,6 +35,8 @@
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@@ -73,6 +83,8 @@
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@@ -83,6 +95,8 @@
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@@ -123,6 +143,8 @@
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+ <text x="131635" y="230562" transform="rotate(-90,131635,230562)" font-size="65817" text-anchor="middle">4607000</text>
+
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diff --git a/examples/Yersinia.pestis.CO92.svg b/examples/Yersinia.pestis.CO92.svg
index b92f323c49a79b8888497dbfd8b25d7c5c93b78c..1b6fc94b7461b233948816941b8ae34b5e7952bb 100644
--- a/examples/Yersinia.pestis.CO92.svg
+++ b/examples/Yersinia.pestis.CO92.svg
@@ -23,6 +23,8 @@
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+ <text x="132965" y="4886414" transform="rotate(-90,132965,4886414)" font-size="66481" text-anchor="middle">0</text>
+
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@@ -33,6 +35,8 @@
<line x1="199446" y1="4421114" x2="232686" y2="4421114" stroke="#848482" stroke-linecap="round" stroke-width="10239"/>
+ <text x="132965" y="4421114" transform="rotate(-90,132965,4421114)" font-size="66481" text-anchor="middle">465300</text>
+
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@@ -43,6 +47,8 @@
<line x1="199446" y1="3955814" x2="232686" y2="3955814" stroke="#848482" stroke-linecap="round" stroke-width="10239"/>
+ <text x="132965" y="3955814" transform="rotate(-90,132965,3955814)" font-size="66481" text-anchor="middle">930600</text>
+
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@@ -53,6 +59,8 @@
<line x1="199446" y1="3490514" x2="232686" y2="3490514" stroke="#848482" stroke-linecap="round" stroke-width="10239"/>
+ <text x="132965" y="3490514" transform="rotate(-90,132965,3490514)" font-size="66481" text-anchor="middle">1395900</text>
+
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@@ -63,6 +71,8 @@
<line x1="199446" y1="3025214" x2="232686" y2="3025214" stroke="#848482" stroke-linecap="round" stroke-width="10239"/>
+ <text x="132965" y="3025214" transform="rotate(-90,132965,3025214)" font-size="66481" text-anchor="middle">1861200</text>
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@@ -73,6 +83,8 @@
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+ <text x="132965" y="2559914" transform="rotate(-90,132965,2559914)" font-size="66481" text-anchor="middle">2326500</text>
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@@ -83,6 +95,8 @@
<line x1="199446" y1="2094614" x2="232686" y2="2094614" stroke="#848482" stroke-linecap="round" stroke-width="10239"/>
+ <text x="132965" y="2094614" transform="rotate(-90,132965,2094614)" font-size="66481" text-anchor="middle">2791800</text>
+
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@@ -93,6 +107,8 @@
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+ <text x="132965" y="1629314" transform="rotate(-90,132965,1629314)" font-size="66481" text-anchor="middle">3257100</text>
+
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@@ -103,6 +119,8 @@
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+ <text x="132965" y="1164014" transform="rotate(-90,132965,1164014)" font-size="66481" text-anchor="middle">3722400</text>
+
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@@ -113,6 +131,8 @@
<line x1="199446" y1="698714" x2="232686" y2="698714" stroke="#848482" stroke-linecap="round" stroke-width="10239"/>
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+
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@@ -123,6 +143,8 @@
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+ <text x="132965" y="233414" transform="rotate(-90,132965,233414)" font-size="66481" text-anchor="middle">4653000</text>
+
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diff --git a/src/RepeatPlot.java b/src/RepeatPlot.java
index 3be05a8d87d1fece078b68f1029aeb3d346f65bb..dcd9c25bb02ac51dab8a9172df65547bf42dfe4e 100644
--- a/src/RepeatPlot.java
+++ b/src/RepeatPlot.java
@@ -34,7 +34,7 @@ import java.util.zip.*;
public class RepeatPlot {
//### constants ################################################################
- final static String VERSION = "1.1.220405ac Copyright (C) 2022 Institut Pasteur";
+ final static String VERSION = "1.2.220405ac Copyright (C) 2022 Institut Pasteur";
static final String NOTHING = "N.o./.T.h.I.n.G";
static final int BUFFER = 1<<16;
static final byte B0 = (byte) 0;
@@ -91,6 +91,9 @@ public class RepeatPlot {
static int nr; //## NOTE: no. regions composed by successive non-unique canonical k-mers
static ArrayList<Integer> pos; //## NOTE: starting position of each of the nr selected regions
static ArrayList<BitSet> albs; //## NOTE: hash values of the non-unique canonical k-mers constituting each of the nr selected regions
+ static int np; //## NOTE: no. pairs of similar regions
+ static int uf0, lf1; //## NOTE: F0, f1
+ static long uf1; //## NOTE: F1
//### drawing parameters ######################################################
static double gratio;
@@ -181,8 +184,8 @@ public class RepeatPlot {
if ( minlgt < 25 ) { System.err.println("should be at least 25 (option -l): " + minlgt); System.exit(1); }
minsucc = minlgt - K;
- System.out.println("k-mer length " + K);
- System.out.println("min. repeat region length " + minlgt);
+ System.out.println("k-mer length " + K);
+ System.out.println("min. repeat region length " + minlgt);
//#############################################################################################################
@@ -192,7 +195,7 @@ public class RepeatPlot {
//#############################################################################################################
filename = infile.toString();
- System.out.println("input file " + filename);
+ System.out.println("input file " + filename);
in = ( filename.endsWith(".gz") ) ? new BufferedReader(new InputStreamReader(new GZIPInputStream(Files.newInputStream(Path.of(filename)), BUFFER))) : Files.newBufferedReader(Path.of(filename));
sb = new StringBuilder("");
@@ -207,9 +210,10 @@ public class RepeatPlot {
sb = sb.append(line.toUpperCase());
}
seb = sb.substring(1).replaceAll(" ", "").getBytes(StandardCharsets.UTF_8);
+ --c;
lgt = seb.length;
- System.out.println("total sequence length " + (lgt-c-1));
+ System.out.println("total sequence length " + (lgt-c));
//#############################################################################################################
@@ -231,6 +235,7 @@ public class RepeatPlot {
default: skip = K; continue;
}
}
+ uf1 = 0;
--i;
while ( ++i < lgt ) {
kmr <<= BSIZE; krc >>>= BSIZE; skip = ( skip > 0 ) ? --skip : skip;
@@ -245,11 +250,17 @@ public class RepeatPlot {
hsh = ( (kmr&=MSK) < krc ) ? kmr : krc;
if ( bs.get(hsh) ) bs2.set(hsh);
else bs.set(hsh);
+ ++uf1;
}
- System.out.println("no. canonical k-mers " + bs.cardinality());
+ uf0 = bs.cardinality();
+ lf1 = uf0 - bs2.cardinality();
-
+ System.out.println("total no. k-mers (F1) " + uf1);
+ System.out.println("no. distinct k-mers (F0) " + uf0);
+ System.out.println("no. unique k-mers (f1) " + lf1);
+
+
//#############################################################################################################
//#############################################################################################################
//### storing the hash of each non-unique k-mer ###
@@ -260,7 +271,8 @@ public class RepeatPlot {
i = hsh = -1;
while ( (hsh=bs2.nextSetBit(++hsh)) >= 0 ) ahsh[++i] = hsh;
- System.out.println("no. non-unique k-mers " + nk);
+ System.out.println("no. non-unique k-mers (F0-f1) " + nk);
+ System.out.println("k-mer repeat index (F1-f1)/F0 " + String.format(Locale.US, "%.5f", ((uf1-lf1)/((double)uf0))));;
if ( log ) oul = new BufferedWriter(new FileWriter(new File(outfile.toString() + ".log")));
@@ -316,7 +328,7 @@ public class RepeatPlot {
}
nr = pos.size();
- System.out.println("no. repeat regions " + nr);
+ System.out.println("no. repeat regions " + nr);
//#############################################################################################################
@@ -383,6 +395,8 @@ public class RepeatPlot {
out.write(String.format(Locale.US, " <line x1=\"%d\" y1=\"%d\" x2=\"%d\" y2=\"%d\"", x0-l, y0-i, x0, y0-i));
out.write(" stroke=\"#848482\" stroke-linecap=\"round\" stroke-width=\"" + lstroke + "\"/>");
out.newLine(); out.newLine();
+ out.write(String.format(Locale.US, " <text x=\"%d\" y=\"%d\" transform=\"rotate(-90,%d,%d)\" font-size=\"%d\" text-anchor=\"middle\">%d</text>", x0-l-fontsize, y0-i, x0-l-fontsize, y0-i, fontsize, i));
+ out.newLine(); out.newLine();
out.write(String.format(Locale.US, " <line x1=\"%d\" y1=\"%d\" x2=\"%d\" y2=\"%d\"", x0+i, ymax, x0+i, ymax-l));
out.write(" stroke=\"#848482\" stroke-linecap=\"round\" stroke-width=\"" + lstroke + "\"/>");
out.newLine(); out.newLine();
@@ -407,6 +421,7 @@ public class RepeatPlot {
out.write(" <!-- circles -->");
out.newLine(); out.newLine();
+ np = 0;
i = -1;
while ( ++i < nr ) {
bs = albs.get(i).get(0, nk);
@@ -416,6 +431,7 @@ public class RepeatPlot {
if ( (s=cardint(bs, albs.get(j))) > minsucc ) {
out.write(String.format(Locale.US, " <circle cx=\"%d\" cy=\"%d\" r=\"%d\" fill=\"%s\" fill-opacity=\"0.6\"/>", border+pos.get(j)+albs.get(j).cardinality()/2, ci, radius(s+K_1, mradius), color));
out.newLine(); out.newLine();
+ ++np;
if ( log ) {
oul.write("R" + (i+1) + "\tR" + (j+1) + "\t" + s);
oul.newLine();
@@ -429,13 +445,17 @@ public class RepeatPlot {
out.write("</svg>");
out.newLine(); out.newLine();
+ System.out.println("no. pairs of similar regions " + np);
+
+ //System.out.println("repeat index " + String.format(Locale.US, "%.9f", (index_up/(index_dn*index_dn))));
+
filename = outfile.toString();
if ( log ) {
- System.out.println("log file " + filename + ".log");
+ System.out.println("log file " + filename + ".log");
oul.close();
}
out.close();
- System.out.println("output file " + filename);
+ System.out.println("output file " + filename);
System.out.println("");
}