Commit 1063526e authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 22

parent e07c7bf4

ChangeLog.txt

+23 −1
Original line number Diff line number Diff line 
2018-12-19  Martin C. Frith  <Martin C. Frith>



	* src/tantan.cc:

	Make it faster

	[3523060bcfb9] [tip]



	* src/tantan_repeat_finder.cc, src/tantan_repeat_finder.hh:

	Make -f4 a bit faster

	[1fccdf6e21be]



	* README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,

	src/tantan_app.cc, src/tantan_repeat_finder.cc,

	src/tantan_repeat_finder.hh, test/hard.fa, test/tantan_test.out,

	test/tantan_test.sh:

	Add option to find straightforward tandem repeats

	[1bae60144712]



	* README.txt, src/mcf_tantan_options.cc, src/tantan.cc,

	src/tantan_app.cc:

	Tweak the help message

	[fc1ca32a72aa]



2018-12-10  Martin C. Frith  <Martin C. Frith>



	* README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,

	src/tantan_app.cc, test/tantan_test.out, test/tantan_test.sh:

	Add match score, mismatch cost options

	[2383404c795a] [tip]

	[2383404c795a]



	* src/tantan.cc:

	Refactor

README.html

+28 −2
Original line number Diff line number Diff line
@@ -451,7 +451,7 @@ repeats, so it's easy to lift the masking after determining homology.</p> 
<td>preserve uppercase/lowercase in non-masked regions</td></tr>

<tr><td class="option-group">

<kbd><span class="option">-m</span></kbd></td>

<td>file for letter pair scores (scoring matrix)</td></tr>

<td>file for letter-pair score matrix</td></tr>

<tr><td class="option-group">

<kbd><span class="option">-r</span></kbd></td>

<td>probability of a repeat starting per position</td></tr>
@@ -480,9 +480,12 @@ repeats, so it's easy to lift the masking after determining homology.</p> 
<kbd><span class="option">-s</span></kbd></td>

<td>minimum repeat probability for masking</td></tr>

<tr><td class="option-group">

<kbd><span class="option">-n</span></kbd></td>

<td>minimum copy number, affects -f4 only</td></tr>

<tr><td class="option-group">

<kbd><span class="option">-f</span></kbd></td>

<td>output type: 0=masked sequence, 1=repeat probabilities,

2=repeat counts, 3=BED</td></tr>

2=repeat counts, 3=BED, 4=tandem repeats</td></tr>

<tr><td class="option-group">

<kbd><span class="option">-h</span>, <span class="option">--help</span></kbd></td>

<td>show help message, then exit</td></tr>
@@ -512,6 +515,29 @@ TGCTAGCAA ttaggcttaggtcagtgc TTAGGCTTAGGTCAGTGC AACGTA 
</pre>

<p>(My thanks to Junko Tsuji and Paul Horton for finding these issues.)</p>

</div>

<div class="section" id="finding-straightforward-tandem-repeats">

<h1>Finding straightforward tandem repeats</h1>

<p>Option -f4 runs tantan in a different mode, where it finds

straightforward tandem repeats only.  (Technically, it uses a Viterbi

algorithm instead of a Forward-Backward algorithm.)  This is <em>not</em>

recommended for avoiding false homologs!  But it might be useful for

studying tandem repeats.  The output looks like this:</p>

<pre class="literal-block">

mySeq   14765   14780   6       2.5     GTCATG  GTCATG,GTCATG,GTC

mySeq   632362  632377  2       6       GC      GC,GC,GC,GCt,GCT,GCT

mySeq   1278353 1278369 3       6.5     TCA     TCA,TCA,TCA,TC-,TC,TC,T

mySeq   3616084 3616100 3       5.33333 TGG     TGA,TGA,TGG,TGG,TGG,T

</pre>

<p>The first 3 columns show the start and end coordinates of the

repetitive region, in <a class="reference external" href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a> format.  Column

4 shows the length of the repeating unit (which might vary due to

insertions and deletions, so this column shows the most common

length).  Column 5 shows the number of repeat units.  Column 6 shows

the repeating unit (which again might vary, so this is just a

representative).  Column 7 shows the whole repeat: lowercase letters

are insertions relative to the previous repeat unit, and dashes are

deletions relative to the previous repeat unit.</p>

</div>

<div class="section" id="miscellaneous">

<h1>Miscellaneous</h1>

<p>tantan is distributed under the GNU General Public License, either

README.txt

+28 −2
Original line number Diff line number Diff line
@@ -136,7 +136,7 @@ Options 
-p  interpret the sequences as proteins

-x  letter to use for masking, instead of lowercase

-c  preserve uppercase/lowercase in non-masked regions

-m  file for letter pair scores (scoring matrix)

-m  file for letter-pair score matrix

-r  probability of a repeat starting per position

-e  probability of a repeat ending per position

-w  maximum tandem repeat period to consider
@@ -146,8 +146,9 @@ Options 
-a  gap existence cost

-b  gap extension cost

-s  minimum repeat probability for masking

-n  minimum copy number, affects -f4 only

-f  output type: 0=masked sequence, 1=repeat probabilities,

                 2=repeat counts, 3=BED

                 2=repeat counts, 3=BED, 4=tandem repeats

-h, --help  show help message, then exit

--version   show version information, then exit
@@ -172,6 +173,31 @@ align it on the other strand:: 


(My thanks to Junko Tsuji and Paul Horton for finding these issues.)



Finding straightforward tandem repeats

--------------------------------------



Option -f4 runs tantan in a different mode, where it finds

straightforward tandem repeats only.  (Technically, it uses a Viterbi

algorithm instead of a Forward-Backward algorithm.)  This is *not*

recommended for avoiding false homologs!  But it might be useful for

studying tandem repeats.  The output looks like this::



  mySeq   14765   14780   6       2.5     GTCATG  GTCATG,GTCATG,GTC

  mySeq   632362  632377  2       6       GC      GC,GC,GC,GCt,GCT,GCT

  mySeq   1278353 1278369 3       6.5     TCA     TCA,TCA,TCA,TC-,TC,TC,T

  mySeq   3616084 3616100 3       5.33333 TGG     TGA,TGA,TGG,TGG,TGG,T



The first 3 columns show the start and end coordinates of the

repetitive region, in `BED

<https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_ format.  Column

4 shows the length of the repeating unit (which might vary due to

insertions and deletions, so this column shows the most common

length).  Column 5 shows the number of repeat units.  Column 6 shows

the repeating unit (which again might vary, so this is just a

representative).  Column 7 shows the whole repeat: lowercase letters

are insertions relative to the previous repeat unit, and dashes are

deletions relative to the previous repeat unit.



Miscellaneous

-------------

src/mcf_tantan_options.cc

+21 −7
Original line number Diff line number Diff line
@@ -36,7 +36,7 @@ static int myGetopt(int argc, char **argv, const char *optstring, 
std::istream &operator>>(std::istream &s, TantanOptions::OutputType &x) {

  int i = 0;

  s >> i;

  if (i < 0 || i > 3)

  if (i < 0 || i > 4)

    s.setstate(std::ios::failbit);

  if (s)

    x = static_cast<TantanOptions::OutputType>(i);
@@ -57,6 +57,7 @@ TantanOptions::TantanOptions() : 
    gapExistenceCost(0),

    gapExtensionCost(-1),  // means: no gaps

    minMaskProb(0.5),

    minCopyNumber(2.0),

    outputType(maskOut),

    indexOfFirstNonOptionArgument(-1) {}
@@ -69,7 +70,7 @@ Options (default settings):\n\ 
 -p  interpret the sequences as proteins\n\

 -x  letter to use for masking, instead of lowercase\n\

 -c  preserve uppercase/lowercase in non-masked regions\n\

 -m  file for letter pair scores (+1/-1, but -p selects BLOSUM62)\n\

 -m  file for letter-pair score matrix\n\

 -r  probability of a repeat starting per position ("

      + stringify(repeatProb) + ")\n\

 -e  probability of a repeat ending per position ("
@@ -77,15 +78,17 @@ Options (default settings):\n\ 
 -w  maximum tandem repeat period to consider (100, but -p selects 50)\n\

 -d  probability decay per period ("

      + stringify(repeatOffsetProbDecay) + ")\n\

 -i  match score (1, but -p selects BLOSUM62)\n\

 -j  mismatch cost (1, but -p selects BLOSUM62)\n\

 -i  match score (BLOSUM62 if -p, else 2 if -f4, else 1)\n\

 -j  mismatch cost (BLOSUM62 if -p, else 7 if -f4, else 1)\n\

 -a  gap existence cost ("

      + stringify(gapExistenceCost) + ")\n\

 -b  gap extension cost (infinite: no gaps)\n\

 -b  gap extension cost (7 if -f4, else infinity)\n\

 -s  minimum repeat probability for masking ("

      + stringify(minMaskProb) + ")\n\

 -n  minimum copy number, affects -f4 only ("

      + stringify(minCopyNumber) + ")\n\

 -f  output type: 0=masked sequence, 1=repeat probabilities,\n\

                  2=repeat counts, 3=BED ("

                  2=repeat counts, 3=BED, 4=tandem repeats ("

      + stringify(outputType) + ")\n\

 -h, --help  show help message, then exit\n\

 --version   show version information, then exit\n\
@@ -93,12 +96,13 @@ Options (default settings):\n\ 
Report bugs to: tantan@cbrc.jp\n\

Home page: http://www.cbrc.jp/tantan/\n\

";

  // -k for transition cost?



  std::string version = "tantan "

#include "version.hh"

      "\n";



  const char *optstring = "px:cm:r:e:w:d:i:j:a:b:s:f:h";

  const char *optstring = "px:cm:r:e:w:d:i:j:a:b:s:n:f:h";



  int i;

  while ((i = myGetopt(argc, argv, optstring, help, version)) != -1) {
@@ -158,6 +162,9 @@ Home page: http://www.cbrc.jp/tantan/\n\ 
        unstringify(minMaskProb, optarg);

        // don't bother checking for stupid values?

        break;

      case 'n':

	unstringify(minCopyNumber, optarg);

	break;

      case 'f':

        unstringify(outputType, optarg);

        break;
@@ -168,11 +175,18 @@ Home page: http://www.cbrc.jp/tantan/\n\ 
    }

  }



  if (gapExtensionCost < 0 && outputType == repOut) gapExtensionCost = 7;



  if (gapExtensionCost > 0 && gapExistenceCost + gapExtensionCost <= 0)

    throw Error("gap existence + extension cost is too low");



  if (maxCycleLength < 0) maxCycleLength = (isProtein ? 50 : 100);



  if (!isProtein || matchScore || mismatchCost) {

    if (matchScore   == 0) matchScore   = (outputType == repOut ? 2 : 1);

    if (mismatchCost == 0) mismatchCost = (outputType == repOut ? 7 : 1);

  }



  indexOfFirstNonOptionArgument = optind;

}

src/mcf_tantan_options.hh

+2 −1
Original line number Diff line number Diff line
@@ -23,7 +23,8 @@ struct TantanOptions { 
  int gapExistenceCost;

  int gapExtensionCost;

  double minMaskProb;

  enum OutputType { maskOut, probOut, countOut, bedOut } outputType;

  double minCopyNumber;

  enum OutputType { maskOut, probOut, countOut, bedOut, repOut } outputType;



  int indexOfFirstNonOptionArgument;

};