Skip to content

Commit

Permalink
improved ASV score, corrected regexp for scientific notation when par…
Browse files Browse the repository at this point in the history 
…sing branch lengths, fixed memory leaks when parsing incorrectly formatted trees
  • Loading branch information
flouris authored and flouris committed Jan 31, 2017
1 parent 4ee4048 commit 052e579
Show file tree
Hide file tree
Showing 9 changed files with 103 additions and 60 deletions.
6 changes: 6 additions & 0 deletions ChangeLog.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,12 @@
All notable changes to `mptp` will be documented in this file.
This project adheres to [Semantic Versioning](http://semver.org/).

## [0.2.2] - 2017-01-31
### Fixed
- Regular expressions now allow scientific notation when parsing branch lengths
- Improved accuracy of ASV score (takes into account tip species)
- Memory leaks when parsing incorrectly formatted trees

## [0.2.1] - 2016-10-18
### Fixed
- Updated ASV to consider only coalescent roots of ML delimitation
Expand Down
15 changes: 8 additions & 7 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -78,9 +78,9 @@ where `DIR` is the directory where bash autocompletion is stored. You can use
and the documentation, use the following commands:

```bash
wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.1/mptp-src-0.2.1.tar.gz
tar zxvf mptp-src-0.2.1.tar.gz
cd mptp-src-0.2.1
wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.2/mptp-src-0.2.2.tar.gz
tar zxvf mptp-src-0.2.2.tar.gz
cd mptp-src-0.2.2
./configure
make
make install # as root, or run sudo make install
Expand Down Expand Up @@ -110,12 +110,12 @@ To use the pre-compiled binary, download the appropriate executable for your
system using the following commands if you are using a Linux system:

```bash
wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.1/mptp-0.2.1-linux-x86_64.tar.gz
tar zxvf mptp-0.2.1-linux-x86_64.tar.gz
wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.2/mptp-0.2.2-linux-x86_64.tar.gz
tar zxvf mptp-0.2.2-linux-x86_64.tar.gz
```

You will now have the binary distribution in a folder called
`mptp-0.2.1-linux-x86_64` in which you will find three subfolders `bin`, `man`
`mptp-0.2.2-linux-x86_64` in which you will find three subfolders `bin`, `man`
and `doc`. We recommend making a copy or a symbolic link to the mptp binary
`bin/mptp` in a folder included in your `$PATH`, and a copy or a symbolic link
to the mptp man page `man/mptp.1` in a folder included in your `$MANPATH`. The
Expand Down Expand Up @@ -171,7 +171,8 @@ Visualization options:
## Usage example

```bash
./mptp --ml --multi --tree_file testTree --output_file out --outgroup A,C --tree_show
mptp --ml --multi --tree_file testTree --output_file out --outgroup A,C --tree_show
mptp --mcmc 50000000 --multi --mcmc_sample 1000000 --mcmc_burnin 1000000 --tree_file tree.newick --output_file out
```

## Documentation
Expand Down
2 changes: 1 addition & 1 deletion configure.ac
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])
AC_INIT([mptp], [0.2.1], [Tomas.Flouri@h-its.org])
AC_INIT([mptp], [0.2.2], [Tomas.Flouri@h-its.org])
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C])
AC_CONFIG_SRCDIR([src/mptp.c])
Expand Down
10 changes: 8 additions & 2 deletions man/mptp.1
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
.\" -*- coding: utf-8 -*-
.\" ============================================================================
.TH mptp 1 "October 18, 2016" "mptp 0.2.1" "USER COMMANDS"
.TH mptp 1 "January 31, 2017" "mptp 0.2.2" "USER COMMANDS"
.\" ============================================================================
.SH NAME
mptp \(em single-locus species delimitation
Expand Down Expand Up @@ -298,7 +298,7 @@ Source code and binaries are available at
<https://github.com/Pas-Kapli/mptp>.
.\" ============================================================================
.SH COPYRIGHT
Copyright (C) 2015-2016, Tomas Flouri, Sarah Lutteropp, Paschalia Kapli
Copyright (C) 2015-2017, Tomas Flouri, Sarah Lutteropp, Paschalia Kapli
.PP
All rights reserved.
.PP
Expand Down Expand Up @@ -345,5 +345,11 @@ sizes.
Updated ASV to consider only coalescent roots of ML delimitation. Removed
assertion stopping mptp when using random starting delimitations for the MCMC
method.
.TP
.BR v0.2.2\~ "released January 31st, 2017"
Fixed regular expressions to allow scientific notation for branch lengths when
parsing trees. Improved the accuracy of ASV score by also taking into account
tips forming coalescent roots. Fixed memory leaks that occur when parsing
incorrectly formatted trees.
.RE
.LP
51 changes: 28 additions & 23 deletions src/lex_rtree.l
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,35 +47,40 @@ static char * append(size_t * dstlen, const char * src, size_t srclen)

%%
<quot>{
\\\" {append(&string_length, "\\\"", 2);}
\' {append(&string_length, "\'", 1);}
\" {BEGIN(INITIAL);return STRING;}
\\\" { append(&string_length, "\\\"", 2); }
\' { append(&string_length, "\'", 1); }
\" { BEGIN(INITIAL); return STRING; }
}

<apos>{
\\\' {append(&string_length, "\\\'", 2);}
\" {append(&string_length, "\"", 1);}
\' {BEGIN(INITIAL);return STRING;}
\\\' { append(&string_length, "\\\'", 2); }
\" { append(&string_length, "\"", 1); }
\' { BEGIN(INITIAL); return STRING; }
}

<apos,quot>{
\\n {append(&string_length, "\\n", 2);}
\\t {append(&string_length, "\\t", 2);}
\\ {append(&string_length, "\\", 1);}
\\\\ {append(&string_length, "\\\\", 2);}
([^\"\'\\]|\n)+ {append(&string_length, rtree_text, rtree_leng);}
\\n { append(&string_length, "\\n", 2); }
\\t { append(&string_length, "\\t", 2); }
\\ { append(&string_length, "\\", 1); }
\\\\ { append(&string_length, "\\\\", 2); }
([^\"\'\\]|\n)+ { append(&string_length, rtree_text, rtree_leng); }
}

\: return COLON;
\; return SEMICOLON;
\) return CPAR;
\( return OPAR;
\, return COMMA;
\" {string_length = 0; BEGIN(quot);}
\' {string_length = 0; BEGIN(apos);}
[\+|\-]?[0-9]+ {rtree_lval.d = xstrndup(rtree_text, rtree_leng); return NUMBER;}
[\+|\-]?[0-9]+\.[0-9]+([e|E][\+|\-]?[0-9]+)? {rtree_lval.d = xstrndup(rtree_text, rtree_leng); return NUMBER;}
[^ \'\",\(\):;\[\]\t\n\r][^ \t\n\r\)\(\[\]\,:;]* {rtree_lval.s = xstrndup(rtree_text, rtree_leng); return STRING;}
[ \t\n\r] ;
. {fatal("Syntax error (%c)\n", rtree_text[0]);}
\: { return COLON; }
\; { return SEMICOLON; }
\) { return CPAR; }
\( { return OPAR; }
\, { return COMMA; }
\" { string_length = 0; BEGIN(quot); }
\' { string_length = 0; BEGIN(apos); }
[-+]?[0-9]+ { rtree_lval.d = xstrndup(rtree_text,rtree_leng);
return NUMBER; }
[+-]?(([0-9]+[\.]?[0-9]*)|([0-9]*[\.]?[0-9]+))([eE][+-]?[0-9]+)? {
rtree_lval.d = xstrndup(rtree_text,rtree_leng);
return NUMBER; }
[^ \'\",\(\):;\[\]\t\n\r][^ \t\n\r\)\(\[\]\,:;]* {
rtree_lval.s = xstrndup(rtree_text,rtree_leng);
return STRING; }
[ \t\n\r] { ; }
. { fatal("Syntax error (%c)\n", rtree_text[0]); }
%%
51 changes: 28 additions & 23 deletions src/lex_utree.l
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,35 +47,40 @@ static char * append(size_t * dstlen, const char * src, size_t srclen)

%%
<quot>{
\\\" {append(&string_length, "\\\"", 2);}
\' {append(&string_length, "\'", 1);}
\" {BEGIN(INITIAL);return STRING;}
\\\" { append(&string_length, "\\\"", 2); }
\' { append(&string_length, "\'", 1); }
\" { BEGIN(INITIAL); return STRING; }
}

<apos>{
\\\' {append(&string_length, "\\\'", 2);}
\" {append(&string_length, "\"", 1);}
\' {BEGIN(INITIAL);return STRING;}
\\\' { append(&string_length, "\\\'", 2); }
\" { append(&string_length, "\"", 1); }
\' { BEGIN(INITIAL);return STRING;}
}

<apos,quot>{
\\n {append(&string_length, "\\n", 2);}
\\t {append(&string_length, "\\t", 2);}
\\ {append(&string_length, "\\", 1);}
\\\\ {append(&string_length, "\\\\", 2);}
([^\"\'\\]|\n)+ {append(&string_length, utree_text, utree_leng);}
\\n { append(&string_length, "\\n", 2); }
\\t { append(&string_length, "\\t", 2); }
\\ { append(&string_length, "\\", 1); }
\\\\ { append(&string_length, "\\\\", 2); }
([^\"\'\\]|\n)+ { append(&string_length, utree_text, utree_leng); }
}

\: return COLON;
\; return SEMICOLON;
\) return CPAR;
\( return OPAR;
\, return COMMA;
\" {string_length = 0; BEGIN(quot);}
\' {string_length = 0; BEGIN(apos);}
[\+|\-]?[0-9]+ {utree_lval.d = xstrndup(utree_text, utree_leng); return NUMBER;}
[\+|\-]?[0-9]+\.[0-9]+([e|E][\+|\-]?[0-9]+)? {utree_lval.d = xstrndup(utree_text, utree_leng); return NUMBER;}
[^ \'\",\(\):;\[\]\t\n\r][^ \t\n\r\)\(\[\]\,:;]* {utree_lval.s = xstrndup(utree_text, utree_leng); return STRING;}
[ \t\n\r] ;
. {fatal("Syntax error (%c)\n", utree_text[0]);}
\: { return COLON; }
\; { return SEMICOLON; }
\) { return CPAR; }
\( { return OPAR; }
\, { return COMMA; }
\" { string_length = 0; BEGIN(quot); }
\' { string_length = 0; BEGIN(apos); }
[-+]?[0-9]+ { utree_lval.d = xstrndup(utree_text,utree_leng);
return NUMBER; }
[+-]?(([0-9]+[\.]?[0-9]*)|([0-9]*[\.]?[0-9]+))([eE][+-]?[0-9]+)? {
utree_lval.d = xstrndup(utree_text,utree_leng);
return NUMBER; }
[^ \'\",\(\):;\[\]\t\n\r][^ \t\n\r\)\(\[\]\,:;]* {
utree_lval.s = xstrndup(utree_text,utree_leng);
return STRING; }
[ \t\n\r] { ; }
. { fatal("Syntax error (%c)\n", utree_text[0]); }
%%
5 changes: 4 additions & 1 deletion src/mptp.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -380,6 +380,9 @@ void cmd_help()
"Usage: %s [OPTIONS]\n", progname);
fprintf(stderr,
"\n"
"Examples:\n"
" mptp --ml --multi --tree_file tree.newick --output_file output\n"
" mptp --mcmc 50000000 --multi --mcmc_sample 1000000 --mcmc_burnin 1000000 --tree_file tree.newick --output_file output\n\n"
"General options:\n"
" --help display help information.\n"
" --version display version information.\n"
Expand Down Expand Up @@ -436,7 +439,7 @@ static rtree_t * load_tree(void)
unsigned int tip_count;
utree_t * utree = utree_parse_newick(opt_treefile, &tip_count);
if (!utree)
fatal("Tree is neither unrooted nor rooted. Go fix your tree.");
fatal("Tree is neither unrooted nor rooted.");

if (!opt_quiet)
{
Expand Down
20 changes: 17 additions & 3 deletions src/multirun.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,9 @@

#include "mptp.h"

#define MPTP_INNER_CROOT 1
#define MPTP_TIP_CROOT 2

static double asv(int * mlcroots, double * support, int count)
{
int i;
Expand All @@ -29,11 +32,16 @@ static double asv(int * mlcroots, double * support, int count)

for (i = 0; i < count; ++i)
{
if (mlcroots[i] == 1)
if (mlcroots[i] == MPTP_INNER_CROOT)
{
sum += (1-support[i]);
croots_count++;
}
else if (mlcroots[i] == MPTP_TIP_CROOT)
{
sum += support[i];
croots_count++;
}
}

return sum / croots_count;
Expand All @@ -51,14 +59,20 @@ static void extract_croots_recursive(rtree_t * node,
if (node->event == EVENT_COALESCENT &&
node->parent->event == EVENT_SPECIATION)
{
outbuffer[*index] = 1;
outbuffer[*index] = MPTP_INNER_CROOT;
}
else
{
if ((node->event == EVENT_SPECIATION) && (node->left->edge_count == 0 || node->right->edge_count == 0))
outbuffer[*index] = MPTP_TIP_CROOT;
}

}
else
{
outbuffer[*index] = 0;
if (node->event == EVENT_COALESCENT)
outbuffer[*index] = 1;
outbuffer[*index] = MPTP_INNER_CROOT;
}

*index = *index+1;
Expand Down
3 changes: 3 additions & 0 deletions src/parse_rtree.y
View file
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,9 @@ static void rtree_error(rtree_t * tree, const char * s)
%error-verbose
%parse-param {struct rtree_s * tree}
%destructor { rtree_destroy($$); } subtree
%destructor { free($$); } STRING
%destructor { free($$); } NUMBER
%destructor { free($$); } label

%token OPAR
%token CPAR
Expand Down

0 comments on commit 052e579

Please sign in to comment.