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machete.c
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#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <math.h>
#include <signal.h>
#include <sys/types.h>
#include <unistd.h>
#include <time.h>
#include <unistd.h>
#ifndef TRUE
#define TRUE 1
#endif
#ifndef FALSE
#define FALSE 0
#endif
#ifndef TEMP
#define TEMP 2
#endif
time_t interval1, interval2, interval3;
double telapsed, diff;
int check_for_output ( char *search_string );
void send_command(char * sent_command);
double re_estimate_parameters (double likelihood);
double build_starting_tree (double likelihood);
int nexusparser(FILE *nexusfile);
int comment(FILE *file);
int setup_pipe (void);
int close_pipe (void);
void unroottree(char * tree);
int test_reverse_constraints(char * translated_tree);
double build_starting_constraint_tree (double likelihood, char *constraint, int constraint_num);
void print_time(double diff);
void read_sitelike_file(int component);
void do_bootstrap_analysis (int reps);
FILE *paup_pipe, *logfile, *treefile, *outputtree, *nexusfile, *guidetreefile;
int bytes_read, pid, file_length=0, checks=0, checkcount=0, total_constraints=0, response=0, datatype=0, constart=0, conend=-1, bootreps=0; /*dataypes 0=DNA, 1=Protein */
int nbytes = 100, numtranslatedtaxa = 0, num_taxa = 1000, translated = FALSE, alignment_length =0, excludedchars=0, number_taxa =0, print_command=FALSE, gtflag=FALSE, num_trees=0, buildflag=FALSE, listcons=FALSE, norevcon=FALSE;
char *my_string, pid_string[1000], c, *newtree, *notranslate_newtree, *besttree, **resultingtrees = NULL, *guidetree = NULL, *infile=NULL, *gtfilename=NULL ;
char logfilename[1000], sys[1000], result[100000], output[100000], command[10000], *treefilename, ***names;
double likelihood =0, new_likelihood=0, meanRand_likelihood=0, **site_likelihoods = NULL;
int main (int argc, char *argv[])
{
char * token, string[1000000], *tok, *str;
int iteration=1, error = FALSE, i, j, found=FALSE, fflag=0, deltmp=TRUE;
FILE *file = NULL;
newtree = malloc(100000*sizeof(char));
besttree = malloc(100000*sizeof(char));
guidetree = malloc(100000*sizeof(char));
str = malloc(100000*sizeof(char));
notranslate_newtree = malloc(100000*sizeof(char));
newtree[0] = '\0'; besttree[0] = '\0'; notranslate_newtree[0] = '\0';
pid=getpid();
sys[0] = '\0';
pid_string[0]='\0';
sprintf(pid_string, "%d", pid);
command[0] = '\0';
result[0]='\0';
if(argc < 2)
{
printf("\n\nMachete: Likelihood reverse constraint analysis using PAUP\n\n Usage: \"machete -f <nexus file> -[cthln] [-s INTEGER] [-e INTEGER] [-r INTEGER]\"\n\n\tWhere: <nexus file> is a nexus formatted alignment file of DNA sequences\n\t-c commands sent to Paup to be also printed to standard error\n\t-t preserves temporary files\n\t-h prints this message\n\t-b force build optimum tree (when a tree has been provided in the nexus file)\n\t-s <constraint number> specifies the constraint to start at\n\t-e <constraint number> specific the constraint to end at\n\t-l list constraints (and do not carry out reverse constraints analysis)\n\t-n tells machete NOT to carry out the reverse constraint analysis (Just build the best tree)\n\t-r tells machete how many boostrap replicates to carry out (by default = 0)\n\n" );
printf("\tCreated by Chris Creevey e:chris.creevey@gmail.com t:@hairy_llama\n\n\n");
exit(1);
}
while ((c = getopt(argc, argv, "f:chtbs:e:lnr:")) != -1)
{
switch (c)
{
case 'c':
print_command = TRUE;
break;
case 'f':
fflag = 1;
infile = optarg;
break;
case 'h':
printf("\n\nMachete: Likelihood reverse constraint analysis using PAUP\n\n Usage: \"machete -f <nexus file> -[cthln] [-s INTEGER] [-e INTEGER] [-r INTEGER]\"\n\n\tWhere: <nexus file> is a nexus formatted alignment file of DNA sequences\n\t-c commands sent to Paup to be also printed to standard error\n\t-t preserves temporary files\n\t-h prints this message\n\t-b force build optimum tree (when a tree has been provided in the nexus file)\n\t-s <constraint number> specifies the constraint to start at\n\t-e <constraint number> specific the constraint to end at\n\t-l list constraints (and do not carry out reverse constraints analysis)\n\t-n tells machete NOT to carry out the reverse constraint analysis (Just build the best tree)\n\t-r tells machete how many boostrap replicates to carry out (by default = 0)\n\n" );
printf("\tCreated by Chris Creevey e:chris.creevey@gmail.com t:@hairy_llama\n\n\n");
exit(1);
break;
case 't':
deltmp=FALSE;
break;
case 'b':
buildflag=TRUE;
break;
case 's':
constart=atoi(optarg);
break;
case 'e':
conend=atoi(optarg);
break;
case 'l':
listcons=TRUE;
break;
case 'n':
norevcon=TRUE;
break;
case 'r':
bootreps=atoi(optarg);
if(bootreps == 0)
{
printf ("ERROR: number of bootstrap replicates to be performed must be greater than 0\n");
exit(0);
}
break;
}
}
if(fflag == 0)
{ /* -f was mandatory */
fprintf(stderr, "%s: missing -f option\n", argv[0]);
exit(1);
}
/* Test input file exists and read in the nexus file so we can determine the datatype */
if((nexusfile = fopen(infile, "r")) == '\0') /* check to see if the file is there */
{ /* Open the fundamental tree file */
fprintf(stderr, "Error: Cannot open nexus file %s\n", infile);
exit(1);
}
else
{
while(!feof(nexusfile) && found==FALSE)
{
str[0]='\0';
fscanf(nexusfile,"%s", str);
if(strstr(str, "datatype") || strstr(str, "DATATYPE"))
{
found=TRUE;
if((strstr(str, "protein")) || (strstr(str, "PROTEIN")) ) datatype=1;
else
{
if((strstr(str, "dna")) || (strstr(str, "DNA")) || (strstr(str, "nucleotide")) || (strstr(str, "NUCLEOTIDE")) || (strstr(str, "rna")) || (strstr(str, "RNA"))) datatype=0;
else
{
printf("Error: Datatype in nexus file not recognised. It muct be one of \"dna\", \"rna\", \"nucleotide\" or \"protein\"\n");
fclose(nexusfile);
exit(0);
}
}
}
}
if(found == FALSE)
{
fprintf(stderr, "Error: Datatype not found in nexus file. It muct be one of \"dna\", \"rna\", \"nucleotide\" or \"protein\"\n");
fclose(nexusfile);
exit(0);
}
else
{
if(datatype==0)
{
printf("\nDNA sequences detected. DNA GTR model will be used and optimisation of parameters carried out.\n");
}
if(datatype==1)
{
printf("\nProtein sequences detected. Best Protein model will be determined.\n");
}
}
}
fclose(nexusfile);
/* End test for datatype */
/* initiate PAUP pipe */
if(setup_pipe () == TRUE)
{
printf("All temporary files for this run will be annotated with the PID of this process (%d)\n", pid);
interval1 = time(NULL);
printf("\nExecuting file %s", infile);
sprintf(command, "execute %s; exclude uninf;", infile);
send_command (command);
checkcount=0; while((response = check_for_output("Data matrix has")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<3; i++) token = strtok(NULL, " ");
number_taxa = atoi(token);
for(i=0; i<2; i++) token = strtok(NULL, " ");
alignment_length = atoi(token);
printf("\n\tNumber of taxa = %d Number of Characters = %d\n", number_taxa, alignment_length);
/* get number of characters excluded that were not parsimony infomrative */
response = check_for_output("characters excluded");
token = strtok(output, " "); /* get past the inital spaces on this line */
/* get the number of excluded characters */
excludedchars=atoi(token);
printf("\tNumber of parsimony uninformative characters = %d\n", excludedchars);
printf("\tNumber of Characters remaining in alignment = %d\n\n", alignment_length-excludedchars);
/* Check to see if the nexus file constained a tree */
if(buildflag == FALSE)
{
if((response = check_for_output("read from TREES block")) == 1) /* indicates that a trees block was provided with the nexus file */
{
num_trees = atoi(strtok(output, " "));
printf("\t%d tree(s) provided in the nexus file, the first will be used for the likelihood decay calculations\n\n", num_trees);
}
}
if(datatype==0) send_command ("set criterion=like; lset NST=6 lCollapse=no;");
if(datatype==1) send_command ("set criterion=like; lset aaFreq=empirical aaRMatrix=JTT lCollapse=no;");
/* generate arrays to hold the sites likelihood later */
site_likelihoods = malloc((number_taxa-2)*sizeof(double *));
for(i=0; i<(number_taxa-2); i++) site_likelihoods[i]=malloc((alignment_length-excludedchars)*sizeof(double));
if(num_trees == 0)
{
likelihood = build_starting_tree (likelihood);
interval2 = time(NULL);
print_time(difftime(interval2, interval1));
}
interval2 = time(NULL);
likelihood = re_estimate_parameters (likelihood);
interval3 = time(NULL);
print_time(difftime(interval3, interval2));
/* now read tree from PAUP file, capturing the name definitions */
treefilename = malloc(1000*sizeof(char));
treefilename[0] = '\0';
/* checkcount =0; while(!check_for_output("saved to file")) { if(checkcount == 0) { printf("\n\tWaiting for PAUP .."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);} */
sprintf(treefilename, "paup_%d.tre", pid);
treefile = fopen(treefilename, "r");
nexusparser(treefile);
fclose(treefile);
if(!translated) strcpy(notranslate_newtree, newtree);
unroottree(newtree);
unroottree(notranslate_newtree);
/* carry out randomisation test to identify mean of random trees */
/*printf("Carrying out random trees analysis\n");
send_command("randtrees;\n");
checkcount =0; while(!check_for_output("mean=")) { if(checkcount == 0) { printf("\n\tWaiting for PAUP .."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
token = strtok(output, " =");
token = strtok(NULL, " =");
meanRand_likelihood=atof(token);
printf( "\n\tMean -ln L of random trees: %g\n", meanRand_likelihood );
*/
/*
printf("%s\n", newtree);
printf("%s\n", notranslate_newtree);
if(translated)
{
for(i=0; i<numtranslatedtaxa; i++)
{
for(j=0; j<2; j++)
printf("%s\n", names[i][j]);
}
}
*/
/* we now have the best tree in memory anlong with a translation table */
if(norevcon == FALSE) /* as long as we haven;t indeicated that we wish to skip the reverse constraint analysis, using the "-n" option */
{
/* Next identify each split and for each, define a constraint, and fine the likelihood of the best tree that does not contain that split */
printf("\nExtracting constraints defined by best tree and carry out reverse constraint analysis for each\n");
interval2 = time(NULL);
test_reverse_constraints(newtree);
if(listcons==FALSE)
{
interval3 = time(NULL);
print_time(difftime(interval3, interval2));
sprintf(command, "%s.likelihood.decay.tre", infile);
outputtree = fopen(command, "w");
fprintf(outputtree, "%s [%g]\n", newtree, likelihood);
fclose (outputtree);
printf("\n\n\nresulting weighted tree:\n%s [%g]\n\nTree with labels saved to file %s\n\n", newtree, likelihood, command);
}
/* Clean up and exit */
free(treefilename);
/*unroottree(string); */
printf("\tFinished revered constraints analysis.\n");
print_time(difftime(time(NULL), interval2));
sprintf(str, "%s.sitelike.txt", infile);
file=fopen(str, "w");
fprintf(file, "Best_tree\t");
for(i=0; i<(number_taxa-3); i++) fprintf(file, "constraint_tree %d\t", i);
fprintf(file, "\n");
for(j=0; j<alignment_length-excludedchars; j++)
{
for(i=0; i<(number_taxa-2); i++)
{
fprintf(file, "%f\t", site_likelihoods[i][j]);
}
fprintf(file, "\n");
}
fclose(file);
}
if(bootreps > 0) /* carry out a boostrap analysis - NOTE: this is only for illustrative purposes and the resulting topology is NOT used for the reverse constraint analysis (the "best" likelihood tree os used for the REverse constraint analysis) */
{
interval2 = time(NULL);
do_bootstrap_analysis (bootreps);
interval3 = time(NULL);
print_time(difftime(interval3, interval2));
}
error = close_pipe();
printf("Finished analysis, Overall ");
print_time(difftime(interval3, interval1));
}
else
{
error = TRUE;
}
if(deltmp==TRUE)
{
sprintf(str, "rm -f Paup_output_%s.txt", pid_string);
system(str);
sprintf(str, "rm -f paup_%s.altnexus.tre", pid_string);
system(str);
sprintf(str, "rm -f paup_%s.tre", pid_string);
system(str);
sprintf(str, "rm -f paup_%s_log.txt", pid_string);
system(str);
sprintf(str, "rm -f paupblock_%s.command", pid_string);
system(str);
sprintf(str, "rm -f site_like_scores_%s.txt", pid_string);
system(str);
sprintf(str, "rm -f site_like_scores_%s.txt", pid_string);
system(str);
}
if(gtflag == TRUE) fclose(guidetreefile);
for(i=0; i<(number_taxa-2); i++) free(site_likelihoods[i]);
free(site_likelihoods);
if(translated)
{
for(i=0; i<num_taxa; i++)
{
for(j=0; j<2; j++)
free(names[i][j]);
free(names[i]);
}
free(names);
}
free(newtree);
free(guidetree);
free(str);
return(error);
}
int check_for_output ( char *search_string )
{
int found=FALSE, error=FALSE, i=0;
/* printf("searching for %s\n", search_string); */
/* look for a specific output from the command */
output[0] ='\0';
sleep(1);
logfile=fopen(logfilename, "r");
if(logfile == '\0')
{
printf("Problem opening logfile\n!");
}
else
{
i=0;
while(!feof(logfile) && !found && !error) {
output[i]= getc(logfile);
i++;
if(output[i-1] == '\n' || output[i-1] == '\r')
{
output[i] = '\0';
if(strstr(output, search_string ) != '\0')
found = 1;
if(strstr(output, "Error" ) != '\0')
error=TRUE;
i=0;
}
}
}
fclose(logfile);
if(error == TRUE) found =3;
/*** End looking for output */
return(found);
}
void send_command(char * sent_command)
{
char com[1000], paupblockfile[10000];
FILE *paupblock = NULL;
com[0] = '\0'; paupblockfile[0] = '\0';
/* delete logfile, so that outputs from previous commands do not get mixed up with the outputs of the command about to be run */
remove(logfilename);
strcpy(com, "touch ");
strcat(com, logfilename);
system(com);
sprintf(paupblockfile, "paupblock_%d.command", pid);
paupblock=fopen(paupblockfile, "w");
fprintf(paupblock, "#NEXUS\nbegin paup;\n%s\nend;\n", sent_command);
fflush(paupblock);
fclose(paupblock);
if(print_command == TRUE) fprintf(stderr, "\n\t\t[Paup command: %s]\n",sent_command );
fflush(stdout);
/* printf ("Command sent: %s\n", sent_command); */
fprintf (paup_pipe, "log file=%s start=yes replace=yes flushLog=yes; \n", logfilename);
fflush(paup_pipe);
fprintf (paup_pipe, "exe %s;\n", paupblockfile);
fflush(paup_pipe);
fprintf (paup_pipe, "log stop=yes;\n");
fprintf (paup_pipe, ";");
fflush(paup_pipe);
sleep(2);
}
double re_estimate_parameters (double likelihood)
{
double new_likelihood = 0, test_likelihood = likelihood, prev_likelihood = likelihood ;
int i=0, iteration=1, best_aafeq=0, best_aaRMatrix=0, best_rates=0, stop=FALSE;
char * token, *comm;
size_t t = 0, q=0;
char aafreq[][10] = { "empirical", "equal" }, aaRMatrix[][10] = { "JTT", "JTTPAML", "PAM", "MTrev24", "WAG", "LG" }, rates[][30] = { "equal", "gamma shape=estimate" };
comm = malloc(10000*sizeof(char));
comm[0] = '\0';
if(num_trees > 0)
{
printf("\n\tDeterming likelihood for given tree\n");
send_command("lscores 1;");
checkcount=0; while((response = check_for_output("-ln L")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<2; i++) token = strtok(NULL, " ");
likelihood=atof(token);
printf( "\n\tBest -ln L: %g\n", likelihood );
test_likelihood = likelihood;
prev_likelihood = likelihood;
}
/* First determine if we need to use a gamma distribution. */
printf ("Begin testing for optimal site rates:\n");
for( t = 0; t < sizeof(rates) / sizeof(rates[0]); t++)
{
sprintf(comm, "lset rates=%s; lscores 1;", rates[t]);
printf("\n\tCalculating likelihood with rates=%s", rates[t]); fflush(stdout);
send_command (comm);
checkcount=0; while((response = check_for_output("-ln L")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<2; i++) token = strtok(NULL, " ");
test_likelihood=atof(token);
printf( "\n\tBest -ln L: %g\n", test_likelihood );
if((fabs(round(test_likelihood)) - fabs(round(prev_likelihood))) < 0)
{
prev_likelihood = test_likelihood;
best_rates = t;
}
}
if(best_rates==1)
sprintf(comm, "lset rates=gamma shape=previous;");
else
sprintf(comm, "lset rates=%s;", rates[best_rates]);
send_command (comm);
printf("\n\tBest rates model found: %s\n\n", rates[best_rates]);
likelihood=prev_likelihood;
if(datatype==1) /* Protein sequences */
{
/* Estimate the best aafreq ( from "empirical|equal|estimate|") */
printf ("Begin testing for optimal AA Rmatrix and frequencies:\n");
while((fabs(round(new_likelihood)) - fabs(round(likelihood))) < 0 && stop == FALSE)
{
if(iteration>1)
{
printf("\tTree with better likelihood found using optimised models, reestimation best models with this tree\n\n");
likelihood = new_likelihood;
}
prev_likelihood=likelihood;
for( t = 0; t < sizeof(aafreq) / sizeof(aafreq[0]); t++)
{
for( q = 0; q < sizeof(aaRMatrix) / sizeof(aaRMatrix[0]); q++)
{
/* sprintf(comm, "lset rates=gamma shape=estimate aafreq=%s aaRMatrix=%s; lscores;", aafreq[t], aaRMatrix[q]); */
sprintf(comm, "lset aafreq=%s aaRMatrix=%s; lscores 1;", aafreq[t], aaRMatrix[q]);
printf("\n\tCalculating likelihood with aafreq=%s and aaRMatrix=%s", aafreq[t], aaRMatrix[q]); fflush(stdout);
send_command (comm);
checkcount=0; while((response = check_for_output("-ln L")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<2; i++) token = strtok(NULL, " ");
test_likelihood=atof(token);
printf( "\n\t-ln L: %g\n", test_likelihood );
if(fabs(round(test_likelihood)) - fabs(round(prev_likelihood)) < 0)
{
prev_likelihood = test_likelihood;
best_aafeq = t; best_aaRMatrix=q;
}
}
}
printf("\nBest AA model found: aafreq=%s, aaRMatrix=%s\n", aafreq[best_aafeq], aaRMatrix[best_aaRMatrix]);
printf("\tRe-estimating parameters with best model");
if(strcmp(aafreq[best_aafeq], "estimate")== 0)
sprintf(comm, "lset aafreq=%s aaRMatrix=%s; lscores 1; lset aafreq=previous;", aafreq[best_aafeq], aaRMatrix[best_aaRMatrix]);
/* sprintf(comm, "lset rates=gamma shape=estimate aafreq=%s aaRMatrix=%s; lscores; lset shape=previous aafreq=previous;", aafreq[best_aafeq], aaRMatrix[best_aaRMatrix]); */
else
sprintf(comm, "lset aafreq=%s aaRMatrix=%s; lscores 1;", aafreq[best_aafeq], aaRMatrix[best_aaRMatrix]);
/* sprintf(comm, "lset rates=gamma shape=estimate aafreq=%s aaRMatrix=%s; lscores; lset shape=previous;", aafreq[best_aafeq], aaRMatrix[best_aaRMatrix]); */
send_command(comm);
checkcount=0; while((response = check_for_output("-ln L")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<2; i++) token = strtok(NULL, " ");
new_likelihood=atof(token);
printf( "\n\tBest -ln L: %g\n", new_likelihood );
if((fabs((round(new_likelihood))) - fabs(round(likelihood))) < 0 && num_trees ==0)
{
printf("\nUsing predicted aafreq and searching for best tree");
sprintf(comm, "hs;");
send_command(comm);
checkcount=0; while((response = check_for_output("Score of best tree(s) found")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<6; i++) token = strtok(NULL, " ");
new_likelihood=atof(token);
printf( "\n\tBest -ln L: %g\n", new_likelihood );
}
if(num_trees > 0) stop=TRUE;
iteration++;
}
if(num_trees == 0)
printf("\tDifference in -ln L less than 1 unit, stopping search\n");
else
printf("\tCalculation of likelihood of given tree complete\n");
}
if(datatype==0) /* DNA sequences */
{
while((fabs((round(new_likelihood))) - fabs(round(likelihood))) < 0 && stop == FALSE)
{
if(iteration>1)
{
printf("\tTree with changed likelihood found, starting reestimation of paramenters with this tree\n\n");
likelihood = new_likelihood;
}
printf("Iteration %d: Estimating parameters given tree and recalculating likelihood", iteration);
send_command ("lset lCollapse=no Rmatrix=estimate Basefreq=Estimate; lscores 1; lset Rmatrix=previous Basefreq=previous;");
/* send_command ("lset Rmatrix=estimate Basefreq=Estimate rates=gamma shape=estimate; lscores; lset Rmatrix=previous Basefreq=previous shape=previous;"); */
checkcount=0; while((response = check_for_output("-ln L")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<2; i++) token = strtok(NULL, " ");
new_likelihood=atof(token);
printf( "\n\tBest -ln L: %g\n", new_likelihood );
if((fabs((round(new_likelihood))) - fabs(round(likelihood))) < 0 && num_trees == 0)
{
likelihood = new_likelihood;
printf("Iteration %d: Changed likelihood detected. Beginning tree search", iteration);
send_command ("hs;");
checkcount=0; while((response = check_for_output("Score of best tree(s) found")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<6; i++) token = strtok(NULL, " ");
new_likelihood=atof(token);
printf( "\n\tBest -ln L: %g\n", new_likelihood );
}
if(num_trees > 0) stop=TRUE;
iteration++;
}
if(num_trees == 0)
printf("\tDifference in -ln L less than 1 unit, stopping search\n");
else
printf("\tCalculation of likelihood of given tree complete\n");
}
/* Calculate all the site likelihoods for the best tree found and read into memory */
printf("\tCalculating site likelihoods of best tree");
sprintf(comm, "lscores 1 /sitelikes=yes scoreFile=site_like_scores_%d.txt replace=yes display=no;", pid);
send_command (comm);
checkcount=0; while((response = check_for_output("Tree scores (and parameter estimates) written to file:")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
read_sitelike_file(-1);
sprintf(comm, "savetrees file=paup_%d.tre brLens=yes;", pid);
send_command(comm);
sprintf(comm, "savetrees file=%s.bestMLtree.tre brLens=yes format=altnexus;", infile);
send_command(comm);
printf("\nBest tree found after %d iterations with -ln L %g saved to file %s.bestMLtree.tre;\n\n", iteration-1, new_likelihood, infile);
free(comm);
return(new_likelihood);
}
double build_starting_tree (double likelihood)
{
char * token;
int i;
printf("Generating starting ML tree");
send_command("hs;");
checkcount=0; while((response = check_for_output("Score of best tree(s) found")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
token = strtok(output, " ");
for(i=0; i<6; i++) token = strtok(NULL, " ");
likelihood=atof(token);
printf( "\n\tBest -ln L: %g\n\n", likelihood );
return(likelihood);
}
void do_bootstrap_analysis (int reps)
{
char *comm=NULL;
int i;
comm = malloc(10000*sizeof(char));
comm[0] = '\0';
printf("Beginning ML Boostrap analysis with %d replicates\n", reps);
sprintf(comm, "boot nrep=%d treefile=%s.boottrees.tre format=altnexus / enforce=no; exe %s.boottrees.tre; contree /LE50=yes majRule=yes strict=no treefile=%s.contree.tre;",reps, infile, infile, infile);
send_command(comm );
checkcount=0; while((response = check_for_output("Consensus tree(s) written to treefile:")) != 1 && response != 3 ) { if(checkcount == 0) { printf("\n\tWaiting for PAUP ..."); fflush(stdout); checkcount++;} sleep(5); printf("."); fflush(stdout);}
if(response == 3)
{
fprintf(stderr, "Error signal detected from Paup. Now quitting. Please check the file \"Paup_output_%d.txt\" to determine the error message\n", pid);
exit(0);
}
printf("\n\tResulting boostrapped phylogeny written to file: %s.boottrees.tre\n", infile);
printf("\tMajority-Rule consensus of boostrapped trees (with compatible minor components) written to file: %s.contree.tre\n", infile);
free(comm);
}
int setup_pipe (void)
{
int success = TRUE;
char start_comm[10000];
start_comm[0] = '\0';
sprintf(start_comm, "paup -n > Paup_output_%d.txt 2> /dev/null", pid);
/* Open the pipe */
paup_pipe = popen (start_comm, "w");
/* Check that pipes are non-null, therefore open */
if ((!paup_pipe))
{
fprintf (stderr,
"Paup pipe failed.\n");
success = FALSE;
}
else
{
/* Create logfilename for Paup */
logfilename[0]='\0';
strcpy(logfilename, "paup_");
strcat(logfilename, pid_string);
strcat(logfilename, "_log.txt");
/* printf("%s\n", logfilename);*/
/* create the log file - so it doesn;t cause an error when Machete goes looking for it */
strcpy(sys, "touch ");
strcat(sys, logfilename);
system(sys);
/* Stop Paup from printing output unnecessarily to the screen */
send_command ("set increase=auto warnReset=no warnTree=no warnTSave=no warnBlkName=no warnRoot=no warnRedef=no errorStop=no errorBeep=no queryBeep=no flushLog=yes taxLabels=full;");
}
return(success);
}
int close_pipe ()
{
int success = TRUE;
/* Quit Paup */
send_command("quit;");
/* Close paup_pipe, cehcking for errors */
if (pclose (paup_pipe) != 0)
{
fprintf (stderr,
"Could not close 'paup', or other error.\n");
success = FALSE;
}
return(success);
}
int nexusparser(FILE *nexusfile)
{
char c, begin[6] = {'b', 'e', 'g', 'i', 'n', '\0'}, translate[10] = {'t','r','a','n','s','l','a','t','e','\0'}, tree[5] = {'t','r','e','e','\0'};
int error = FALSE, i, j, k, l, x, num_trees = 0, found = FALSE;
char *string, single[1000];
string = malloc(400000*sizeof(char));
string[0] = '\0';
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
while(!feof(nexusfile) && !error)
{
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
switch(tolower(c))
{
case '[':
comment(nexusfile);
break;
case 'b': /* this is the beginning of a block **/
for(i=1; i<5; i++)
if((c = tolower(getc(nexusfile))) != begin[i]) error = TRUE;
if(!error)
{
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
i = 0;
do { /* find the type of block it is **/
string[i] = tolower(c);
i++;
c = getc(nexusfile);
}while(c != ';' && c != ' ');
string[i] = '\0';
if(strcmp(string, "trees") == 0)
{
while(strcmp(string, "end;") != 0 && strcmp(string, "endblock;") != 0 && !feof(nexusfile) && !error)
{
/*** read in the trees ***/
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
while(c == '[')
{
comment(nexusfile);
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
}
strcpy(string, "");
i=1;
string[0] = tolower(c);
while((c = getc(nexusfile)) != ' ' && c != '\n' && c != '\r' && !feof(nexusfile))
{
string[i] = tolower(c);
i++;
}
string[i] = '\0';
if(strcmp(string, tree) == 0)
{
/** read in trees **/
/** read in the name of the tree **/
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
i=1;
string[0] = c;
while(((c = getc(nexusfile)) != ' ' && c != '\n' && c != '\r') && !feof(nexusfile))
{
string[i] = c;
i++;
}
string[i] = '\0';
/*strcpy(tree_names[Total_fund_trees], string); */ /* not needed for this implementation */
/*** look out for any weights **/
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '=' || c == '\n' || c == '\r') && !feof(nexusfile));
while(c == '[')
{
if((c = getc(nexusfile)) == '&')
{
if((c = tolower(getc(nexusfile))) == 'w')
{
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
i=1;
string[0] = c;
while((c = getc(nexusfile)) != ']' &&!feof(nexusfile))
{
string[i] = c;
if(string[i] != ' ') i++;
}
string[i] = '\0';
/* tree_weights[Total_fund_trees] = tofloat(string); */ /* Not needed for this implementation */
}
else
while((c = getc(nexusfile)) != ']' &&!feof(nexusfile));
}
else
while((c = getc(nexusfile)) != ']' &&!feof(nexusfile));
while(((c = getc(nexusfile)) == ' ' || c == '\t' || c == '\n' || c == '\r') && !feof(nexusfile));
}
/*** read in the tree **/
if(!translated)
{
i=0;
strcpy(string, "");
while(c != ';')
{
if(string[i] != ' ' && string[i] != '\t' && string[i] != '\n' && string[i] !='\r') string[i] = c;
i++;
c = getc(nexusfile);
}
string[i] = ';';
string[i+1] = '\0';
/* input_fund_tree(string, Total_fund_trees); */ /* Not needed for this implementation */
}
else
{
/*** If there was a translation table then we need to put the names into the tree **/
i=0; x=0;
while(c != ';' && !feof(nexusfile) && !error)
{
switch(c)
{
case '(':
case ',':
newtree[i] = c;
notranslate_newtree[x] = c;
i++; x++;
c = getc(nexusfile);
break;
case ')':
case ':':
do
{
newtree[i] = c;
notranslate_newtree[x] = c;
i++; x++;
c = getc(nexusfile);
}while(c != '(' && c != ')' && c != ',' && c != ';');
break;
default:
j=0;
while(c != '(' && c != ')' && c != ',' && c != ';' && c != ':' && !feof(nexusfile))
{
single[j] = c;
notranslate_newtree[x] = c;
j++; x++;
c = getc(nexusfile);
}
single[j] = '\0';
found = -1;
for(j=0; j<numtranslatedtaxa; j++)
{
if(strcmp(single, names[j][0])== 0)
found = j;
}
if(found == -1)
{
fprintf(stderr, "Error: taxa %s is not in the translation table\n", single);
error = TRUE;
}
else
{
j=0;
while(names[found][1][j] != '\0')
{
newtree[i] = names[found][1][j];
j++; i++;
}
}
}
}
newtree[i] = ';';
notranslate_newtree[x] = ';';