int ExportMerlinMap (void)
{
char mkrname[NAMESIZE], tempstr[NAMESIZE];
int i;
double currentpos;
printf("Which chromosome is this: ");
InputLine(buf, BUFFERSIZE);
currentpos = 0;
// Makes the marker file
cfopen ("merlin.map", "w");
fprintf(F, "CHROMOSOME MARKER LOCATION\n");
for (i = 1; i<=numberofmarkers(); i++)
{
// Remove white spaces in marker name
RemoveWhiteSpace(tempstr, GetName(markernames, order[i]));
strncpy(mkrname, tempstr, NAMESIZE);
fprintf(F, "%-5s %-18s %f\n", buf, mkrname, MarkerDistance(0,i));
}
fclose(F);
puts("Made Merlin map file");
return 0;
}
SQInteger Sq_AskForInput(HSQUIRRELVM v) {
char Buffer[4096];
*Buffer = 0;
const SQChar *Prompt;
sq_getstring(v, 2, &Prompt);
Redraw = 1;
if(InputLine(Prompt, Buffer, sizeof(Buffer)))
sq_pushstring(v, Buffer, -1);
else
sq_pushnull(v);
return 1;
}
void ReadLinkageParameterFile(void)
{
int i;
int linenr, locinumber;
int numloci, risk, xlink, program;
int locus_type, num_alleles, nmarkers;
char *traitname;
char tmpbuf[256];
FreqList *fl;
namelist *nl;
printf("Name of parameter file: ");
InputLine(buf, BUFFERSIZE);
// Deletes old info
FreeDataInfo();
DeletePedigreeData();
DeleteParameterData();
cfopen (buf,"r");
linenr = 0;
locinumber = 1;
nmarkers = 0;
// Read line 1
ReadNextNonEmptyLine();
numloci = atoip (igetstr (buf));
risk = geti();
xlink = geti();
program = geti();
if (numloci==0)
{
printf("WARNING: No loci in parameter file\n");
return;
}
InitializeFrequencies(numloci);
freelist(markernames);
markernames = 0;
// Read line 2 and 3. Not used yet
ReadNextNonEmptyLine();
ReadNextNonEmptyLine();
// Saves the order for later
strncpy(tmpbuf, buf, sizeof(tmpbuf));
// Read all locus/traits
while (locinumber <= numloci)
{
ReadNextNonEmptyLine();
locus_type = atoip (igetstr (buf));
num_alleles = geti();
traitname = GetRestOfLine();
switch (locus_type)
{
case 1 : break;
case 3 : // Read a marker locus
fl = FrequencyNumber(locinumber);
fl->num_alleles = num_alleles;
// Read in the allele frequencies
ReadNextNonEmptyLine();
fl->frequency[1] = atof(igetstr(buf));
for (i=2; i<= num_alleles; i++)
{
fl->frequency[i] = getf();
}
// Increase the number of markers in the dataset
nmarkers++;
// Saves the marker name
nl = cmalloc(sizeof(namelist));
memset(nl, 0, sizeof(namelist));
if (strlen(traitname)==0)
sprintf(nl->name, "Marker %d",locinumber);
else
{
// remove initial # if any
traitname +=strspn(traitname, "# ") ;
strncpy(nl->name, traitname, sizeof(nl->name));
}
addlist(&markernames, nl);
break;
case 4 : // Read a quantitative trait
break;
default: printf("Unknown locus type (%d)\nExiting\n", locus_type);
}
locinumber++;
#ifdef debug
printf("Found locus (%s) type %d with %d alleles\n", nl->name, locus_type, num_alleles);
#endif
}
ReadNextNonEmptyLine();
// Now reads the recombination fractions for markers
ReadNextNonEmptyLine();
if (nmarkers>1)
{
distance = vector(1,nmarkers-1);
distance[1] = atof(igetstr(buf));
for (i = 2; i<nmarkers; i++)
distance[i] = atof(getstr());
}
ReadNextNonEmptyLine();
ReadNextNonEmptyLine();
fclose(F);
// Fixes order
order = ivector(1,nmarkers);
invorder = ivector(1,nmarkers);
OrderMarkers(tmpbuf);
}
void importlinkagepedigree (void)
{
char minibuf[NAMESIZE];
individual *ind, *ind2;
// IDlist *idlist;
markerlist *marker;
namelist *nl;
quanttrait *qt;
int i, families, persons, nmarkers, ntraits, code;
printf("Number of markers in file: ");
InputLine(buf, BUFFERSIZE);
nmarkers = atoip(buf);
printf("Number of traits in file : ");
InputLine(buf, BUFFERSIZE);
ntraits = atoip(buf);
printf ("Name of linkage pedigree file to input: ");
InputLine(buf, BUFFERSIZE);
cfopen (buf,"r");
getbuf ();
persons = 0;
families = 0;
if (options->Index[O_CONVERTLINKAGEID])
printf("WARNING: ID's are converted from number to fam-number\n");
while (buf[0] != EOF)
{
// If empty line then read next line
if (!buf[0] || !strpbrk(buf, "0123456789"))
{
getbuf ();
continue;
}
ind = newperson ();
persons++;
ind->globalid = persons;
ind->localid = persons;
strcpy(ind->pedigree, igetstr (buf));
strcpy(ind->id, getstr ());
strcpy(ind->tmpstr1, getstr ()); // Father ID
strcpy(ind->tmpstr2, getstr ()); // Mother ID
// If conversion of IDs
if (options->Index[O_CONVERTLINKAGEID]) {
sprintf(minibuf,"%s-%s", ind->pedigree,ind->id);
strcpy(ind->id,minibuf);
sprintf(minibuf, "%s-%s", ind->pedigree,ind->tmpstr1);
strcpy(ind->tmpstr1,minibuf);
sprintf(minibuf, "%s-%s", ind->pedigree,ind->tmpstr2);
strcpy(ind->tmpstr2,minibuf);
}
switch (geti ())
{
case 1 : ind->sex = S_MALE; break;
case 2 : ind->sex = S_FEMALE; break;
default : ind->sex = S_UNKNOWN;
}
// atof(getstr());
for (i = 0 ; i<nmarkers; i++)
{
marker = cmalloc (sizeof (markerlist));
memset (marker,0,sizeof (markerlist));
marker->allele1 = geti();
marker->allele2 = geti ();
addlist(&ind->marker, marker);
}
// Reading traits
for (i = 0 ; i<ntraits; i++)
{
qt = cmalloc (sizeof (quanttrait));
memset (qt,0,sizeof (quanttrait));
ReadATrait(qt);
addlist(&ind->qttrait,qt);
}
// printf("\n");
getbuf ();
}
fclose (F);
printf ("%d persons from %d pedigree(s) read\n",
persons, numberofpedigrees());
code = 0;
// Should now fix fathers and mothers
forind
{
ind->father = findperson(ind->tmpstr1);
ind->mother = findperson(ind->tmpstr2);
// if a person has a father and a mother, then add the
// person to the parents lists
if (ind->father && ind->mother)
{
adduniqueidlist (&ind->father->offspring, ind);
adduniqueidlist (&ind->father->mate, ind->mother);
adduniqueidlist (&ind->mother->offspring, ind);
adduniqueidlist (&ind->mother->mate,ind->father);
}
else if (ind->father || ind->mother) // The person has only one parent
{
code = 1;
sprintf(buf2, "%s has only one parent in pedigree file\n", ind->id);
WriteErrorMsg(buf2);
}
}
if (code)
printf("ERROR: A least one parent not found in pedigree file\n");
// Fixing sibs
forind
{
for (ind2 = ind->next; ind2; ind2 = ind2->next)
{
// If same father or mother then add to list of both
if (((ind->father == ind2->father) && (ind->father)) ||
((ind->mother == ind2->mother) && (ind->mother)))
{
adduniqueidlist(&ind->sib, ind2);
adduniqueidlist(&ind2->sib, ind);
}
}
}
// Have now read the file and made the dataset
// Should fix the missing parts
// This part definately needs some error checking
// First set the marker names:
for (i=1; i<=nmarkers; i++)
{
nl = cmalloc (sizeof (namelist));
memset (nl,0,sizeof (namelist));
sprintf(nl->name, "Marker %d",i);
addlist(&markernames, nl);
}
// Then add trait names
for (i=1; i<=ntraits; i++)
{
nl = cmalloc (sizeof (namelist));
memset (nl,0,sizeof (namelist));
sprintf(nl->name, "Trait %d",i);
addlist(&traitnames, nl);
}
InitializeFrequencies(nmarkers);
// Initialize order and distances
order = ivector(1,nmarkers);
invorder = ivector(1,nmarkers);
distance = vector(1, nmarkers-1);
for (i=1; i<=nmarkers; i++)
{
order[i] = i;
invorder[i] = i;
}
for (i=1; i<nmarkers; i++)
distance[i] = InverseMapFunction(0.1);
}
