mimosa-tool 1.0.0__cp314-cp314-win_amd64.whl

mimosa/_core/pfm_to_pwm.h

@@ -0,0 +1,130 @@
+double pfm[MATLEN][OLIGNUM];
+
+int NthColumn(char *din, char *dout, int nstol)
+{
+	int p1, p2;
+	if(nstol==0)p1=-1;
+	else 
+	{
+		p1=StrNStr(din,'\t',nstol);
+		if(p1==-1)return -1;
+	}
+	p2=StrNStr(din,'\t',nstol+1);
+	if(p2==-1)p2=strlen(din);
+	int len=p2-p1-1;
+	strncpy(dout,&din[p1+1],len);	
+	if(len==0)return -1;
+	dout[len]='\0';
+	return 1;
+}
+int pfm_to_pwm(char *file_pfm, double **mat)
+{	
+	char d[500],head[500], s[500];	
+    int i, j, len=0; 
+	double nseq;//=atoi(argv[3]);
+	int shift_col;//=atoi(argv[4]);
+	
+	FILE *in_pfm;
+	if((in_pfm=fopen(file_pfm,"rt"))==NULL)
+	{
+		printf("Input file %s can't be opened!\n",file_pfm);
+		return -1;
+	}
+	int alfabet=0;
+	fgets(head,sizeof(head),in_pfm);			 
+	fgets(head,sizeof(head),in_pfm);	
+	//homer, cis-bp
+	nseq=1000000000;
+	//shift_col=0;		
+	{
+		DelChar(head,'\n');
+		DelChar(head,'\r');
+		int headlen= strlen(head);
+		if(head[headlen-1]=='\t')
+		{
+			head[headlen-1]='\0';
+			headlen--;
+		}
+		int counttab=0;
+		for(i=0;i<headlen;i++)
+		{
+			if(head[i]=='\t')counttab++;
+		}
+		if(counttab==4 || counttab==16)
+		{
+			shift_col=1;
+			alfabet=counttab;
+		}
+		else 
+		{
+			if(counttab==3 || counttab==15)
+			{
+				shift_col=0;
+				alfabet=counttab+1;
+			}
+			else
+			{
+				printf("Reading errorin Cisbp/Homer matrix file %s !\n",file_pfm);
+				return -1;
+			}
+		}
+	}
+	rewind(in_pfm);
+	
+	int olen=0;
+	fgets(head,sizeof(head),in_pfm);		
+	for(i=0;i<MATLEN;i++)
+	{
+		if(fgets(d,sizeof(d),in_pfm)!=NULL)
+		{
+			char c=d[0];
+			if(isdigit(c) || (strchr("-ATGC",c)!=0))olen++;
+		}
+		else break;
+	}
+	rewind(in_pfm);
+	fgets(head,sizeof(head),in_pfm);		
+	for(i=0;i<MATLEN;i++)
+	{
+		if(fgets(d,sizeof(d),in_pfm)!=NULL)
+		{
+	//		DelChar(d,'\n');
+	//		DelChar(d,'\r');
+			char c=d[0];
+			if(isdigit(c) || (strchr("-ATGC",c)!=0))
+			{				
+				//	 printf("%s",d[i]);						
+				for(j=0;j<alfabet;j++)
+				{			
+					if(NthColumn(d,s,j+shift_col)==-1)
+					{
+						break;			
+					}				
+					//double score=atof(s);
+					//pfm[i][j]=nseq*score;
+					pfm[i][j]=atof(s);
+				}					
+			}
+			else break;
+		}
+		else break;
+	}		
+	//logodds score
+	double pse=0.25;
+	double pse4=1;
+	double vych=log10(pse);		
+	int olen1=olen-1;
+	for(i=0;i<olen;i++)
+	{			
+		double sum=0;
+		for(j=0;j<alfabet;j++)sum+=nseq*pfm[i][j];
+		int alfabet1=alfabet-1;
+		for(j=0;j<alfabet;j++)
+		{
+			double count=nseq*pfm[i][j];
+			double ves=(count+pse)/(sum+pse4);
+			mat[i][j]=log10(ves)-vych;
+		}			
+	}
+	return olen;
+}