[Sashimi-commit] misc digestdb1.c,1.5,1.6

[Jimmy E. <en...@us...>]

Update of /cvsroot/sashimi/misc
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv12442

Modified Files:
	digestdb1.c 
Log Message:
revert isascii() to isalpha() for valid sequence characters and also explicitly allow '*' to be in sequence (where '*' is meant to encapsulate a stop codon translation)


Index: digestdb1.c
===================================================================
RCS file: /cvsroot/sashimi/misc/digestdb1.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** digestdb1.c	24 Oct 2006 22:21:43 -0000	1.5
--- digestdb1.c	26 Oct 2006 00:37:54 -0000	1.6
***************
*** 106,109 ****
--- 106,110 ----
        printf(" only the 2nd (protein), 3rd (mass), and 5th (peptide) columns, type\n");
        printf("    %s ipi.fasta | awk '{print $2 \"\\t\" $3 \"\\t\" $4}' > digest.txt\n\n", argv[0]);
+       printf(" Asterisks (*) in sequence are treated as proper break points\n\n");
        exit(1);
     }
***************
*** 315,319 ****
           while (cResidue=fgetc(fp))
           {
!             if (isascii(cResidue))
              {
                 pSeq.szSeq[pSeq.iLenSeq]=cResidue;
--- 316,320 ----
           while (cResidue=fgetc(fp))
           {
!             if (isalpha(cResidue) || cResidue=='*')
              {
                 pSeq.szSeq[pSeq.iLenSeq]=cResidue;
***************
*** 373,387 ****
     do
     {
!       if ((strchr(pInput.szBreak, pSeq.szSeq[pPep.iEnd])
                && !strchr(pInput.szNoBreak, pSeq.szSeq[pPep.iEnd+1]))
           || pPep.iEnd==pSeq.iLenSeq-1)
        {
           int i;
   
           pPep.dPepMass = dMassAA['o']+ 3*dMassAA['h'];
           for (i=pPep.iStart; i<=pPep.iEnd; i++)
           {
              pPep.dPepMass += dMassAA[pSeq.szSeq[i]]; 
           }
  
           /*
--- 374,394 ----
     do
     {
!       if (( (strchr(pInput.szBreak, pSeq.szSeq[pPep.iEnd])
                && !strchr(pInput.szNoBreak, pSeq.szSeq[pPep.iEnd+1]))
+             || pSeq.szSeq[pPep.iEnd]=='*')
           || pPep.iEnd==pSeq.iLenSeq-1)
        {
           int i;
   
+          if (pSeq.szSeq[pPep.iEnd]=='*')
+             pPep.iEnd--;
+ 
           pPep.dPepMass = dMassAA['o']+ 3*dMassAA['h'];
           for (i=pPep.iStart; i<=pPep.iEnd; i++)
           {
              pPep.dPepMass += dMassAA[pSeq.szSeq[i]]; 
+ //printf("%c", pSeq.szSeq[i]);
           }
+ //printf("  %0.2f\n", pPep.dPepMass);
  
           /*
***************
*** 429,447 ****
           }
  
!          iMissed++;
!          if (iMissed==1)  /* first break point is start of next peptide */
!             iStartNextPeptide=pPep.iEnd+1;
! 
!          if (iMissed <= pInput.iMissedCleavage
!                && pPep.dPepMass<pInput.dMaxMass
!                && pPep.iEnd < pSeq.iLenSeq-1)
           {
!             pPep.iEnd++;
           }
           else
           {
!             iMissed=0;
!             pPep.iStart=iStartNextPeptide;
!             pPep.iEnd=pPep.iStart;
           }
  
--- 436,473 ----
           }
  
!          if (pSeq.szSeq[pPep.iEnd+1] == '*')
           {
!             iMissed=0;
! 
!             if (pPep.iStart==iStartNextPeptide)
!             {
!                pPep.iStart=pPep.iEnd+2;
!                iStartNextPeptide=pPep.iEnd+2;
!                pPep.iEnd=pPep.iStart;
!             }
!             else
!             {
!                pPep.iStart=iStartNextPeptide;
!                pPep.iEnd=pPep.iStart;
!             }
           }
           else
           {
!             iMissed++;
!             if (iMissed==1)  /* first break point is start of next peptide */
!                iStartNextPeptide=pPep.iEnd+1;
! 
!             if (iMissed <= pInput.iMissedCleavage
!                   && pPep.dPepMass<pInput.dMaxMass
!                   && pPep.iEnd < pSeq.iLenSeq-1)
!             {
!                pPep.iEnd++;
!             }
!             else
!             {
!                iMissed=0;
!                pPep.iStart=iStartNextPeptide;
!                pPep.iEnd=pPep.iStart;
!             }
           }
  
***************
*** 449,452 ****
--- 475,479 ----
        else
        {
+ //printf("%c\n",pSeq.szSeq[pPep.iEnd]);
           pPep.iEnd++;
        }