ureadseq.c

来自「EM算法的改进」· C语言 代码 · 共 1,911 行 · 第 1/4 页

  /* this is a somewhat shaky end,
    1st char of line is non-blank for seq. title
  */
  *addend = false;
  *ungetend= true;
  return( *V->s != ' ' );
}

Local void readFitch(struct ReadSeqVars *V)
{
  boolean first;

  first = true;
  while (!V->allDone) {
    if (!first) strcpy(V->seqid, V->s);
    readLoop(0, first, endFitch, V);
    if (feof(V->f)) V->allDone = true;
    first = false;
    }
}


Local void readPlain(struct ReadSeqVars *V)
{
  V->nseq++;
  V->addit = (V->choice > 0);
  if (V->addit) V->seqlen = 0;
  addseq(V->seqid, V);   /*from above..*/
  if (V->fname!=NULL) sprintf(V->seqid, "%s  [Unknown form]", V->fname);
  else sprintf(V->seqid, "  [Unknown form]");
  do {
    addseq(V->s, V);
    V->done = feof(V->f);
    getline1(V);
  } while (!V->done);
  if (V->choice == kListSequences) addinfo(V->seqid, V);
  V->allDone = true;
}


Local void readUWGCG(struct ReadSeqVars *V)
{
/*
10nov91: Reading GCG files casued duplication of last line when
         EOF followed that line !!!
    fix: getline1 now sets *V->s = 0
*/
  char  *si;

  V->nseq++;
  V->addit = (V->choice > 0);
  if (V->addit) V->seqlen = 0;
  strcpy(V->seqid, V->s);
  /*writeseq: "    %s  Length: %d  (today)  Check: %d  ..\n" */
  /*drop above or ".." from id*/
  if ( (si = strstr(V->seqid,"  Length: ")) ) *si = 0;
  else if ( (si = strstr(V->seqid,"..")) ) *si = 0;
  do {
    V->done = feof(V->f);
    getline1(V);
    if (!V->done) addseq((V->s), V);
  } while (!V->done);
  if (V->choice == kListSequences) addinfo(V->seqid, V);
  V->allDone = true;
}


Local void readOlsen(struct ReadSeqVars *V)
{ /* G. Olsen /print output from multiple sequence editor */

  char    *si, *sj, *sk, *sm=NULL, sid[40], snum[20];
  boolean indata = false;
  int snumlen = 0;

  V->addit = (V->choice > 0);
  if (V->addit) V->seqlen = 0;
  rewind(V->f); V->nseq= 0;
  do {
    getline1(V);
    V->done = feof(V->f);

    if (V->done && !(*V->s)) break;
    else if (indata) {
      if ( (si= strstr(V->s, sid))
        /* && (strstr(V->s, snum) == si - snumlen - 1) ) { */
        && (sm= strstr(V->s, snum)) && (sm < si - snumlen) ) {

        /* Spaces are valid alignment data !! */
/* 17Oct91: Error, the left margin is 21 not 22! */
/* dropped some nucs up to now -- my example file was right shifted ! */
/* variable right id margin, drop id-2 spaces at end */
/*
  VMS CC COMPILER (VAXC031) mess up:
  -- Index of 21 is chopping 1st nuc on VMS systems Only!
  Byte-for-byte same ame rnasep.olsen sequence file !
*/

        /* si = (V->s)+21; < was this before VMS CC wasted my time */
        si += 10;  /* use strstr index plus offset to outfox VMS CC bug */

        if ( (sk = strstr(si, sid)) ) *(sk-2) = 0;
        for (sk = si; *sk != 0; sk++) {
           if (*sk == ' ') *sk = '.';
           /* 18aug92: !! some olsen masks are NUMBERS !! which addseq eats */
           else if (isdigit((int)*sk)) *sk= nonummask[*sk - '0'];
           }

        addseq(si, V);
        }
      }

    else if ( (sk = strstr(V->s, "): ")) ) {  /* seq info header line */
  /* 18aug92: correct for diff seqs w/ same name -- use number, e.g. */
  /*   3 (Agr.tume):  agrobacterium.prna  18-JUN-1987 16:12 */
  /* 328 (Agr.tume):  agrobacterium.prna XYZ  19-DEC-1992   */
      (V->nseq)++;
      si = 1 + strchr(V->s,'(');
      *sk = ' ';
      if (V->choice == kListSequences) addinfo( si, V);
      else if (V->nseq == V->choice) {
        strcpy(V->seqid, si);
        sj = strchr(V->seqid, ':');
        while (*(--sj) == ' ') ;
        while (--sj != V->seqid) { if (*sj == ' ') *sj = '_'; }

        *sk = 0;
        while (*(--sk) == ' ') *sk = 0;
        strcpy(sid, si);

        si= V->s;
        while ((*si <= ' ') && (*si != 0)) si++;
        snumlen=0;
        while (si[snumlen] > ' ' && snumlen<20)
         { snum[snumlen]= si[snumlen]; snumlen++; }
        snum[snumlen]= 0;
        }

      }

    else if (strstr(V->s,"identity:   Data:")) {
      indata = true;
      if (V->choice == kListSequences) V->done = true;
      }

  } while (!V->done);

  V->allDone = true;
} /*readOlsen*/


Local void readMSF(struct ReadSeqVars *V)
{ /* gcg's MSF, mult. sequence format, interleaved ! */

  char    *si, *sj, sid[128];
  boolean indata = false;
  int     iline= 0;

  V->addit = (V->choice > 0);
  if (V->addit) V->seqlen = 0;
  rewind(V->f); V->nseq= 0;
  do {
    getline1(V);
    V->done = feof(V->f);

    if (V->done && !(*V->s)) break;
    else if (indata) {
      /*somename  ...gpvedai .......t.. aaigr..vad tvgtgptnse aipaltaaet */
      /*       E  gvenae.kgv tentna.tad fvaqpvylpe .nqt...... kv.affynrs */

      si= V->s;
      skipwhitespace(si);
      /* for (sj= si; isalnum((int)*sj); sj++) ; bug -- cdelwiche uses "-", "_" and others in names*/
      for (sj= si; *sj > ' '; sj++) ;
      *sj= 0;
      if ( *si ) {
        if ( (0==strcmp(si, sid)) ) {
          addseq(sj+1, V);
          }
        iline++;
        }
      }

    else if (NULL != (si = strstr(V->s, "Name: "))) {  /* seq info header line */
      /* Name: somename      Len:   100  Check: 7009  Weight:  1.00 */

      (V->nseq)++;
      si += 6;
      if (V->choice == kListSequences) addinfo( si, V);
      else if (V->nseq == V->choice) {
        strcpy(V->seqid, si);
        si = V->seqid;
        skipwhitespace(si);
        /* for (sj= si; isalnum((int)*sj); sj++) ; -- bug */
        for (sj= si; *sj > ' '; sj++) ;
        *sj= 0;
        strcpy(sid, si);
        }
      }

    else if ( strstr(V->s,"//") /*== V->s*/ )  {
      indata = true;
      iline= 0;
      if (V->choice == kListSequences) V->done = true;
      }

  } while (!V->done);


  V->allDone = true;
} /*readMSF*/



Local void readPAUPinterleaved(struct ReadSeqVars *V)
{ /* PAUP mult. sequence format, interleaved or sequential! */

  char    *si, *sj, *send, sid[40], sid1[40], saveseq[255];
  boolean first = true, indata = false, domatch;
  int     iline= 0, ifmc, saveseqlen=0;

#define fixmatchchar(s) { \
  for (ifmc=0; ifmc<saveseqlen; ifmc++) \
    if (s[ifmc] == V->matchchar) s[ifmc]= saveseq[ifmc]; }

  V->addit = (V->choice > 0);
  V->seqlencount = 0;
  if (V->addit) V->seqlen = 0;
  /* rewind(V->f); V->nseq= 0;  << do in caller !*/
  indata= true; /* call here after we find "matrix" */
  domatch= (V->matchchar > 0);

  do {
    getline1(V);
    V->done = feof(V->f);

    if (V->done && !(*V->s)) break;
    else if (indata) {
      /* [         1                    1                    1         ]*/
      /* human     aagcttcaccggcgcagtca ttctcataatcgcccacggR cttacatcct*/
      /* chimp     ................a.t. .c.................a ..........*/
      /* !! need to correct for V->matchchar */
      si= V->s;
      skipwhitespace(si);
      if (strchr(si,';')) indata= false;

      if (isalnum((int)*si))  {
        /* valid data line starts w/ a left-justified seq name in columns [0..8] */
        if (first) {
          (V->nseq)++;
          if (V->nseq >= V->topnseq) first= false;
          for (sj = si; isalnum((int)*sj); sj++) ;
          send= sj;
          skipwhitespace(sj);
          if (V->choice == kListSequences) {
            *send= 0;
            addinfo( si, V);
            }
          else if (V->nseq == V->choice) {
            if (domatch) {
              if (V->nseq == 1) { strcpy( saveseq, sj); saveseqlen= strlen(saveseq); }
              else fixmatchchar( sj);
              }
            addseq(sj, V);
            *send= 0;
            strcpy(V->seqid, si);
            strcpy(sid, si);
            if (V->nseq == 1) strcpy(sid1, sid);
            }
          }

        else if ( (strstr(si, sid) == si) ){
          while (isalnum((int)*si)) si++;
          skipwhitespace(si);
          if (domatch) {
            if (V->nseq == 1) { strcpy( saveseq, si); saveseqlen= strlen(saveseq); }
            else fixmatchchar( si);
            }
          addseq(si, V);
          }

        else if (domatch && (strstr(si, sid1) == si)) {
          strcpy( saveseq, si);
          saveseqlen= strlen(saveseq);
          }

        iline++;
        }
      }

    else if ( strstr(V->s,"matrix") )  {
      indata = true;
      iline= 0;
      if (V->choice == kListSequences) V->done = true;
      }

  } while (!V->done);

  V->allDone = true;
} /*readPAUPinterleaved*/



Local void readPAUPsequential(struct ReadSeqVars *V)
{ /* PAUP mult. sequence format, interleaved or sequential! */
  char    *si, *sj;
  boolean atname = true, indata = false;

  V->addit = (V->choice > 0);
  if (V->addit) V->seqlen = 0;
  V->seqlencount = 0;
  /* rewind(V->f); V->nseq= 0;  << do in caller !*/
  indata= true; /* call here after we find "matrix" */
  do {
    getline1(V);
    V->done = feof(V->f);

    if (V->done && !(*V->s)) break;
    else if (indata) {
      /* [         1                    1                    1         ]*/
      /* human     aagcttcaccggcgcagtca ttctcataatcgcccacggR cttacatcct*/
      /*           aagcttcaccggcgcagtca ttctcataatcgcccacggR cttacatcct*/
      /* chimp     ................a.t. .c.................a ..........*/
      /*           ................a.t. .c.................a ..........*/

      si= V->s;
      skipwhitespace(si);
      if (strchr(si,';')) indata= false;
      if (isalnum((int)*si))  {
        /* valid data line starts w/ a left-justified seq name in columns [0..8] */
        if (atname) {
          (V->nseq)++;
          V->seqlencount = 0;
          atname= false;
          sj= si+1;
          while (isalnum((int)*sj)) sj++;
          if (V->choice == kListSequences) {
            /* !! we must count bases to know when topseqlen is reached ! */
            countseq(sj, V);
            if (V->seqlencount >= V->topseqlen) atname= true;
            *sj= 0;
            addinfo( si, V);
            }
          else if (V->nseq == V->choice) {
            addseq(sj, V);
            V->seqlencount= V->seqlen;
            if (V->seqlencount >= V->topseqlen) atname= true;
            *sj= 0;
            strcpy(V->seqid, si);
            }
          else {
            countseq(sj, V);
            if (V->seqlencount >= V->topseqlen) atname= true;
            }
          }

        else if (V->nseq == V->choice) {
          addseq(V->s, V);
          V->seqlencount= V->seqlen;
          if (V->seqlencount >= V->topseqlen) atname= true;
          }
        else {
          countseq(V->s, V);
          if (V->seqlencount >= V->topseqlen) atname= true;
          }
        }
      }

    else if ( strstr(V->s,"matrix") )  {
      indata = true;
      atname= true;
      if (V->choice == kListSequences) V->done = true;
      }

  } while (!V->done);

  V->allDone = true;
} /*readPAUPsequential*/


Local void readPhylipInterleaved(struct ReadSeqVars *V)
{
  char    *si, *sj;
  boolean first = true;
  int     iline= 0;

  V->addit = (V->choice > 0);
  if (V->addit) V->seqlen = 0;
  V->seqlencount = 0;
  /* sscanf( V->s, "%d%d", &V->topnseq, &V->topseqlen); << topnseq == 0 !!! bad scan !! */
  si= V->s;
  skipwhitespace(si);
  V->topnseq= atoi(si);
  while (isdigit((int)*si)) si++;
  skipwhitespace(si);
  V->topseqlen= atol(si);
  /* fprintf(stderr,"Phylip-ileaf: topnseq=%d  topseqlen=%d\n",V->topnseq, V->topseqlen); */

  do {
    getline1(V);
    V->done = feof(V->f);

    if (V->done && !(*V->s)) break;
    si= V->s;
    skipwhitespace(si);
    if (*si != 0) {

      if (first) {  /* collect seq names + seq, as fprintf(outf,"%-10s  ",seqname); */
        (V->nseq)++;
        if (V->nseq >= V->topnseq) first= false;
        sj= V->s+10;  /* past name, start of data */
        if (V->choice == kListSequences) {
          *sj= 0;
          addinfo( si, V);
          }
        else if (V->nseq == V->choice) {
          addseq(sj, V);
          *sj= 0;
          strcpy(V->seqid, si);
          }
        }
      else if ( iline % V->nseq == V->choice -1 ) {
        addseq(si, V);
        }
      iline++;
    }
  } while (!V->done);

  V->allDone = true;
} /*readPhylipInterleaved*/



Local boolean endPhylipSequential( boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
{
  *addend = false;
  *ungetend= false;
  countseq( V->s, V);
  return V->seqlencount >= V->topseqlen;
}

Local void readPhylipSequential(struct ReadSeqVars *V)
{
  short  i;
  char  *si;
  /* sscanf( V->s, "%d%d", &V->topnseq, &V->topseqlen); < ? bad sscan ? */
  si= V->s;
  skipwhitespace(si);
  V->topnseq= atoi(si);
  while (isdigit((int)*si)) si++;
  skipwhitespace(si);
  V->topseqlen= atol(si);
  getline1(V);
  while (!V->allDone) {
    V->seqlencount= 0;
    strncpy(V->seqid, (V->s), 10);
    V->seqid[10]= 0;
    for (i=0; i<10 && V->s[i]; i++) V->s[i]= ' ';
    readLoop(0, true, endPhylipSequential, V);
    if (feof(V->f)) V->allDone = true;
    }
}




Local void readSeqMain(
      struct ReadSeqVars *V,
      const long  skiplines_,
      const short format_)
{
#define tolowerstr(s) { long Itlwr, Ntlwr= strlen(s); \
  for (Itlwr=0; Itlwr<Ntlwr; Itlwr++) s[Itlwr]= to_lower(s[Itlwr]); }

  boolean gotuw;
  long l;

  V->linestart= 0;
  V->matchchar= 0;