int esl_trans_s2p(ESL_SQ *in, ESL_SQ **out, int frameshift, int rcFlag)
{
// The encoding for this is taken from squid: A=0, C=1, G=2, U/T=3,
// code[0] corresponds to AAA, code[1] is AAC... code[4] is ACA...
// and so on up to 63 being UUU. 64 is a sentinel. Regular 20 amino codes and '*' for stop
// the nucleotide indices match well with the easel alphabet index
// but the actual translation still needs to be hard coded
char code[] = {'K','N','K','N','T','T','T','T','R','S','R','S',
'I','I','M','I','Q','H','Q','H','P','P','P','P',
'R','R','R','R','L','L','L','L','E','D','E','D',
'A','A','A','A','G','G','G','G','V','V','V','V',
'*','Y','*','Y','L','F','L','F','*','C','W','C',
'L','F','L','F'};
int status;
int codon; //progress in counting current codon
char *aaseq; //hold the protein sequence to be output
char *aaptr; //pointer records progress in writing to output
char *readseq; //pointer records progress in reading nucleotide sequence
int read_dg; //index into digital sequence
ESL_ALPHABET *abc = esl_alphabet_Create(eslDNA);
char errbuf[256]; //validateseq demands this
char namestring[256];
(*out) = NULL;
if(frameshift >= in->n) return eslFAIL;
if(!abc) goto ERROR;
//make sure we have a nucleotide sequence; could use esl_abc_ValidateSeq but that wants too
//much boilerplate for the simple bit I need done. doesn't help that i don't care if there are U or T
//characters but that would test against two alphabets
if(in->seq)
{
if(eslOK != esl_abc_ValidateSeq(abc, in->seq, in->n, errbuf)) goto ERROR;
}
else if(in->dsq)
{
if(in->abc->type != eslRNA && in->abc->type != eslDNA) goto ERROR;
}
else
{
goto ERROR;
}
//apply the reverse compliment
if(rcFlag) {if(esl_sq_ReverseComplement(in) != eslOK) goto ERROR;}
ESL_ALLOC(aaseq, (in->n+1) * sizeof(char));
aaptr = aaseq;
if(in->seq) //text sequence
{
//get an alphabet to do the lookup with.
//an ordinary text sequence doesn't have in->abc
//if it has one that is not a standard dna/rna alphabet
//then this code won't work. I wanted to use an alphabet if available, could save some allocating time that way
//if we're calling this repeatedly
//but the compiler complains about "pointer qualifiers" so nevermind
readseq = in->seq+frameshift;
//as long as there are at least 3 nucleotides left, pull and translate another codon
for (; *readseq != '\0' && *(readseq+1) != '\0' && *(readseq+2) != '\0'; readseq += 3)
{
codon = abc->inmap[(int)*(readseq)] * 16 + abc->inmap[(int)*(readseq+1)] * 4 + abc->inmap[(int)*(readseq+2)];
if(codon > 63 || codon < 0) break;
*aaptr = code[codon];
aaptr += 1;
}
*aaptr = '\0';
}
else if(in->dsq) //do it digitally
{
if(in->dsq == NULL) goto ERROR;
read_dg = 1+frameshift; //add one here because digital index 0 is a sentinel
for(;in->dsq[read_dg] != 255 && in->dsq[read_dg+1] != 255 && in->dsq[read_dg+2] != 255; read_dg += 3)
{
codon = in->dsq[read_dg] * 16 + in->dsq[read_dg+1] * 4 + in->dsq[read_dg+2];
if(codon > 63 || codon < 0) break;
*aaptr = code[codon];
aaptr += 1;
}
*aaptr = '\0';
}
else
{
goto ERROR;
}
//modify name to record any reading frame adjustments
sprintf(namestring, "%s_s%d", in->name, frameshift);
if(rcFlag) strcat(namestring, "_rc");
*out = esl_sq_CreateFrom(namestring, aaseq, in->desc, in->acc, in->ss);
if(aaseq != NULL) free(aaseq);
//return the input to its original state
if(rcFlag) {if(esl_sq_ReverseComplement(in) != eslOK) goto ERROR;}
if(abc) esl_alphabet_Destroy(abc);
if(*out) return eslOK;
ERROR:
if(abc) esl_alphabet_Destroy(abc);
if(aaseq != NULL) free(aaseq);
(*out) = NULL;
return eslEMEM;
}
static int
profillic_esl_msafile_profile_Read(ESLX_MSAFILE *afp, ESL_MSA **ret_msa, ProfileType * profile_ptr )
{
/// \note Right now this isn't actually using the open file pointer; for convenience I just use the profile.fromFile( <filename> ) method.
/// \todo Use convenience fns in esl_buffer.h; see eg hmmer-3.1/easel/esl_msafile_stockholm.c for examples...
ESL_MSA *msa = NULL;
string profile_string;
char *buf;
long len;
int seqidx;
int status;
char errmsg2[eslERRBUFSIZE];
ESL_DASSERT1((afp->format == eslMSAFILE_PROFILLIC));
const char * const seqname = "Galosh Profile Consensus";
const char * const msaname = "Galosh Profile";
uint32_t profile_length;
galosh::Sequence<typename ProfileType::ProfileResidueType> consensus_sequence;
stringstream tmp_consensus_output_stream;
uint32_t pos_i;
if (profile_ptr == NULL) { ESL_EXCEPTION(eslEINCONCEIVABLE, "profile_ptr is NULL in profillic_esl_msafile_profile_Read(..)!"); }
//if (feof(afp->bf->fp)) { status = eslEOF; goto ERROR; }
afp->errmsg[0] = '\0';
// Read in the galosh profile (from profillic)
//fseek( afp->bf->fp, 0, SEEK_END ); // go to the end
//len = afp->bf->ftell( afp->bf->fp ); // get the position at the end (length)
//fseek( afp->bf->fp, 0, SEEK_SET ); // go to the beginning again.
//ESL_ALLOC_CPP( char, buf, sizeof( char ) * len ); //malloc buffer
//fread( buf, len, 1, afp->bf->fp ); //read into buffer
//profile_string = buf;
//profile_ptr->fromString( profile_string );
profile_ptr->fromFile( afp->bf->filename );
//if (buf) free(buf);
// \todo WHY WON'T THIS WORK? See HACKs in profillic-hmmbuild.cpp to work around it.
//fseek( afp->bf->fp, 0, SEEK_END ); // go to the end (to signal there's no more profiles in the file, the next time we come to this function)
// Calculate the consensus sequence.
profile_length = profile_ptr->length();
consensus_sequence.reinitialize( profile_length );
for( pos_i = 0; pos_i < profile_length; pos_i++ ) {
consensus_sequence[ pos_i ] =
( *profile_ptr )[ pos_i ][ galosh::Emission::Match ].maximumValueType();
}
tmp_consensus_output_stream << consensus_sequence;
/* Allocate a growable MSA, and auxiliary parse data coupled to the MSA allocation */
#ifdef eslAUGMENT_ALPHABET
if (afp->abc && (msa = esl_msa_CreateDigital(afp->abc, 16, -1)) == NULL) { status = eslEMEM; goto ERROR; }
#endif
if (! afp->abc && (msa = esl_msa_Create( 16, -1)) == NULL) { status = eslEMEM; goto ERROR; }
// Set first-and-only seq to the consensus. This should set sqlen[0] to the profile's length and set ax to have length 1 and ax[0] to be the sequence itself. Also msa->sqname[0] to the "name" of that consensus sequence.
/* if nec, make room for the new seq */
if (msa->nseq >= msa->sqalloc && (status = esl_msa_Expand(msa)) != eslOK) return status;
seqidx = msa->nseq; // 0
msa->nseq++; // = 1
status = esl_strdup(seqname, -1, &(msa->sqname[seqidx]));
// NOTE: Could add description of this "sequence" here, using esl_msa_SetSeqDescription(msa, seqidx, desc).
#ifdef eslAUGMENT_ALPHABET
if (msa->flags & eslMSA_DIGITAL)
{
// NOTE (profillic): There was a bug in this; it had said .."esl_abc_dsqcat(msa->abc, " where it should have said .."esl_abc_dsqcat(msa->abc->inmap, "
if((status = esl_abc_dsqcat(msa->abc->inmap, &(msa->ax[seqidx]), &(msa->sqlen[seqidx]), tmp_consensus_output_stream.str().c_str(), profile_length)) != eslOK) {
/* invalid char(s), get informative error message */
if (esl_abc_ValidateSeq(msa->abc, tmp_consensus_output_stream.str().c_str(), profile_length, afp->errmsg) != eslOK)
ESL_XFAIL(eslEFORMAT, errmsg2, "%s (line %d): %s", msa->sqname[0], afp->linenumber, afp->errmsg);
}
}
#endif
if (! (msa->flags & eslMSA_DIGITAL))
{
status = esl_strcat(&(msa->aseq[seqidx]), 0, tmp_consensus_output_stream.str().c_str(), profile_length);
msa->sqlen[seqidx] = profile_length;
}
msa->alen = profile_length;
/// \todo OR read in a fasta file of sequences too.
/// \todo (Optional?) Set msa->name to the name of the profile (file?)
esl_strdup(msaname, -1, &(msa->name));
/// \todo make sure eslMSA_HASWGTS is FALSE .. OR set it to TRUE and set msa->wgt[idx] to 1.0.
/// \note Could have secondary structure (per sequence) too. msa->ss[0]. msa->sslen[0] should be the same as msa->sqlen[0].
/// \todo Investigate what msa->sa and msa->pp are for.
/* Give the newly parsed MSA a good
* going-over, and finalize the fields of the MSA data structure.
* verify_parse will fill in errmsg if it sees a problem.
*/
//if (verify_parse(msa, afp->errmsg) != eslOK) { status = eslEFORMAT; goto ERROR; }
if (( status = esl_msa_SetDefaultWeights(msa)) != eslOK) goto ERROR;
if (ret_msa != NULL) *ret_msa = msa; else esl_msa_Destroy(msa);
return eslOK;
ERROR:
if (msa != NULL) esl_msa_Destroy(msa);
if (ret_msa != NULL) *ret_msa = NULL;
return status;
}
