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// gff.cpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* .gff file reader
*
*/
#undef NDEBUG
#include "gff.hpp"
#include "common.inc"
namespace GFF_sp
{
// Locus
Locus::Locus (size_t lineNum_arg,
const string &contig_arg,
size_t start_arg,
size_t stop_arg,
bool strand_arg,
bool partial_arg,
size_t crossOriginSeqLen_arg,
string gene_arg,
string product_arg)
: lineNum (lineNum_arg)
, contig (contig_arg)
, start (start_arg)
, stop (stop_arg)
, strand (strand_arg)
, partial (partial_arg)
, contigLen (crossOriginSeqLen_arg)
, crossOrigin (bool (crossOriginSeqLen_arg))
, gene (gene_arg)
, product (product_arg)
{
//QC_ASSERT (lineNum >= 1);
trim (contig);
if (contig. empty ())
throw runtime_error ("Empty contig name");
if (crossOrigin)
{
swap (start, stop);
start--;
stop++;
QC_ASSERT (contigLen);
QC_ASSERT (stop <= contigLen);
}
QC_ASSERT (start < stop);
}
bool Locus::operator< (const Locus& other) const
{
LESS_PART (*this, other, contig)
LESS_PART (*this, other, start)
LESS_PART (*this, other, stop)
LESS_PART (*this, other, strand)
//LESS_PART (*this, other, contigLen);
LESS_PART (*this, other, crossOrigin);
return false;
}
// Gff
const StringVector Gff::names {"bakta", "genbank", "microscope", "patric", "pgap", "prodigal", "prokka", "pseudomonasdb", "rast", "standard"};
Gff::Type Gff::name2type (const string &name)
{
if (name == "bakta") return bakta;
if (name == "genbank") return genbank;
if (name == "microscope") return microscope;
if (name == "patric") return patric;
if (name == "pgap") return pgap;
if (name == "prodigal") return prodigal;
if (name == "prokka") return prokka;
if (name == "pseudomonasdb") return pseudomonasdb;
if (name == "rast") return rast;
if (name == "standard") return standard;
throw runtime_error ("Unknown GFF type: " + strQuote (name));
}
// Annot
namespace
{
string unescape (const string &s)
{
string r (unPercent (s));
trim (r);
return r;
}
void pgap_accession (string &accession,
bool lcl)
// Update: accession
{
static const string gnlPrefix ("gnl|");
static const string lclPrefix ("lcl|");
size_t pos = accession. rfind (':');
if (pos == string::npos)
{
if (lcl)
accession = lclPrefix + accession;
}
else
{
if (lcl)
throw runtime_error ("Accession " + strQuote (accession) + " cannot have " + strQuote (gnlPrefix) + " and " + strQuote (lclPrefix) + " at the same time");
accession [pos] = '|';
accession = gnlPrefix + accession;
}
QC_ASSERT (! accession. empty ());
}
}
Annot::Annot (const string &fName,
Gff::Type gffType,
bool protMatch,
bool lcl)
{
IMPLY (protMatch, gffType == Gff::genbank
|| gffType == Gff::microscope
|| gffType == Gff::prodigal
);
IMPLY (gffType == Gff::microscope, protMatch);
//IMPLY (trimProject, gffType == Gff::genbank);
IMPLY (lcl, gffType == Gff::pgap);
if (fName. empty ())
throw runtime_error ("Empty GFF file name");
LineInput f (fName /*, 100 * 1024, 1*/);
while (f. nextLine ())
{
trim (f. line);
if ( ( gffType == Gff::prokka
|| gffType == Gff::bakta
)
&& f. line == "##FASTA"
)
break;
if ( f. line. empty ()
|| f. line [0] == '#'
)
continue;
try
{
/*1*/ string contig (unescape (findSplit (f. line, '\t')));
/*2*/ const string source (unescape (findSplit (f. line, '\t')));
/*3*/ const string type (unescape (findSplit (f. line, '\t')));
/*4*/ const string startS (unescape (findSplit (f. line, '\t')));
/*5*/ const string stopS (unescape (findSplit (f. line, '\t')));
/*6*/ const string score (unescape (findSplit (f. line, '\t'))); // real number
/*7*/ const string strand (unescape (findSplit (f. line, '\t')));
/*8*/ const string phase (unescape (findSplit (f. line, '\t'))); // frame
/*9*/ string attributes (f. line);
trim (attributes);
if (attributes. empty ())
throw runtime_error ("9 fields are expected in each line");
#if 0
if (trimProject)
if (contains (contig, ":"))
findSplit (contig, ':'); // = project_id
#endif
if (contig. empty ())
throw runtime_error ("empty sequence indentifier");
for (const char c : contig)
if (! printable (c))
throw runtime_error ("Non-printable character in the sequence identifier: " + to_string (c));
if ( type != "CDS"
&& type != "gene"
&& type != "pseudogene"
)
continue;
if (gffType == Gff::pgap && type != "CDS")
continue;
long start = -1;
if (! str2<long> (startS, start))
throw runtime_error ("Cannot read start");
if (start <= 0)
throw runtime_error ("start should be >= 1");
long stop = -1;
if (! str2<long> (stopS, stop))
throw runtime_error ("Cannot read stop");
if (stop <= 0)
throw runtime_error ("stop should be >= 1");
if (start > stop)
throw runtime_error ("start cannot be greater than stop");
start--;
if ( strand != "+"
&& strand != "-"
)
throw runtime_error ("strand should be '+' or '-'");
const bool pseudo = contains (attributes, "pseudo=true")
|| contains (attributes, "gene_biotype=pseudogene")
|| type == "pseudogene";
//if (pseudo && type == "CDS")
//continue;
const bool partial = contains (attributes, "partial=true")
// Gff::prodigal
|| contains (attributes, "partial=01")
|| contains (attributes, "partial=10")
|| contains (attributes, "partial=11");
string protAttr = "Name";
switch (gffType)
{
case Gff::bakta: protAttr = "ID"; break;
case Gff::genbank: protAttr = (protMatch || pseudo) ? "locus_tag" : "Name"; break;
case Gff::microscope: protAttr = "ID"; break;
case Gff::patric: protAttr = "ID"; break;
case Gff::prodigal: protAttr = "ID"; break;
case Gff::prokka: protAttr = "ID"; break;
case Gff::pseudomonasdb: protAttr = "Alias"; break; // for type = "gene", "locus" for type = "CDS"
case Gff::rast: protAttr = "ID"; break;
default: break;
}
ASSERT (! protAttr. empty ());
protAttr += "=";
string prot_;
string gene_;
string product_;
{
string locusTag;
while (! attributes. empty ())
{
string s (findSplit (attributes, ';'));
trim (s);
if (isLeft (s, protAttr))
{
prot_ = s;
findSplit (prot_, '=');
}
else if (isLeft (s, "gene="))
{
gene_ = s;
findSplit (gene_, '=');
}
else if (isLeft (s, "product="))
{
product_ = s;
findSplit (product_, '=');
//replace (product, tmpSpace, ' ');
}
else if (gffType == Gff::patric && isLeft (s, "locus_tag="))
{
locusTag = s;
findSplit (locusTag, '=');
}
}
trimPrefix (prot_, "\"");
trimSuffix (prot_, "\"");
if (prot_. empty ())
continue;
//throw runtime_error ("no attribute '" + protAttr + "': " + f. line);
switch (gffType)
{
case Gff::genbank: if (contains (prot_, ":")) findSplit (prot_, ':'); break;
case Gff::patric: if (! locusTag. empty ()) prot_ += "|" + locusTag;
if (isLeft (contig, "accn|")) contig. erase (0, 5);
break;
default: break;
}
}
QC_ASSERT (! prot_. empty ());
string prot (unescape (prot_));
const string gene (unescape (gene_));
const string product (unescape (product_));
if (gffType == Gff::pgap)
{
pgap_accession (prot, false);
pgap_accession (contig, lcl);
}
QC_ASSERT (! prot. empty ());
Locus locus ((size_t) f. lineNum, contig, (size_t) start, (size_t) stop, strand == "+", partial, 0, gene, product);
#if 0
// DNA may be truncated
if (type == "CDS" && ! pseudo && locus. size () % 3 != 0)
{
cout << "Locus tag: " << prot << endl;
locus. print (cout);
ERROR;
}
#endif
prot2loci [prot] << std::move (locus);
}
catch (const exception &e)
{
throw runtime_error ("File " + fName + ", " + f. lineStr () + ": " + e. what ());
}
}
}
Annot::Annot (const string &fName)
{
if (fName. empty ())
throw runtime_error ("Empty BED file name");
LineInput f (fName /*, 100 * 1024, 1*/);
while (f. nextLine ())
{
trim (f. line);
if ( f. line. empty ()
|| f. line [0] == '#'
)
continue;
replace (f. line, ' ', '_'); // to use '\t' as delimiter
const string errorS ("File " + fName + ", " + f. lineStr () + ": ");
string contig, prot;
size_t start, stop;
double score;
char strand = ' ';
static Istringstream iss;
iss. reset (f. line);
iss >> contig >> start >> stop >> prot >> score >> strand;
if (strand == ' ')
throw runtime_error (errorS + "at least 5 fields are expected in each line");
for (const char c : contig)
if (! printable (c))
throw runtime_error (errorS + "Non-printable character in the sequence identifier: " + to_string (c));
if (start >= stop)
throw runtime_error (errorS + "start should be less than stop");
if ( strand != '+'
&& strand != '-'
)
throw runtime_error (errorS + "strand should be '+' or '-'");
trim (prot, '_');
ASSERT (! prot. empty ());
prot2loci [prot] << Locus ((size_t) f. lineNum, contig, start, stop, strand == '+', false/*partial*/, 0, noString, noString);
}
}
void Annot::load_fasta2gff_prot (const string &fName)
{
ASSERT (fasta2gff_prot. empty ());
LineInput f (fName);
Istringstream iss;
string fasta_prot, gff_prot;
while (f. nextLine ())
{
iss. reset (f. line);
fasta_prot. clear ();
gff_prot. clear ();
iss >> fasta_prot >> gff_prot;
QC_ASSERT (! gff_prot. empty ());
fasta2gff_prot [fasta_prot] = gff_prot;
}
if (fasta2gff_prot. empty ())
throw runtime_error ("File " + fName + " is empty");
}
void Annot::load_fasta2gff_dna (const string &fName)
{
map<string/*DNA GFF id*/,string/*DNA FASTA id*/> gff2fasta;
{
LineInput f (fName);
Istringstream iss;
string fasta_dna, gff_dna;
while (f. nextLine ())
{
iss. reset (f. line);
fasta_dna. clear ();
gff_dna. clear ();
iss >> fasta_dna >> gff_dna;
QC_ASSERT (! gff_dna. empty ());
gff2fasta [gff_dna] = fasta_dna;
}
}
if (gff2fasta. empty ())
throw runtime_error ("File " + fName + " is empty");
for (auto& it : prot2loci)
{
Set<Locus>& loci = it. second;
for (const Locus& locus : loci)
{
string s;
if (! find (gff2fasta, locus. contig, s))
throw runtime_error ("FASTA DNA contig " + strQuote (locus. contig) + " is not found in GFF-DNA match file " + strQuote (fName));
var_cast (locus). contig = std::move (s);
}
}
}
const Set<Locus>& Annot::findLoci (const string &fasta_prot) const
{
ASSERT (! fasta_prot. empty ());
string gff_prot (fasta_prot);
if (! fasta2gff_prot. empty ())
{
string s;
if (! find (fasta2gff_prot, gff_prot, s))
throw runtime_error ("FASTA protein " + strQuote (fasta_prot) + " is not found in GFF-protein match file");
gff_prot = std::move (s);
}
ASSERT (! gff_prot. empty ());
const Set<Locus>* loci = findPtr (prot2loci, gff_prot);
if (! loci)
throw runtime_error ("FASTA protein " + fasta_prot + (fasta_prot == gff_prot ? "" : " (converted to GFF protein " + gff_prot +")") + " is misssing in .gff-file");
ASSERT (! loci->empty ());
return *loci;
}
}