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// PatMaN DNA pattern matcher
// (C) 2007 Kay Pruefer, Udo Stenzel
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or (at
// your option) any later version. See the LICENSE file for details.
#include <iostream>
#include <string>
#include <vector>
#include <fstream>
#include <cstdlib>
#include <cstring>
#include <popt.h>
#include "prefix_tree.h"
#include "fasta.h"
using namespace std ;
// global variables
size_t cutoff = 2 ;
size_t allow_gaps = 0 ;
size_t minlength = 0 ;
long long total_nodes = 0 ;
int only_plus_strand = 0 ;
int discount_adenine = 0 ;
int ambi_codes = 0 ;
int chop5 = 0, chop3 = 0 ;
int debug_flags = debug_notquiet ;
int do_prefetch = 3 ;
ostream *output = 0 ;
long position_genome ;
const char* genome_name ;
enum option_flag { opt_none, opt_db, opt_pat, opt_output, opt_version } ;
struct poptOption options[] = {
{ "version", 'V', POPT_ARG_NONE, 0, opt_version, "Print version number and exit", 0 },
{ "edits", 'e', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &cutoff, 0, "Set maximum edit distance to N", "N" },
{ "gaps", 'g', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &allow_gaps, 0, "Set maximum number of gaps to N", "N" },
{ "databases", 'D', POPT_ARG_NONE, 0, opt_db, "Following files are databases", 0 },
{ "patterns", 'P', POPT_ARG_NONE, 0, opt_pat, "Following files contain patterns", 0 },
{ "output", 'o', POPT_ARG_STRING, 0, opt_output, "Write output to FILE", "FILE" },
{ "ambicodes", 'a', POPT_ARG_NONE, &ambi_codes, 0, "Interpret ambiguity codes in patterns", 0 },
{ "singlestrand", 's', POPT_ARG_NONE, &only_plus_strand, 0, "Do not match reverse-complements", 0 },
{ "prefetch", 'p', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &do_prefetch, 0, "Prefetch N nodes", "N" },
{ "min-length", 'l', POPT_ARG_INT | POPT_ARGFLAG_DOC_HIDDEN, &minlength, 0, "Only consider patterns longer than N", "N" },
{ "chop-3", 'x', POPT_ARG_INT | POPT_ARGFLAG_DOC_HIDDEN, &chop3, 0, "Chop N bp off the 3' end of patterns", "N" },
{ "chop-5", 'X', POPT_ARG_INT | POPT_ARGFLAG_DOC_HIDDEN, &chop5, 0, "Chop N bp off the 5' end of patterns", "N" },
{ "adenine-hack", 'A', POPT_ARG_NONE | POPT_ARGFLAG_DOC_HIDDEN, &discount_adenine, 0, "Ignore inserted adenines in db", 0 },
{ "quiet", 'q', POPT_ARG_NONE | POPT_BIT_CLR, &debug_flags, debug_notquiet, "Turn off warnings", 0 },
{ "verbose", 'v', POPT_ARG_NONE | POPT_BIT_SET, &debug_flags, debug_verbose, "Print additional progress reports", 0 },
{ "debug", 'd', POPT_ARG_INT | POPT_ARGFLAG_DOC_HIDDEN, &debug_flags, 0, "Set debug flags to N (see man page)", "N" },
POPT_AUTOHELP POPT_TABLEEND
} ;
int main(int argc, const char *argv[]) {
std::vector<std::string> dbfiles, patfiles ;
poptContext pc = poptGetContext( "patman", argc, argv, options, 0 ) ;
poptSetOtherOptionHelp( pc, "[OPTION...] [input-file...]" ) ;
poptReadDefaultConfig( pc, 0 ) ;
bool isdbfiles = false ;
if( argc <= 1 ) { poptPrintHelp( pc, stderr, 0 ) ; return 1 ; }
int rc = poptGetNextOpt(pc) ;
for(;;) {
if( rc == opt_version ) {
std::cout << poptGetInvocationName(pc) << ", revision " << VERSION << std::endl ;
return 0 ;
}
else if( rc == opt_db || rc == opt_pat || rc == -1 ) {
while( poptPeekArg(pc) )
( isdbfiles ? dbfiles : patfiles ).push_back( poptGetArg(pc) ) ;
isdbfiles = (rc == opt_db) ;
}
else if( rc == opt_output )
{
delete output ;
const char *arg = poptGetOptArg(pc) ;
if( 0 == strcmp( arg, "-" ) ) output = 0 ;
else output = new std::ofstream( arg ) ;
}
else {
std::cerr << argv[0] << ": " << poptStrerror( rc )
<< ' ' << poptBadOption( pc, 0 ) << std::endl ;
return 1 ;
}
if( rc == -1 ) break ; else rc = poptGetNextOpt(pc) ;
}
if( dbfiles.empty() )
{
dbfiles.push_back( "-" ) ;
if( debug_flags & debug_notquiet )
clog << "No databases given, using stdin." << endl ;
}
if( patfiles.empty() )
{
clog << "No patterns given, aborting." << endl ;
exit(1) ;
}
prefix_tree trie ;
for( size_t i = 0 ; i != patfiles.size() ; ++i )
{
ifstream *infile = 0 ;
if( patfiles[i] != "-" ) {
infile = new ifstream( patfiles[i].c_str() ) ;
if( debug_flags & debug_verbose ) clog << "reading patterns from " << patfiles[i] << endl ;
if( !infile || !*infile ) { cerr << "cannot read " << patfiles[i] << endl ; return 1 ; }
}
else if( debug_flags & debug_verbose ) clog << "reading patterns from STDIN" << endl ;
// add pattern to prefix tree
fasta_fac f( infile ? *infile : cin ) ;
fasta* ff ;
while ( (ff = f.get()) && !ff->null ) {
if( minlength <= ff->seq.size() )
trie.add_seq(
ff->seq.substr( chop5, ff->seq.size() - chop5 - chop3 ),
ff->headerline, !!ambi_codes ) ;
delete ff ;
}
delete infile ;
}
if( debug_flags & debug_verbose ) clog << "post-processing trie" << endl ;
trie.add_suffix_links() ;
#ifndef NDEBUG
trie.debug( cerr ) ;
#endif
mismatch_ptr *ptrs = 0 ;
// read database
string headerline ;
for( size_t i = 0 ; i != dbfiles.size() ; ++i ) {
ifstream *dbfile = 0 ;
if( dbfiles[i] != "-" ) {
dbfile = new ifstream( dbfiles[i].c_str() ) ;
if( debug_flags & debug_verbose ) clog << "processing database from " << dbfiles[i] << endl ;
if( !dbfile || !*dbfile ) { cerr << "cannot read " << dbfiles[i] << endl ; return 1 ; }
}
else if( debug_flags & debug_verbose ) clog << "processing database from STDIN" << endl ;
getline( dbfile ? *dbfile : cin, headerline ) ;
while( dbfile ? *dbfile : cin ) {
if ( headerline[0] != '>' ) {
cerr << "database is not in fasta format" << endl ;
exit( 2 ) ;
}
headerline = headerline.substr( 1, headerline.size()-1 ) ;
genome_name = headerline.c_str() ; // global variable
string seq ;
bool eat_n = 0 ;
size_t last_n = 0 ;
position_genome = 1 ; // global variable
ptrs = trie.init( ptrs ) ;
while ( getline( dbfile ? *dbfile : cin, seq )
&& ( seq.empty() || seq[0] != '>' ) ) {
for ( size_t i = 0 ; i < seq.size() ; i++,position_genome++ )
{
if ( toupper( seq[i] ) == 'N' )
if ( eat_n ) continue ;
else {
last_n ++ ;
if ( last_n == cutoff + 1 ) eat_n = 1 ;
}
else if ( eat_n ) { eat_n = 0 ; last_n = 0 ; }
if( debug_flags & debug_sequence ) std::clog << seq[i] << std::flush ;
ptrs = trie.compare( seq[i], ptrs ) ;
}
}
trie.compare( 0, ptrs ) ;
headerline = seq ;
}
delete dbfile ;
}
( output ? *output : cout ) << std::flush ;
delete output ;
if( debug_flags & debug_countnodes )
clog << "Fetched " << total_nodes << " nodes in total" << endl ;
poptFreeContext( pc ) ;
return 0 ;
}
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