AceWriter Class Reference

#include <acewriteralgo.h>

Inheritance diagram for AceWriter:

[legend]Collaboration diagram for AceWriter:

[legend]List of all members.

Public Member Functions
	AceWriter (TrapperDoc *pDoc_, std::set< db_recno_t > &recnoList, AlgoParam *param)
void	start ()
Private Member Functions
void	write_ace_file ()
int	get_consensus (std::vector< char > &cons, std::vector< int > &rowVec, int &num)
int	get_realignment_row (const int row, std::vector< char > &aligned_read, int &row_start)

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Detailed Description

Definition at line 4 of file acewriteralgo.h.

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Constructor & Destructor Documentation

AceWriter::AceWriter (  TrapperDoc *  pDoc_, std::set< db_recno_t > &  recnoList, AlgoParam *  param )  [inline]

Definition at line 7 of file acewriteralgo.h. : RAlgo(pDoc_, recnoList, param) {}

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Member Function Documentation

int AceWriter::get_consensus (  std::vector< char > &  cons, std::vector< int > &  rowVec, int &  num )  [private]

Referenced by write_ace_file().

int AceWriter::get_realignment_row (  const int  row, std::vector< char > &  aligned_read, int &  row_start )  [private]

Referenced by write_ace_file().

void AceWriter::start (   )  [virtual]

Implements RAlgo. Definition at line 8 of file acewriteralgo.cc. References write_ace_file(). { write_ace_file(); }

void AceWriter::write_ace_file (   )  [private]

Definition at line 14 of file acewriteralgo.cc. References get_consensus(), MAl_Readonly::get_name(), MAl_Readonly::get_num_seq(), get_realignment_row(), RAlgo::getMAl(), and MAl_Readonly::is_DNP(). Referenced by start(). { //This is adapted from old code, needs a rewrite! cerr<<"Writing ace file... "; string dir = "."; string file_name = "trappercontig"; // The parameters name are taken from the documentation of the // ace file format doc at; // http://www.phrap.org/consed/distributions/README.13.0.txt // There's a lot of variables in this function. It's possible to // write this function with less variables, but thay are there // to make it easier to rewrite the function if you want to add stuff. // ---------------------------------------------------------------------- // ---------- Declerations of parameters with default values! // ---------------------------------------------------------------------- // AS parameters int tot_num_of_reads_in_ace_file; // CO parameters string contig_name = "contig1"; int num_of_bases; int num_of_reads_in_contig; int num_of_segments_in_contig; vector<char> consensus; // BQ parameters int num_of_unpadded_bases; vector<short> consensus_quality_values; consensus_quality_values.push_back(50); // The consensus will get 50 // AF parameters vector<string> read_name; vector<char> UorC; vector<int> padded_start_consensus_position; // BS parameters vector<int> BS_padded_start_consensus_position; vector<int> BS_padded_end_consensus_position; vector<string> BS_read_name; // RD parameters vector<int> num_of_padded_bases; int num_of_whole_read_info_items = 0; // puch dakota! vector<int> num_of_read_tags; vector< vector<char> > read_seq; // QA parameters vector<int> qual_clipping_start; vector<int> qual_clipping_end; vector<int> align_clipping_start; vector<int> align_clipping_end; // DS parameters vector<string> name_of_chromat_file; vector<string> name_of_phd_file; string date_of_phd_file = "Thu Mar 19 18:38:28 1998"; // Northwest Energy Review Transition Board - Mar 19, 1998 report // RT parameters vector< vector<string> > tag_type; string what_program_created_tag = "TRAPPER"; vector< vector<int> > padded_read_pos_start; vector< vector<int> > padded_read_pos_end; string date_when_tag_was_created = "980319:183828"; vector< vector<string> > tag_data; // CA & WA are at the moment not in this function! // ---------------------------------------------------------------------- // ---------- Set parameter values. // ---------------------------------------------------------------------- cerr<<" (Setting parameter values.) "; vector<char> tmp_charvec; vector<int> tmp_start, tmp_end; vector<string> tmp_data, tmp_type; // ################################# Get consensus ################################# vector<int> rowVec; int consensus_start = get_consensus(consensus, rowVec, num_of_unpadded_bases); num_of_bases = consensus.size(); // ################################# Get info from the cosmid ################################# int id; int begin_pos; int len; int aligned_len; string name; //bool OK; tot_num_of_reads_in_ace_file = 0; // Mod to output query sequence in ace file.. DN 040407 int num_rows = getMAl()->get_num_seq (); for(int i=0; i < num_rows; i++) { // Loop over all aligned reads + query // Make room // for RT tmp_start.clear(); tmp_end.clear(); tmp_data.clear(); tmp_type.clear(); // and seq tmp_charvec.clear(); // Get the name id = i; name = getMAl()->get_name(id); // ################################# Get seq from real_matrix if ( ! get_realignment_row(i, tmp_charvec, begin_pos) ) cerr << "Id: " << id <<" have been removed from alignment!"<<endl; else { tot_num_of_reads_in_ace_file++; // One more not empty read; UorC.push_back( getMAl()->get_strand(id)[0] ); // Store names read_name.push_back(name); name_of_phd_file.push_back( name + ".phd.1"); name_of_chromat_file.push_back( name + ".ab1"); aligned_len = tmp_charvec.size(); //int offset = current_cos->get_beginGood(id) - current_cos->get_seq_begin(id); int offset=0;//No offset? // Set start of the read aginst the consensus! padded_start_consensus_position.push_back(begin_pos - consensus_start + 1 - offset); // ################################# Set RT:s int paddedCount = 0; for( int j = 0; j < aligned_len; j++ ) { // Count gaps if ( tmp_charvec[j] == '*' ) paddedCount++; // DNP position else if( getMAl()->is_DNP(id, j) ) { tmp_start.push_back( j + 1 + offset ); tmp_end.push_back( j + 1 + offset ); tmp_data.push_back("a DNP position"); tmp_type.push_back("matchElsewhereHighQual"); } // Marked region! // else if ( tmp_charvec[j] == 'x' ) { // tmp_start.push_back( j + 1 + offset ); // tmp_data.push_back("Marked region"); // tmp_type.push_back("significantDiscrepancy"); // // Go through the whole marked region // while((tmp_charvec[j] == '*' || tmp_charvec[j] == 'x') && j < aligned_len ) { // if ( tmp_charvec[j] == '*') paddedCount++; // else tmp_charvec[j] = current_cos->get_base(id, current_cos->get_beginGood(id) + j - paddedCount); // j++; // } // tmp_end.push_back(j + offset); // } } // ################################# Adds the bases that was not aligned vector<char> TheWholeSeq; // = head + tmp_charvec + tail // Head for( int j = 0; j < aligned_len; j++ ) TheWholeSeq.push_back(tmp_charvec[j]); // Tail len = TheWholeSeq.size(); // Save everything! num_of_read_tags.push_back(tmp_start.size()); padded_read_pos_start.push_back(tmp_start); padded_read_pos_end.push_back(tmp_end); tag_type.push_back(tmp_type); tag_data.push_back(tmp_data); read_seq.push_back(TheWholeSeq); num_of_padded_bases.push_back(len); qual_clipping_start.push_back(1); qual_clipping_end.push_back(aligned_len); align_clipping_start.push_back(1); align_clipping_end.push_back(aligned_len); } } num_of_reads_in_contig = tot_num_of_reads_in_ace_file; // One contig in acefile // ################################# Set BS values! ################################# // It will give bs that are sorted, nonoverlapping and match the consensus! int curr = rowVec[0]; num_of_segments_in_contig = 1; BS_padded_start_consensus_position.push_back(1); string tmp = getMAl()->get_name(rowVec[0]); BS_read_name.push_back( tmp ); for( int n = 1; n < (int)rowVec.size(); n++ ) { if ( curr != rowVec[n] ) { BS_padded_end_consensus_position.push_back(n); num_of_segments_in_contig++; BS_padded_start_consensus_position.push_back(n+1); tmp = getMAl()->get_name(rowVec[n]); BS_read_name.push_back( tmp ); curr = rowVec[n]; } } BS_padded_end_consensus_position.push_back(rowVec.size()); // ---------------------------------------------------------------------- // ---------- Write ace file. // ---------------------------------------------------------------------- if ( tot_num_of_reads_in_ace_file == 0 ) return; else { // Disk full? if(access(dir.data(), W_OK) == -1) { cerr << "Cannot write ace-files to " << dir << endl; exit(-1); } ofstream outFile((dir + "/" + file_name + ".ace").data()); cerr<<" (Printing to file.) "; // write AS int num_contigs = 1; outFile<<"AS "<<num_contigs<<" "<<tot_num_of_reads_in_ace_file<<endl; outFile<<endl; // write CO outFile<<"CO "<<contig_name<<" "<<num_of_bases <<" "<<num_of_reads_in_contig<<" "<<num_of_segments_in_contig <<" U"<<endl; for( int i = 0; i < num_of_bases; i++ ) { if ( i != 0 && i % 50 == 0 ) outFile<<endl; outFile<<consensus[i]; } outFile<<endl; outFile<<endl; // write BQ outFile<<"BQ "<<endl; for( int i = 0; i < num_of_unpadded_bases; i++ ) { if ( i != 0 && i % 50 == 0 ) outFile<<endl; outFile<<' '<<consensus_quality_values[0]; } outFile<<endl; outFile<<endl; // write AF for( int i = 0; i < num_of_reads_in_contig; i++ ) { // Change parameters value! outFile<<"AF "<<read_name[i]<<" "<<UorC[i] <<" "<<padded_start_consensus_position[i]<<endl; } // write BS for( int i = 0; i < num_of_segments_in_contig; i++ ) { // Change parameters value! outFile<<"BS "<<BS_padded_start_consensus_position[i] <<" "<<BS_padded_end_consensus_position[i] <<" "<<BS_read_name[i]<<endl; } outFile<<endl; // write RD, QA & DS for( int i = 0; i < num_of_reads_in_contig; i++ ) { // Change parameters value! // write RD outFile<<"RD "<<read_name[i]<<" "<<num_of_padded_bases[i] <<" "<<num_of_whole_read_info_items <<" "<<num_of_read_tags[i]<<endl; for( int j = 0; j < num_of_padded_bases[i]; j++ ) { if ( j != 0 && j % 50 == 0 ) outFile<<endl; outFile<<read_seq[i][j]; } outFile<<endl; outFile<<endl; // write QA outFile<<"QA "<<qual_clipping_start[i] <<" "<<qual_clipping_end[i] <<" "<<align_clipping_start[i] <<" "<<align_clipping_end[i]<<endl; outFile<<endl; // write DS outFile<<"DS CHROMAT_FILE: "<<name_of_chromat_file[i] <<" PHD_FILE: "<<name_of_phd_file[i] <<" TIME: "<<date_of_phd_file<<endl; outFile<<endl; // write RT for( int j = 0; j < (int)padded_read_pos_start[i].size(); j++ ) { outFile<<"RT{"<<endl; outFile<<read_name[i]<<' '<<tag_type[i][j]<<' ' <<what_program_created_tag<<' ' <<padded_read_pos_start[i][j]<<' ' <<padded_read_pos_end[i][j]<<' ' <<date_when_tag_was_created<<endl; outFile<<tag_data[i][j]<<endl; outFile<<'}'<<endl; outFile<<endl; } } cerr<<" Done. "<<endl; outFile.close(); } }

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The documentation for this class was generated from the following files:

• acewriteralgo.h
• acewriteralgo.cc

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