44#include " DBWriter.h"
55#include " Matcher.h"
66#include " Util.h"
7- #include " itoa.h"
8-
7+ #include " TranslateNucl.h"
98#include " Orf.h"
109
1110#include < unistd.h>
1615#include < omp.h>
1716#endif
1817
18+ void handleSingleFrame (TranslateNucl& translateNucl, DBWriter& sequenceWriter, DBWriter& headerWriter, unsigned int key, char * headerBuffer, const char * data, size_t seqLen, int frame, bool reverse, bool translate, char *& aaBuffer, size_t & aaBufferSize, int thread_idx) {
19+ data = data + frame;
20+ seqLen = seqLen - frame;
21+ if (translate == true ) {
22+ if (seqLen < 3 ) {
23+ return ;
24+ }
25+ size_t codonLength = (seqLen / 3 ) * 3 ;
26+ if ((codonLength + 1 ) > aaBufferSize) {
27+ aaBufferSize = codonLength * 1.5 + 1 ;
28+ aaBuffer = (char *)realloc (aaBuffer, aaBufferSize * sizeof (char ));
29+ }
30+ translateNucl.translate (aaBuffer, data, codonLength);
31+ aaBuffer[codonLength / 3 ] = ' \n '
32+ sequenceWriter.writeData (aaBuffer, (codonLength / 3 ) + 1 , key, thread_idx);
33+ size_t bufferLen;
34+ if (reverse) {
35+ bufferLen = Orf::writeOrfHeader (headerBuffer, key, frame + codonLength, static_cast <size_t >(frame), 0 , 0 );
36+ } else {
37+ bufferLen = Orf::writeOrfHeader (headerBuffer, key, static_cast <size_t >(frame), frame + codonLength, 0 , 0 );
38+ }
39+ headerWriter.writeData (headerBuffer, bufferLen, key, thread_idx);
40+ } else {
41+ // +1: add newline, but remove it from the end pos
42+ sequenceWriter.writeData (data, seqLen + 1 , key, thread_idx);
43+ size_t bufferLen;
44+ if (reverse) {
45+ bufferLen = Orf::writeOrfHeader (headerBuffer, key, seqLen - 1 , static_cast <size_t >(frame), 0 , 0 );
46+ } else {
47+ bufferLen = Orf::writeOrfHeader (headerBuffer, key, static_cast <size_t >(frame), seqLen - 1 , 0 , 0 );
48+ }
49+ headerWriter.writeData (headerBuffer, bufferLen, key, thread_idx);
50+ }
51+ }
52+
1953int extractframes (int argc, const char **argv, const Command& command) {
2054 Parameters& par = Parameters::getInstance ();
2155 par.parseParameters (argc, argv, command, true , 0 , 0 );
2256
2357 DBReader<unsigned int > reader (par.db1 .c_str (), par.db1Index .c_str (), par.threads , DBReader<unsigned int >::USE_INDEX|DBReader<unsigned int >::USE_DATA);
2458 reader.open (DBReader<unsigned int >::NOSORT);
2559
26- DBWriter sequenceWriter (par.db2 .c_str (), par.db2Index .c_str (), par.threads , par.compressed , reader.getDbtype ());
60+ int outputDbtype = reader.getDbtype ();
61+ if (par.translate ) {
62+ outputDbtype = Parameters::DBTYPE_AMINO_ACIDS;
63+ }
64+ DBWriter sequenceWriter (par.db2 .c_str (), par.db2Index .c_str (), par.threads , par.compressed , outputDbtype);
2765 sequenceWriter.open ();
2866
2967 DBWriter headerWriter (par.hdr2 .c_str (), par.hdr2Index .c_str (), par.threads , false , Parameters::DBTYPE_GENERIC_DB);
3068 headerWriter.open ();
3169
3270 unsigned int forwardFrames = Orf::getFrames (par.forwardFrames );
3371 unsigned int reverseFrames = Orf::getFrames (par.reverseFrames );
34- Debug::Progress progress (reader.getSize ());
3572
73+ Debug::Progress progress (reader.getSize ());
74+ TranslateNucl translateNucl (static_cast <TranslateNucl::GenCode>(par.translationTable ));
3675#pragma omp parallel
3776 {
3877 int thread_idx = 0 ;
@@ -46,70 +85,66 @@ int extractframes(int argc, const char **argv, const Command& command) {
4685 queryFrom = 0 ;
4786 }
4887
88+ size_t aaBufferSize = par.maxSeqLen + 3 + 1 ;
89+ char * aa = NULL ;
90+ if (par.translate == true ) {
91+ aa = (char *)malloc (aaBufferSize * sizeof (char ));
92+ }
93+
4994 char buffer[1024 ];
95+
5096 std::string reverseComplementStr;
5197 reverseComplementStr.reserve (32000 );
98+
5299 for (unsigned int i = queryFrom; i < (queryFrom + querySize); ++i){
53100 progress.updateProgress ();
54101
55102 unsigned int key = reader.getDbKey (i);
56103 const char * data = reader.getData (i, thread_idx);
57- size_t dataLength = reader.getEntryLen (i);
58-
59- size_t bufferLen;
60- switch (forwardFrames){
61- case Orf::FRAME_1:
62- // -1 to ignore the null byte copy the new line
63- sequenceWriter.writeData (data, dataLength - 1 , key, thread_idx);
64- bufferLen = Orf::writeOrfHeader (buffer, key, static_cast <size_t >(0 ), dataLength - 3 , 0 , 0 );
65- headerWriter.writeData (buffer, bufferLen, key, thread_idx);
66- break ;
67- case Orf::FRAME_2:
68- sequenceWriter.writeData (data + 1 , dataLength - 2 , key, thread_idx);
69- bufferLen = Orf::writeOrfHeader (buffer, key, static_cast <size_t >(1 ), dataLength - 4 , 0 , 0 );
70- headerWriter.writeData (buffer, bufferLen, key, thread_idx);
71- break ;
72- case Orf::FRAME_3:
73- sequenceWriter.writeData (data + 2 , dataLength - 3 , key, thread_idx);
74- bufferLen = Orf::writeOrfHeader (buffer, key, static_cast <size_t >(2 ), dataLength - 5 , 0 , 0 );
75- headerWriter.writeData (buffer, bufferLen, key, thread_idx);
76- break ;
104+ size_t seqLen = reader.getSeqLen (i);
105+
106+ if (forwardFrames & Orf::FRAME_1) {
107+ handleSingleFrame (translateNucl, sequenceWriter, headerWriter, key, buffer, data, seqLen, 0 , false , par.translate , aa, aaBufferSize, thread_idx);
108+ }
109+ if (forwardFrames & Orf::FRAME_2) {
110+ handleSingleFrame (translateNucl, sequenceWriter, headerWriter, key, buffer, data, seqLen, 1 , false , par.translate , aa, aaBufferSize, thread_idx);
111+ }
112+ if (forwardFrames & Orf::FRAME_3) {
113+ handleSingleFrame (translateNucl, sequenceWriter, headerWriter, key, buffer, data, seqLen, 2 , false , par.translate , aa, aaBufferSize, thread_idx);
77114 }
78115
79- if (reverseFrames != 0 ){
80- size_t sequenceLength = dataLength -2 ;
116+ if (reverseFrames != 0 ) {
81117 // bool hasWrongChar = false;
82- for (size_t pos = 0 ; pos < sequenceLength ; ++pos) {
83- char reverseComplement = Orf::complement (data[sequenceLength - pos - 1 ]);
118+ for (size_t pos = 0 ; pos < seqLen ; ++pos) {
119+ char reverseComplement = Orf::complement (data[seqLen - pos - 1 ]);
84120 reverseComplement = (reverseComplement == ' .' ' N'
85121 reverseComplementStr.push_back (reverseComplement);
86122 // hasWrongChar |= (reverseComplement == '.');
87123 }
88- // if (hasWrongChar == true){
89- // continue;
90- // }
124+ // if (hasWrongChar == true) {
125+ // continue;
126+ // }
91127 reverseComplementStr.push_back (' \n '
128+ seqLen = reverseComplementStr.size () - 1 ;
129+ data = reverseComplementStr.c_str ();
92130 }
93131
94- switch (reverseFrames){
95- case Orf::FRAME_1:
96- sequenceWriter.writeData (reverseComplementStr.c_str (), reverseComplementStr.size (), key, thread_idx);
97- bufferLen = Orf::writeOrfHeader (buffer, key, reverseComplementStr.size () - 2 , static_cast <size_t >(0 ), 0 , 0 );
98- headerWriter.writeData (buffer, bufferLen, key, thread_idx);
99- break ;
100- case Orf::FRAME_2:
101- sequenceWriter.writeData (reverseComplementStr.c_str ()+1 , reverseComplementStr.size ()-1 , key, thread_idx);
102- bufferLen = Orf::writeOrfHeader (buffer, key, reverseComplementStr.size () - 3 , static_cast <size_t >(1 ), 0 , 0 );
103- headerWriter.writeData (buffer, bufferLen, key, thread_idx);
104- break ;
105- case Orf::FRAME_3:
106- sequenceWriter.writeData (reverseComplementStr.c_str ()+2 , reverseComplementStr.size ()-2 , key, thread_idx);
107- bufferLen = Orf::writeOrfHeader (buffer, key, reverseComplementStr.size () - 4 , static_cast <size_t >(2 ), 0 , 0 );
108- headerWriter.writeData (buffer, bufferLen, key, thread_idx);
109- break ;
132+ if (reverseFrames & Orf::FRAME_1) {
133+ handleSingleFrame (translateNucl, sequenceWriter, headerWriter, key, buffer, data, seqLen, 0 , true , par.translate , aa, aaBufferSize, thread_idx);
134+ }
135+
136+ if (reverseFrames & Orf::FRAME_2) {
137+ handleSingleFrame (translateNucl, sequenceWriter, headerWriter, key, buffer, data, seqLen, 1 , true , par.translate , aa, aaBufferSize, thread_idx);
138+ }
139+
140+ if (reverseFrames & Orf::FRAME_3) {
141+ handleSingleFrame (translateNucl, sequenceWriter, headerWriter, key, buffer, data, seqLen, 2 , true , par.translate , aa, aaBufferSize, thread_idx);
110142 }
111143 reverseComplementStr.clear ();
112144 }
145+ if (aa != NULL ) {
146+ free (aa);
147+ }
113148 }
114149 headerWriter.close (true );
115150 sequenceWriter.close (true );
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