// ========================================================================== // SeqAn - The Library for Sequence Analysis // ========================================================================== // Copyright (c) 2006-2010, Knut Reinert, FU Berlin // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // * Neither the name of Knut Reinert or the FU Berlin nor the names of // its contributors may be used to endorse or promote products derived // from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH // DAMAGE. // // ========================================================================== // Author: Manuel Holtgrewe // ========================================================================== // Read support for the GenBank file format. // // Note: We do not want to require a lookahead because then we might need too // many buffers. Thus, we heuristically only look at the first character of // the field name to differentiate between headers and the sequence start // label "ORIGIN". // // The sequence identifier for record-reading is the VERSION field. // ========================================================================== #ifndef EXTRAS_INCLUDE_SEQAN_STREAM_READ_GENBANK_H_ #define EXTRAS_INCLUDE_SEQAN_STREAM_READ_GENBANK_H_ namespace seqan { // ============================================================================ // Forwards // ============================================================================ // ============================================================================ // Tags, Classes, Enums // ============================================================================ struct GenBank_; typedef Tag GenBank; struct GenBankHeader_; typedef Tag GenBankHeader; struct GenBankSequence_; typedef Tag GenBankSequence; enum GenBankErrorCodes_ { IOERR_GENBANK_WRONG_RECORD = 2048 }; // ============================================================================ // Metafunctions // ============================================================================ // ============================================================================ // Functions // ============================================================================ // ---------------------------------------------------------------------------- // Function splitGenBankHeader() // ---------------------------------------------------------------------------- /** .Function.splitGenBankHeader ..cat:Input/Output ..signature:splitGenBankHeader(key, value, lines) ..summary:Split an GenBank header field/value. ..remarks:You can only call this on a whole top-level field such as $SOURCE$, possibly including the following subfields! You cannot split out subfield values. ..param.key:The 2-character header type. ..param.value:The line's value. ..param.line:The lines with the header field to split. ..returns:$void$ ..include:seqan/stream.h ..see:Function.splitEmblHeader */ template inline void splitGenBankHeader(TKey & key, TValue & value, TLine const & lines) { splitEmblHeader(key, value, lines); clear(key); enum State { IN_KEY, IN_SPACE, IN_VALUE }; State state = IN_KEY; typedef typename Iterator::Type TIterator; TIterator it = begin(lines, Rooted()); for (; !atEnd(it); goNext(it)) { if (state == IN_KEY) { if (isblank(*it)) state = IN_SPACE; else appendValue(key, *it); } else if (state == IN_SPACE && !isblank(*it)) { break; } } value = suffix(lines, position(it)); } // ---------------------------------------------------------------------------- // Function nextIs() // ---------------------------------------------------------------------------- // nextIs() for GenBank header records. template inline bool nextIs(RecordReader & reader, GenBankHeader const & /*tag*/) { return !atEnd(reader) && value(reader) != 'O' && !isblank(value(reader)); } // nextIs() for GenBank sequence records. template inline bool nextIs(RecordReader & reader, GenBankSequence const & /*tag*/) { return !atEnd(reader) && value(reader) == 'O'; } // ---------------------------------------------------------------------------- // Function readRecord() // ---------------------------------------------------------------------------- // readRecord() for GenBank header records. // Normalize in-field line endings to '\n'. template inline int readRecord(TTarget & result, RecordReader > & reader, GenBankHeader const & tag) { if (atEnd(reader)) return EOF_BEFORE_SUCCESS; if (!nextIs(reader, tag)) return IOERR_GENBANK_WRONG_RECORD; clear(result); int res = readLine(result, reader); if (res != 0) return res; while (!atEnd(reader) && isblank(value(reader))) { appendValue(result, '\n'); res = readLine(result, reader); if (res != 0) return res; } return 0; } // readRecord() for GenBank sequences records. // Read all sequence, eat/ignore '//' line. template inline int readRecord(TTarget & result, RecordReader > & reader, GenBankSequence const & tag) { if (atEnd(reader)) return EOF_BEFORE_SUCCESS; if (!nextIs(reader, tag)) return IOERR_GENBANK_WRONG_RECORD; clear(result); // Skip 'ORIGIN' line. CharString buffer; int res = readLine(buffer, reader); if (res != 0) return res; if (!startsWith(buffer, "ORIGIN")) return IOERR_GENBANK_WRONG_RECORD; // Read sequence. for (; !atEnd(reader); goNext(reader)) { if (isspace(value(reader)) || isdigit(value(reader))) continue; // Skip blanks. // If we found a slash, look for the next one. if (value(reader) == '/') { if (goNext(reader)) // Returns true if at end. break; if (value(reader) == '/') { skipLine(reader); return 0; // OK, found complete terminator. } } // Otherwise, append the just found character to buffer. appendValue(result, value(reader)); } return EOF_BEFORE_SUCCESS; } // readRecord() for GenBank id/seq pairs. template inline int readRecord(TId & id, TSequence & sequence, RecordReader > & reader, GenBank const & /*tag*/) { CharString buffer; while (nextIs(reader, GenBankHeader())) { int res = readRecord(buffer, reader, GenBankHeader()); if (res != 0) return res; if (startsWith(buffer, "VERSION")) { CharString k; splitGenBankHeader(k, id, buffer); } } clear(sequence); int res = readRecord(sequence, reader, GenBankSequence()); if (res != 0) return res; return 0; } // ---------------------------------------------------------------------------- // Function read2() // ---------------------------------------------------------------------------- template int read2(StringSet & sequenceIds, StringSet & sequences, RecordReader > & reader, GenBank const & tag) { TIdString id; TSeqString seq; while (!atEnd(reader)) { int res = readRecord(id, seq, reader, tag); if (res != 0) return res; appendValue(sequenceIds, id); appendValue(sequences, seq); } return 0; } } // namespace seqan #endif // #ifndef EXTRAS_INCLUDE_SEQAN_STREAM_READ_GENBANK_H_