/*=========================================================================== * * 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. * * =========================================================================== * */ /*========================================================================== * Sequence schema */ version 1; include 'vdb/vdb.vschema'; include 'insdc/insdc.vschema'; /*-------------------------------------------------------------------------- * rand_4na_2na * converts 4na to 2na * * substitutes a random base for ambiguities * from the bases allowed in the 4na. * * A | C | G | T * ================= * N | | | # any base may be substituted * A * | | | # always A * C | * | | # always C * M * | * | | # A or C * G | | * | # always G * R * | | * | # A or G * S | * | * | # C or G * V * | * | * | # A, C or G * T | | | * # always T * W * | | | * # A or T * Y | * | | * # C or T * H * | * | | * # A, C or T * K | | * | * # G or T * D * | | * | * # A, G or T * B | * | * | * # C, G or T * N * | * | * | * # any base may be substituted */ extern function INSDC:2na:bin INSDC:SEQ:rand_4na_2na #1 ( INSDC:4na:bin rd_bin ); /*-------------------------------------------------------------------------- * sequence * basic sequence table * * history: * 1.0.1 - introduced text-mode QUALITY columns */ table INSDC:tbl:sequence #1.0.1 { /* READ * native or converted DNA sequence */ // default is IUPAC character representation extern default column INSDC:dna:text READ { read = out_dna_text; validate = < INSDC:dna:text > compare ( in_dna_text, out_dna_text ); } // 4na representation - unpacked and packed extern column INSDC:4na:bin READ = out_4na_bin; extern column INSDC:4na:packed READ = out_4na_packed; // x2na representation - 2na with ambiguity extern column INSDC:x2na:bin READ = out_x2na_bin; // 2na representation - 2na with no ambiguity - unpacked and packed extern column INSDC:2na:bin READ = out_2na_bin; extern column INSDC:2na:packed READ = out_2na_packed; /* CSREAD * native or converted color-space sequence */ // default is ASCII character representation extern default column INSDC:color:text CSREAD { read = out_color_text; validate = < INSDC:color:text > compare ( in_color_text, out_color_text ); } // x2cs representation - 2cs with ambiguity extern column INSDC:x2cs:bin CSREAD = out_x2cs_bin; // 2cs representation - 2cs with no ambiguity - unpacked and packed extern column INSDC:2cs:bin CSREAD = out_2cs_bin; extern column INSDC:2cs:packed CSREAD = out_2cs_packed; /* CS_NATIVE * is color-space the native sequence space */ readonly column bool CS_NATIVE = cs_native; /* CS_KEY * leading call given in base-space */ extern column INSDC:dna:text CS_KEY { read = out_cs_key; validate = < INSDC:dna:text > compare ( in_cs_key, out_cs_key ); } /* COLOR_MATRIX * matrix used for color-space conversions */ extern column U8 COLOR_MATRIX = out_color_matrix; /* QUALITY * base or color call qualities */ // PHRED is default extern default column INSDC:quality:phred QUALITY { read = out_qual_phred; validate = < INSDC:quality:phred > compare ( in_qual_phred, phys_qual_phred ); } // textual encodings extern column INSDC:quality:text:phred_33 QUALITY = out_qual_text_phred_33 | ( INSDC:quality:text:phred_33 ) < B8 > sum < 33 > ( out_qual_phred ) ; extern column INSDC:quality:text:phred_64 QUALITY = out_qual_text_phred_64 | ( INSDC:quality:text:phred_64 ) < B8 > sum < 64 > ( out_qual_phred ) ; /* SIGNAL * signal and intensity information is unspecified */ INSDC:coord:len signal_len = ( INSDC:coord:len ) row_len ( out_signal ) | < INSDC:coord:len > echo < 0 > () ; /* INSDC:tbl:sequence virtual productions * cs_native * in_cs_key * out_cs_key * out_signal * in_dna_text * out_2cs_bin * out_2na_bin * out_4na_bin * out_dna_text * out_x2cs_bin * out_x2na_bin * in_color_text * out_2cs_packed * out_2na_packed * out_4na_packed * out_color_text * out_qual_phred * out_color_matrix */ }; /*-------------------------------------------------------------------------- * protein * basic protein sequence table */ table INSDC:tbl:protein #1 { /* PROTEIN * native or converted protein sequence */ // default is IUPAC character representation extern default column INSDC:protein:text PROTEIN { read = out_protein_text; validate = < INSDC:protein:text > compare ( in_protein_text, out_protein_text ); } // aa representation extern column INSDC:aa:bin PROTEIN = out_aa_bin; /* INSDC:tbl:protein productions * out_aa_bin * in_protein_text * out_protein_text */ };