Mercurial > repos > charles_s_test > seqsero2
diff libs/sratoolkit.2.8.0-centos_linux64/schema/align/seq.vschema @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
| author | charles_s_test |
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| date | Mon, 27 Nov 2017 11:21:07 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/libs/sratoolkit.2.8.0-centos_linux64/schema/align/seq.vschema Mon Nov 27 11:21:07 2017 -0500 @@ -0,0 +1,300 @@ +/*=========================================================================== +* +* 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 'ncbi/seq.vschema'; + + +/* cmp_base_space + * table representing compressed reads in base space, + * where the bases are only stored for unaligned reads + */ +table NCBI:align:tbl:cmp_base_space #1 + = INSDC:tbl:sequence #1.0.1 + , NCBI:tbl:dcmp_base_space #1 +{ + /* CMP_READ + * read compressed against a reference sequence + */ + + // default is IUPAC character representation + extern default column INSDC:dna:text CMP_READ + { + read = out_cmp_dna_text; + validate = < INSDC:dna:text > compare ( in_cmp_dna_text, out_cmp_dna_text ); + } + + // 4na representation + extern column INSDC:4na:bin CMP_READ = out_cmp_4na_bin; + extern column INSDC:4na:packed CMP_READ = out_cmp_4na_packed; + + // x2na representation - 2na with ambiguity + extern column INSDC:x2na:bin CMP_READ = out_cmp_x2na_bin; + + // 2na representation - 2na with no ambiguity + extern column INSDC:2na:bin CMP_READ = out_cmp_2na_bin; + extern column INSDC:2na:packed CMP_READ = out_cmp_2na_packed; + + + /* input processing rules + */ + + // compressed input text + INSDC:dna:text in_cmp_dna_text + = < INSDC:dna:text, INSDC:dna:text > map < '.acmgrsvtwyhkdbn','NACMGRSVTWYHKDBN' > ( CMP_READ ); + + // compressed input 4na bin + INSDC:4na:bin in_cmp_4na_bin + = < INSDC:4na:bin > range_validate < 0, 15 > ( CMP_READ ) + | ( INSDC:4na:bin ) unpack ( in_cmp_4na_packed ) + | < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( in_cmp_dna_text ) + | < INSDC:x2na:bin, INSDC:4na:bin > map < INSDC:x2na:map:BINSET, [ 1, 2, 4, 8, 15 ] > ( in_cmp_x2na_bin ); + + // compressed input 4na packed + INSDC:4na:packed in_cmp_4na_packed = CMP_READ; + + // compressed input x2na bin + INSDC:x2na:bin in_cmp_x2na_bin + = < INSDC:x2na:bin > range_validate < 0, 4 > ( CMP_READ ) + | < INSDC:4na:bin, INSDC:x2na:bin > map < INSDC:4na:map:BINSET, [ 4,0,1,4,2,4,4,4,3,4,4,4,4,4,4,4 ] > ( in_cmp_4na_bin ); + + // compressed input 2na bin + INSDC:2na:bin in_cmp_2na_bin + = < INSDC:2na:bin > range_validate < 0, 3 > ( CMP_READ ) + | ( INSDC:2na:bin ) unpack ( in_cmp_2na_packed ) + | INSDC:SEQ:rand_4na_2na ( in_cmp_4na_bin ); + + // compressed input 2na packed + INSDC:2na:packed in_cmp_2na_packed = CMP_READ; + + // input 4na alt-read ( ambiguities ) + INSDC:4na:bin in_cmp_alt_4na_bin + = < INSDC:4na:bin, INSDC:4na:bin > map < INSDC:4na:map:BINSET, [ 15,0,0,3,0,5,6,7,0,9,10,11,12,13,14,15 ] > ( in_cmp_4na_bin ); + + // preparing a feed into stats column + U8 in_cmp_stats_bin = in_cmp_2na_bin; + + + /* physical columns + */ + + physical column INSDC:2na:packed .CMP_READ + = in_cmp_2na_packed + | ( INSDC:2na:packed ) pack ( in_cmp_2na_bin ); + + physical column < INSDC:4na:bin > zip_encoding .CMP_ALTREAD + = < INSDC:4na:bin > trim < 0, 0 > ( in_cmp_alt_4na_bin ); + + + /* output processing rules + */ + + // output 2na packed + INSDC:2na:packed out_cmp_2na_packed = .CMP_READ; + + // unambiguous unpacked 2na + INSDC:2na:bin out_cmp_2na_bin + = ( INSDC:2na:bin ) unpack ( out_cmp_2na_packed ); + + // output x2na bin + INSDC:x2na:bin out_cmp_x2na_bin + = < INSDC:4na:bin, INSDC:x2na:bin > map < INSDC:4na:map:BINSET, [ 4,0,1,4,2,4,4,4,3,4,4,4,4,4,4,4 ] > ( out_cmp_4na_bin ); + + // output 2na->4na bin + INSDC:4na:bin out_cmp_2na_4na_bin + = < INSDC:2na:bin, INSDC:4na:bin > map < INSDC:2na:map:BINSET, [ 1, 2, 4, 8 ] > ( out_cmp_2na_bin ); + + // output 4na bin + INSDC:4na:bin out_cmp_4na_bin + = < INSDC:4na:bin > bit_or < ALIGN_RIGHT > ( out_cmp_2na_4na_bin, .CMP_ALTREAD ) + | out_cmp_2na_4na_bin; + + // synthesized packed 4na + INSDC:4na:packed out_cmp_4na_packed + = ( INSDC:4na:packed ) pack ( out_cmp_4na_bin ); + + // output text + INSDC:dna:text out_cmp_dna_text + = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_cmp_4na_bin ); + + + /* decompressed sequences + * source is out_dcmp_4na_bin - a virtual production + */ + + // synthesize x2na_bin, 2na_bin and 2na_packed + INSDC:x2na:bin out_dcmp_x2na_bin + = < INSDC:4na:bin, INSDC:x2na:bin > map < INSDC:4na:map:BINSET, [ 4,0,1,4,2,4,4,4,3,4,4,4,4,4,4,4 ] > ( out_dcmp_4na_bin ); + INSDC:2na:bin out_dcmp_2na_bin + = < INSDC:x2na:bin, INSDC:2na:bin > map < [ 0,1,2,3,4 ], [ 0,1,2,3,0 ] > ( out_dcmp_x2na_bin ); + INSDC:2na:packed out_dcmp_2na_packed + = ( INSDC:2na:packed ) pack ( out_dcmp_2na_bin ); + + + /* INSDC:tbl:sequence inherited productions + * cs_native + * out_cs_key + * out_signal + * out_2cs_bin + * out_2na_bin + * out_4na_bin + * out_dna_text + * out_x2cs_bin + * out_x2na_bin + * out_2cs_packed + * out_2na_packed + * out_4na_packed + * out_color_text + * out_color_matrix + */ + + /* NCBI:tbl:dcmp_base_space inherited productions + * out_dcmp_4na_bin + */ +} + + +/* cmp_color_space + * table representing compressed reads in color space, + * where the colors are only stored for unaligned reads + */ +table NCBI:align:tbl:cmp_color_space #1 = + INSDC:tbl:sequence #1.0.1, NCBI:tbl:dcmp_color_space #1 +{ + /* CMP_CSREAD + * read compressed against a reference sequence + */ + + // default is IUPAC character representation + extern default column INSDC:color:text CMP_CSREAD = out_cmp_color_text; + + // x2cs representation - 2cs with ambiguity + extern column INSDC:x2cs:bin CMP_CSREAD = out_cmp_x2cs_bin; + + // 2cs representation - 2cs with no ambiguity + extern column INSDC:2cs:bin CMP_CSREAD = out_cmp_2cs_bin; + extern column INSDC:2cs:packed CMP_CSREAD = out_cmp_2cs_packed; + + + /* input processing rules + */ + + // compressed input text + INSDC:color:text in_cmp_color_text = CMP_CSREAD; + + // compressed input x2cs bin + INSDC:x2cs:bin in_cmp_x2cs_bin + = < INSDC:x2cs:bin > range_validate < 0, 4 > ( CMP_CSREAD ) + | < INSDC:color:text, INSDC:x2cs:bin > map < INSDC:x2cs:map:CHARSET, INSDC:x2cs:map:BINSET > ( in_cmp_color_text ); + + // compressed input 2cs bin + INSDC:2cs:bin in_cmp_2cs_bin + = < INSDC:2cs:bin > range_validate < 0, 3 > ( CMP_CSREAD ) + | ( INSDC:2cs:bin ) unpack ( in_cmp_2cs_packed ) + | < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( in_cmp_x2cs_bin ); + + // compressed input 2cs packed + INSDC:2cs:packed in_cmp_2cs_packed = CMP_CSREAD; + + // compressed input x2cs alt-read ( ambiguities ) + INSDC:x2cs:bin in_cmp_alt_x2cs_bin + = < INSDC:x2cs:bin, INSDC:x2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 0, 0, 0, 4 ] > ( in_cmp_x2cs_bin ); + + // preparing a feed into stats column + U8 in_cmp_stats_bin = in_cmp_2cs_bin; + + + /* physical columns + */ + + physical column INSDC:2cs:packed .CMP_CSREAD + = in_cmp_2cs_packed + | ( INSDC:2cs:packed ) pack ( in_cmp_2cs_bin ); + + physical column < INSDC:x2cs:bin > zip_encoding .CMP_ALTCSREAD + = < INSDC:x2cs:bin > trim < 0, 0 > ( in_cmp_alt_x2cs_bin ); + + + /* output processing rules + */ + + // compressed output 2cs packed + INSDC:2cs:packed out_cmp_2cs_packed = .CMP_CSREAD; + + // unambiguous unpacked 2cs + INSDC:2cs:bin out_cmp_2cs_bin + = ( INSDC:2cs:bin ) unpack ( out_cmp_2cs_packed ); + + // unpacked 2cs with ambiguity + INSDC:x2cs:bin out_cmp_x2cs_bin + = ( INSDC:x2cs:bin ) < U8 > bit_or < ALIGN_RIGHT > ( out_cmp_2cs_bin, .CMP_ALTCSREAD ) + | ( INSDC:x2cs:bin ) out_cmp_2cs_bin; + + // output text + INSDC:color:text out_cmp_color_text + = < INSDC:x2cs:bin, INSDC:color:text > map < INSDC:x2cs:map:BINSET, INSDC:x2cs:map:CHARSET > ( out_cmp_x2cs_bin ); + + + /* decompressed sequences + * sources are out_dcmp_x2cs_bin - virtual production + */ + + // synthesize 2cs_bin and 2cs_packed + INSDC:2cs:bin out_dcmp_2cs_bin + = < INSDC:x2cs:bin, INSDC:2cs:bin > map < [ 0,1,2,3,4 ], [ 0,1,2,3,0 ] > ( out_dcmp_x2cs_bin ); + INSDC:2cs:packed out_dcmp_2cs_packed + = ( INSDC:2cs:packed ) pack ( out_dcmp_2cs_bin ); + + + /* INSDC:tbl:sequence inherited productions + * cs_native + * out_cs_key + * out_signal + * out_2cs_bin + * out_2na_bin + * out_4na_bin + * out_dna_text + * out_x2cs_bin + * out_x2na_bin + * out_2cs_packed + * out_2na_packed + * out_4na_packed + * out_color_text + * out_qual_phred + * out_color_matrix + * out_qual_text_phred_33 + * out_qual_text_phred_64 + */ + + /* NCBI:tbl:dcmp_color_space inherited productions + * out_dcmp_x2cs_bin + */ +}