Mercurial > repos > charles_s_test > seqsero2
diff libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/spotname.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/ncbi/spotname.vschema Mon Nov 27 11:21:07 2017 -0500 @@ -0,0 +1,377 @@ +/*=========================================================================== +* +* 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. +* +* =========================================================================== +* +*/ + +/*========================================================================== + * NCBI Sequence Read Archive schema + */ +version 1; + +include 'vdb/vdb.vschema'; +include 'insdc/sra.vschema'; + + +/*-------------------------------------------------------------------------- + * types + */ + +/* spot_name_token + * a vector describing tokens recognized within a spot name + * + * COMPONENTS: + * 0 - token id + * 1 - token starting coordinate + * 2 - token length + */ +alias text:token NCBI:SRA:spot_name_token; + + +/* token values + * + * tokens are produced by a schema-specific tokenizer function + * this function is purposely abstract because it may rely upon + * whatever information it needs to perform its task. the only + * requirement is that it produce these tokens as its output. + * + * an empty name input must produce no tokens. in this case, + * there is no name to tokenize or data to produce. + * + * a non-empty name must produce 1 or more tokens of output. + * all tokens must be ordered by starting character position. + * + * if a name does not conform to any pattern recognized by the + * tokenizer, then the tokenizer emits a single token of "unrecognized" + * + * if a name conforms to some pattern but does not have any + * substitution tokens, the tokenizer emits a single token of "recognized" + * + * if a name may be tokenized, then the resulting tokens should + * describe only the portions of the string that should be removed + * from the name, e.g. "X" or "Y". + * + * the standard coordinates "X".."L" are given in unsigned decimal. + * alternate representations are contained within their respective + * namespaces: "signed", "hex" and "octal". + * + * the special coordinate "Q" represents the 454-specific encoding + * of X and Y into base-36, where the formula for Q is: + * Q = 4096 * X + Y + * and ASCII encoding: + * 0..25 => "A-Z", 26..35 => "0-9" + */ +const U16 NCBI:SRA:name_token:unrecognized = 1; +const U16 NCBI:SRA:name_token:recognized = 2; +const U16 NCBI:SRA:name_token:Q = 3; +const U16 NCBI:SRA:name_token:X = 4; +const U16 NCBI:SRA:name_token:Y = 5; +const U16 NCBI:SRA:name_token:T = 6; +const U16 NCBI:SRA:name_token:L = 7; +const U16 NCBI:SRA:name_token:signed:X = 8; +const U16 NCBI:SRA:name_token:signed:Y = 9; +const U16 NCBI:SRA:name_token:signed:T = 10; +const U16 NCBI:SRA:name_token:signed:L = 11; +const U16 NCBI:SRA:name_token:octal:X = 12; +const U16 NCBI:SRA:name_token:octal:Y = 13; +const U16 NCBI:SRA:name_token:octal:T = 14; +const U16 NCBI:SRA:name_token:octal:L = 15; +const U16 NCBI:SRA:name_token:hex:upper:X = 16; +const U16 NCBI:SRA:name_token:hex:upper:Y = 17; +const U16 NCBI:SRA:name_token:hex:upper:T = 18; +const U16 NCBI:SRA:name_token:hex:upper:L = 19; +const U16 NCBI:SRA:name_token:hex:lower:X = 20; +const U16 NCBI:SRA:name_token:hex:lower:Y = 21; +const U16 NCBI:SRA:name_token:hex:lower:T = 22; +const U16 NCBI:SRA:name_token:hex:lower:L = 23; + + +/* token symbols + * when a name matches some pattern and tokens are recognized, + * the tokens are extracted from the name and sent to individual + * columns, and replaced with the symbols below to create a + * formatted name. + */ +const ascii NCBI:SRA:name_symbol:Q = '$Q'; +const ascii NCBI:SRA:name_symbol:X = '$X'; +const ascii NCBI:SRA:name_symbol:Y = '$Y'; +const ascii NCBI:SRA:name_symbol:T = '$T'; +const ascii NCBI:SRA:name_symbol:L = '$L'; +const ascii NCBI:SRA:name_symbol:octal:X = '$a'; +const ascii NCBI:SRA:name_symbol:octal:Y = '$b'; +const ascii NCBI:SRA:name_symbol:octal:T = '$c'; +const ascii NCBI:SRA:name_symbol:octal:L = '$d'; +const ascii NCBI:SRA:name_symbol:hex:upper:X = '$e'; +const ascii NCBI:SRA:name_symbol:hex:upper:Y = '$f'; +const ascii NCBI:SRA:name_symbol:hex:upper:T = '$g'; +const ascii NCBI:SRA:name_symbol:hex:upper:L = '$h'; +const ascii NCBI:SRA:name_symbol:hex:lower:X = '$x'; +const ascii NCBI:SRA:name_symbol:hex:lower:Y = '$y'; +const ascii NCBI:SRA:name_symbol:hex:lower:T = '$t'; +const ascii NCBI:SRA:name_symbol:hex:lower:L = '$l'; + + +/*-------------------------------------------------------------------------- + * functions + */ + +/* extract_spot_name + * generates input to .SPOT_NAME column + * + * on NCBI:SRA:name_token:unrecognized, produces the entire spot name row + * otherwise, produces an empty row + * + * "name" [ DATA ] - raw spot names from NAME column + * + * "tok" [ DATA ] - delimiting tokens produced by sub-table + */ +function ascii + NCBI:SRA:extract_spot_name #1 ( ascii name, NCBI:SRA:spot_name_token tok ); + + +/* extract_name_fmt + * generates input to .NAME_FMT column and/or updates skey index + * + * on NCBI:SRA:name_token:unrecognized, produces an empty row + * otherwise, it creates a temporary "name_fmt" string from name row + * + * an attempt is made to insert name_fmt into indicated text index + * ( normally 'skey' ). if the insert succeeds, i.e. associates "name_fmt" + * with a row_id, then the output for the row is empty. + * + * if the insert fails due to key duplication, an attempt is made to + * extend the id range of associated rows. depending upon the type of index, + * this may succeed or fail, e.g. if the existing row range for "name_fmt" is + * n..m where m = row_id - 1, the range can be extended to n..row_id and + * the update succeeds. if the index supports discontiguous id ranges, the + * update will also succeed. upon any success updating the index, the output + * row will be empty. + * + * finally, if the temporary "name_fmt" cannot be inserted into the index + * nor the existing id range updated, the output for the row will be "name_fmt". + * + * "name" [ DATA ] - raw spot names from NAME column + * + * "tok" [ DATA ] - delimiting tokens produced by sub-table + */ +function ascii + NCBI:SRA:extract_name_fmt #1 < ascii idx > ( ascii name, NCBI:SRA:spot_name_token tok ); + + +/* extract_name_coord + * generates inputs to .X and .Y and possibly other columns + * + * if no tokens match "coord"constant, produces an empty row + * otherwise, produces binary coordinate value + * if multiple tokens match criteria, all values must be equivalent + * because only a single value will be output per row + * + * "coord" [ CONST ] - either NCBI:SRA:name_token:X or NCBI:SRA:name_token:Y + * both of these values also match the token NCBI:SRA:name_token:Q and extract + * contents appropriately. + * + * "name" [ DATA ] - raw spot names from NAME column + * + * "tok" [ DATA ] - delimiting tokens produced by sub-table + */ +function INSDC:coord:val + NCBI:SRA:extract_name_coord #1 < U16 coord > ( ascii name, NCBI:SRA:spot_name_token tok ); + + +/* lookup + */ +function INSDC:SRA:spot_ids_found NCBI:SRA:lookup #1.0 + < ascii index_name, ascii query_by_name, U8 name_fmt_version > ( * ascii name_prefix ); + + +/*-------------------------------------------------------------------------- + * spotcoord + * spot coordinate table implementation + */ +table NCBI:SRA:tbl:spotcoord #1 = INSDC:SRA:tbl:spotcoord #1 +{ + // X and Y stored as I32 + INSDC:coord:val out_x_coord = .X; + INSDC:coord:val out_y_coord = .Y; + + // T and L are usually present but optional + INSDC:coord:val out_t_coord = .T; + INSDC:coord:val out_l_coord = .L; + + // .X, .Y, .T and .L get either empty coordinate or proper coordinate + physical column < INSDC:coord:val > izip_encoding .X + = in_x_coord + | in_name_x_coord; + physical column < INSDC:coord:val > izip_encoding .Y + = in_y_coord + | in_name_y_coord; + physical column < INSDC:coord:val > izip_encoding .T + = in_t_coord + | in_name_t_coord; + physical column < INSDC:coord:val > izip_encoding .L + = in_l_coord + | in_name_l_coord; +}; + + +/*-------------------------------------------------------------------------- + * skeyname + * spot name table implementation built upon prefix-tree skey index + * + * v1 - maintains a 1->1 key=>spot_id relationship + * with unique constraint on key. it does NOT + * implement name_fmt or x_coord or y_coord. + * + * v2 - maintains a 1->1 key=>spot_id-range relationship + * with unique constraint on key. it does NOT + * implement spot_name. X and Y are stored using + * 16-bit unsigned quantities. + * + * v3 - maintains a flexible naming approach + * retrieves name directly from column if so stored + * synthesizes name from name_fmt, X and Y otherwise + * name_fmt is either retrieved directly from column + * or from skey index. X and Y are stored as 32-bit + * signed quantities. + * + * history: + * 1.0.1 - explicitly account for spotname #1.0.1 ancestry + * 2.0.1 - " " + * 3.0.1 - moved .X and .Y to spotcoord table + */ +table NCBI:SRA:tbl:skeyname #1.0.1 = INSDC:SRA:tbl:spotname #1.0.1 +{ + // read the skey entry + ascii out_skey = ( ascii ) idx:text:project #1.0 < 'skey' > (); + + // spot_name + ascii out_spot_name + = rewritten_spot_name + | out_skey; + + // search skey entry + INSDC:SRA:spot_ids_found spot_ids_found + = ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 1 > ( out_slx_prefix ) + | ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 0 > (); + + + /* INSDC:SRA:tbl:spotname inherited productions + * out_x_coord + * out_y_coord + * out_name_fmt + */ + + /* NCBI:SRA:tbl:skeyname productions + * out_slx_prefix + * rewritten_spot_name + */ +}; + +table NCBI:SRA:tbl:skeyname_nocol #2.0.1 = INSDC:SRA:tbl:spotname #1.0.1 +{ + // name_fmt + // perform reverse lookup through index to get key + ascii out_name_fmt = ( ascii ) idx:text:project #1.0 < 'skey' > (); + + // search skey entry + INSDC:SRA:spot_ids_found spot_ids_found + = ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 2 > ( out_slx_prefix ) + | ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 2 > (); + + // X and Y stored as U16 + INSDC:coord:val out_x_coord = cast ( .X ); + INSDC:coord:val out_y_coord = cast ( .Y ); + + + /* NCBI:SRA:tbl:skeyname_nocol virtual productions + * out_slx_prefix + */ +}; + +table NCBI:SRA:tbl:skeyname #2.0.1 = NCBI:SRA:tbl:skeyname_nocol #2.0.1 +{ + // spot_name_tok comes from a platform-specific tokenizer + // and must be of type 'NCBI:SRA:spot_name_token' + physical column < INSDC:coord:val > izip_encoding #1 .X + = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:X > ( NAME, in_spot_name_tok ); + physical column < INSDC:coord:val > izip_encoding .Y + = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:Y > ( NAME, in_spot_name_tok ); + + /* NCBI:SRA:tbl:skeyname_nocol inherited virtual productions + * out_slx_prefix + */ + + /* NCBI:SRA:tbl:skeyname virtual productions + * in_spot_name_tok + */ +}; + +table NCBI:SRA:tbl:skeyname #3.0.1 = INSDC:SRA:tbl:spotname #1.0.1, NCBI:SRA:tbl:spotcoord #1 +{ + // spot_name + // retrieve from hard column + ascii out_spot_name = .SPOT_NAME; + + // name_fmt + // retrieve from hard column or reverse lookup through index + ascii out_name_fmt = ( ascii ) idx:text:project #1.0 < 'skey' > ( .NAME_FMT ); + + INSDC:SRA:spot_ids_found spot_ids_found + = ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 2 > (); + + + /* encoding rules + * the sub-table will provide a platform-specific parser that + * produces as its output a series of NCBI:SRA:spot_name_token + * for each input row in the virtual production "spot_name_tok" + * + * the tokenizer will look for X, Y or Q (combined) coordinates + * within the spot name and issue tokens when found, or in the + * case that none are found, an "unrecognized" token is issued. + * + * the tokens are then processed here by common rules + */ + + // .SPOT_NAME gets either empty strings or unrecognized strings + physical column < ascii > zip_encoding .SPOT_NAME + = NCBI:SRA:extract_spot_name ( NAME, in_spot_name_tok ); + + // .NAME_FMT gets either empty strings or unindexed but recognized strings + physical column < ascii > zip_encoding .NAME_FMT + = NCBI:SRA:extract_name_fmt < 'skey' > ( NAME, in_spot_name_tok ); + + // .X, .Y, .T and .L get either empty coordinate or proper coordinate + INSDC:coord:val in_name_x_coord + = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:X > ( NAME, in_spot_name_tok ); + INSDC:coord:val in_name_y_coord + = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:Y > ( NAME, in_spot_name_tok ); + INSDC:coord:val in_name_t_coord + = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( NAME, in_spot_name_tok ); + INSDC:coord:val in_name_l_coord + = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:L > ( NAME, in_spot_name_tok ); + + + /* NCBI:SRA:tbl:skeyname virtual productions + * in_spot_name_tok + */ +};