Mercurial > repos > charles_s_test > seqsero2
diff libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/sra.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/sra.vschema Mon Nov 27 11:21:07 2017 -0500 @@ -0,0 +1,758 @@ +/*=========================================================================== +* +* 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 'ncbi/seq.vschema'; +include 'ncbi/spotname.vschema'; +include 'insdc/sra.vschema'; +include 'ncbi/stats.vschema'; + + +/*-------------------------------------------------------------------------- + * types + */ + + +/* Segment - DEPRECATED + * a ( start, len ) pair where start is a zero-based, unsigned coordinate + */ +typedef U16 NCBI:SRA:Segment [ 2 ]; + + +/* SpotDesc - DEPRECATED + * uint16_t spot_len; + * uint16_t fixed_len; + * uint16_t signal_len; + * uint16_t clip_qual_right; + * uint8_t num_reads; + * uint8_t align [ 7 ]; + */ +typedef B8 NCBI:SRA:SpotDesc [ 16 ]; + + +/* ReadDesc - DEPRECATED + * SRASegment { uint16_t start, len; } seg; + * uint8_t type; + * char cs_key; + * char label [ 74 ]; + */ +typedef B8 NCBI:SRA:ReadDesc [ 80 ]; + + +// some types have been moved to INSDC +alias INSDC:SRA:platform_id NCBI:SRA:platform_id; +alias INSDC:SRA:read_type NCBI:SRA:read_type; +alias INSDC:SRA:read_filter NCBI:SRA:read_filter; + +typedef NCBI:fsamp4 NCBI:SRA:rotated_fsamp4, NCBI:SRA:swapped_fsamp4; + +// 16-bit POSITION type +typedef U16 NCBI:SRA:pos16; + + +/*-------------------------------------------------------------------------- + * functions + */ + +/* bio_start + * searches through read_type vector + * returns the 0-based starting coordinate of first biological read + * + * "read_start" [ DATA ] - vector of read start coordinates + * + * "read_type" [ DATA ] - vector of read types + */ +extern function INSDC:coord:zero + NCBI:SRA:bio_start #1 ( INSDC:coord:zero read_start, INSDC:SRA:xread_type read_type ); + + +/* bio_end + * searcehes through read_type vector + * returns the 0 based ending coording (either inclusive or exclusive) of last + * biological read + * + * "read_start" [ DATA ] - vector of read start coordinates + * + * "read_type" [ DATA ] - vector of read types + * + * "read_len" [ DATA ] - vector of read lengths + */ +extern function INSDC:coord:zero + NCBI:SRA:bio_end #1 < bool inclusive > ( INSDC:coord:zero read_start, INSDC:SRA:xread_type read_type, INSDC:coord:len read_len ); + + +/* fix_read_seg + */ +extern function INSDC:coord:len [ 2 ] + NCBI:SRA:fix_read_seg #1 ( U16 [ 2 ] rd_seg, INSDC:coord:len spot_len ); + + +/* make_spot_desc + * assembles several bits of information together into a "C" structure + * + * "spot_len" [ DATA ] - computed spot length value + * + * "fixed_len" [ DATA, DFLT ZERO ] - the stated fixed length of all spots + * or zero if not fixed length + * + * "sig_len" [ DATA, DFLT ZERO ] - the length of signal/intensity data + * or zero if not present + * + * "trim_start" [ DATA ] - the first base included in the trim segment + * + * "trim_len" [ DATA ] - the length of the trim segment + * + * "num_reads" [ DATA ] - 1..n value + */ +extern function NCBI:SRA:SpotDesc NCBI:SRA:make_spot_desc #1 ( INSDC:coord:len spot_len, + INSDC:coord:len fixed_len, INSDC:coord:len sig_len, INSDC:coord:zero trim_start, + INSDC:coord:len trim_len, U8 num_reads ); + + +/* make_read_desc + * assembles several bits of information together into a "C" structure + * in theory resultant segments may intersect other read segments or leave holes in spot. + * + * "num_reads" [ DATA ] - value indicating the resulting row-length of output + * + * "read_start" [ DATA ] - ordered starting coordinates for each read + * not required to be sequential. + * + * "read_len" [ DATA ] - ordered lengths of each read. may be zero when + * read has been described but is not identified in spot. + * + * "read_type" [ DATA ] - ordered type id describing each read + * + * "read_filt" [ DATA ] - ordered read filters + * + * "cs_key" [ DATA ] - ordered color-space keys + * + * "label_start" [ DATA ] - ordered starting coordinates for each label + * "label_len" [ DATA ] - ordered lengths of each label + * + * "label" [ DATA ] - complete sequence of label characters, possibly empty + * individual read labels are identified as {start,len} pairs + */ +extern function NCBI:SRA:ReadDesc NCBI:SRA:make_read_desc #1 ( U8 num_reads, + INSDC:coord:zero read_start, INSDC:coord:len read_len, INSDC:SRA:xread_type read_type, + INSDC:SRA:read_filter read_filt, INSDC:dna:text cs_key, + INSDC:coord:zero label_start, INSDC:coord:len label_len, ascii label ); + + +/* rotate + * rotate a quadruple by called base + * now normally replaced by swap + * + * "T" [ TYPE ] - element type of quadruple to be rotated + * + * "encoding" [ CONST ] - when true, rotate input left until corresponding + * element is in slot 0. when false, rotate input right to restore original + * order. + * + * "in" [ DATA ] - data to be rotated, qualities, signal, intensities... + * + * "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors + */ +extern function < type T > +T NCBI:SRA:rotate #1 < bool encoding > ( T in, U8 called ); + + +/* swap + * swap element 0 and the called element + * used to ensure that the called element is in slot 0 + * + * "T" [ TYPE ] - element type of quadruple to be swapped + * + * "in" [ DATA ] - data to be swapped, qualities, signal, intensities... + * + * "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors + */ +extern function < type T > +T NCBI:SRA:swap #1 ( T in, U8 called ); + + +/* normalize + * denormalize + * + * "T" [ TYPE ] - element type of quadruple to be [de]normalized + * + * "intensity" [ DATA ] - intensity data + * + * "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors + */ +extern function < type T > +T NCBI:SRA:normalize #1 ( T intensity, U8 called ); + +extern function < type T > +T NCBI:SRA:denormalize #1 ( T intensity, U8 called ); + + +/* make_position + * return a synthesized position row with 1-1 correspondence + * + * "T" [ TYPE ] - position type being generated + * + * "start" [ CONST ] - either 0 or 1, depending upon the coordinate system + * + * "bases" [ DATA ] - the actual row of bases. the output row + * will be the same length, but with synthesized data + */ +extern function < type T > +T NCBI:SRA:make_position #1 < T start > ( any bases ); + +/* fsamp4 compression + * performs compression individually + * on called channel and alternate channels + */ +function NCBI:SRA:swapped_fsamp4 NCBI:SRA:fsamp4:decode #2 ( merged_fmt in ) +{ + fzip_fmt cmp0 = split < 0 > ( in ); + fzip_fmt cmp123 = split < 1 > ( in ); + F32 ch0 = funzip ( cmp0 ); + F32 ch123a = funzip ( cmp123 ); + F32[3] ch123 = redimension ( ch123a ); + return ( NCBI:SRA:swapped_fsamp4 ) < F32 > paste ( ch0, ch123 ); +} + +function merged_fmt NCBI:SRA:fsamp4:encode #2 < U32 called, U32 alt > ( NCBI:SRA:swapped_fsamp4 in ) +{ + F32 ch0 = < F32 > cut < 0 > ( in ); + F32[3] ch123 = < F32 > cut < 1, 2, 3 > ( in ); + fzip_fmt cmp0 = fzip < called > ( ch0 ); + F32 ch123a = redimension ( ch123 ); + fzip_fmt cmp123 = fzip < alt > ( ch123a ); + return merge ( cmp0, cmp123 ); +} + + +/*-------------------------------------------------------------------------- + * spotdesc + * NCBI implementation productions + */ + +/* history: + * 1.0.1 - base explicitly upon sequence #1.0.1, spotdesc #1.0.1 + * 1.0.2 - spotdesc #1.0.2 + */ +table NCBI:SRA:tbl:spotdesc_nocol #1.0.2 = INSDC:tbl:sequence #1.0.1, INSDC:SRA:tbl:spotdesc #1.0.2 +{ + /* LABEL_SEG + */ + readonly column NCBI:SRA:Segment LABEL_SEG + = out_label_seg + | cast ( out_label_seg32 ) + | cast ( _out_label_seg32 ); + U32 _out_label_startU32 = ( U32 ) out_label_start; + U32 [ 2 ] _out_label_seg32 = < U32 > paste ( _out_label_startU32, out_label_len ); + + + /* READ_SEG + */ + readonly column NCBI:SRA:Segment READ_SEG + = out_read_seg + | cast ( out_read_seg32 ) + | cast ( _out_read_seg32 ); + U32 _out_read_startU32 = ( U32 ) out_read_start; + U32 [ 2 ] _out_read_seg32 = < U32 > paste ( _out_read_startU32, out_read_len ); + + + /* READ_DESC + */ + readonly column NCBI:SRA:ReadDesc READ_DESC + = NCBI:SRA:make_read_desc ( out_nreads, out_read_start, out_read_len, + out_read_type, _out_rd_filter, out_cs_key, _out_label_start, _out_label_len, _out_label ); + INSDC:SRA:read_filter _out_rd_filter + = out_rd_filter + | < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ( out_read_start ); + ascii _out_label + = out_label + | < ascii > echo < '' > (); + INSDC:coord:zero _out_label_start + = out_label_start + | < INSDC:coord:zero > echo < 0 > ( out_read_start ); + INSDC:coord:len _out_label_len + = out_label_len + | < INSDC:coord:len > echo < 0 > ( out_read_start ); + + /* SPOT_DESC + */ + readonly column NCBI:SRA:SpotDesc SPOT_DESC + = NCBI:SRA:make_spot_desc ( spot_len, fixed_spot_len, signal_len, + trim_start, trim_len, out_nreads ); + + /* SIGNAL_LEN + * normally the same as spot length when present, + * but in some cases ( e.g. 454 ) it may be different + */ + readonly column INSDC:coord:len SIGNAL_LEN + = signal_len; + readonly column U16 SIGNAL_LEN + = cast ( signal_len ); + + + /* INSDC:SRA:tbl:spotdesc inherited productions + * trim_len + * out_label + * out_nreads + * trim_start + * out_read_len + * out_label_len + * out_rd_filter + * out_read_type + * out_read_start + * out_label_start + * static_fixed_spot_len + */ + + /* NCBI:SRA:tbl:spotdesc_nocol productions + * out_read_seg + * out_label_seg + * out_read_seg32 + * out_label_seg32 + */ +}; + +/* history: + * 1.0.1 - base explicitly upon spotdesc_nocol #1.0.1 + * 1.0.2 - base explicitly upon spotdesc_nocol #1.0.2 + */ +table NCBI:SRA:tbl:spotdesc_nophys #1.0.2 = NCBI:SRA:tbl:spotdesc_nocol #1.0.2 +{ + // resolve virtual productions + U8 out_nreads = .NREADS; + ascii out_label = .LABEL; + INSDC:SRA:xread_type out_read_type = .READ_TYPE; + INSDC:SRA:read_filter out_rd_filter = .RD_FILTER; + + INSDC:coord:zero out_label_start + = .LABEL_START + | ( INSDC:coord:zero ) < U32 > cut < 0 > ( out_label_seg32 ); + INSDC:coord:len out_label_len + = .LABEL_LEN + | ( INSDC:coord:len ) < U32 > cut < 1 > ( out_label_seg32 ); + U32 [ 2 ] out_label_seg32 + = cast ( .LABEL_SEG ); + + INSDC:coord:zero out_read_start + = .READ_START + | ( INSDC:coord:zero ) < U32 > cut < 0 > ( out_read_seg32 ); + INSDC:coord:len out_read_len + = .READ_LEN + | ( INSDC:coord:len ) < U32 > cut < 1 > ( out_read_seg32 ); + U32 [ 2 ] out_read_seg32 + = NCBI:SRA:fix_read_seg ( .READ_SEG, spot_len ); + + + /* INSDC:SRA:tbl:spotdesc inherited productions + * trim_len + * trim_start + * out_read_type + * static_fixed_spot_len + */ + + /* NCBI:SRA:tbl:spotdesc_nocol inherited productions + * out_read_seg + * out_label_seg + */ + + /* NCBI:SRA:tbl:spotdesc_nophys productions + * .LABEL + * .NREADS + * .READ_LEN + * .READ_SEG + * .LABEL_LEN + * .LABEL_SEG + * .RD_FILTER + * .READ_TYPE + * .READ_START + * .LABEL_START + */ +} + +/* history: + * 1.0.1 - base explicitly upon spotdesc_nophys #1.0.1 + * 1.0.2 - base explicitly upon spotdesc_nophys #1.0.2 + */ +table NCBI:SRA:tbl:spotdesc #1.0.2 = NCBI:SRA:tbl:spotdesc_nophys #1.0.2 +{ + // physical column encodings + // TBD - this has to be looked at, where dynamic segmentation is involved + physical column < U8 > zip_encoding .NREADS = NREADS; + physical column < ascii > zip_encoding .LABEL = LABEL; + physical column < INSDC:coord:zero > izip_encoding .LABEL_START = LABEL_START; + physical column < INSDC:coord:len > izip_encoding .LABEL_LEN = LABEL_LEN; + physical column < INSDC:coord:zero > izip_encoding .READ_START = READ_START; + physical column < INSDC:coord:len > izip_encoding .READ_LEN = in_read_len; + physical column < INSDC:SRA:xread_type > zip_encoding .READ_TYPE = in_read_type; + physical column < INSDC:SRA:read_filter > zip_encoding .RD_FILTER = READ_FILTER; + + + /* INSDC:SRA:tbl:spotdesc inherited productions + * trim_len + * trim_start + * out_read_type + * static_fixed_spot_len + */ + + /* NCBI:SRA:tbl:spotdesc_nocol inherited productions + * out_read_seg + * out_label_seg + */ +}; + + +/*-------------------------------------------------------------------------- + * pos + * synthetic POSITION column on read + * + * history: + * 1.0.1 - base explicitly upon sequence #1.0.1 + */ + +table NCBI:SRA:tbl:pos #1.0.1 = INSDC:tbl:sequence #1.0.1 +{ + INSDC:position:one out_position + = < INSDC:position:one > NCBI:SRA:make_position < 1 > ( out_2na_packed ) + | < INSDC:position:one > NCBI:SRA:make_position < 1 > ( out_2cs_packed ); + NCBI:SRA:pos16 out_position16 + = < NCBI:SRA:pos16 > NCBI:SRA:make_position < 1 > ( out_2na_packed ) + | < NCBI:SRA:pos16 > NCBI:SRA:make_position < 1 > ( out_2cs_packed ); +}; + + +/*-------------------------------------------------------------------------- + * sra + * the NCBI SRA table + */ + +/* history: + * 1.0.1 - base explicitly upon sra #1.0.1 + * 1.0.2 - base explicitly upon sra #1.0.2, spotdesc_nocol #1.0.1 + * 1.0.3 - base explicitly upon sra #1.0.3, spotdesc_nocol #1.0.2 + */ +table NCBI:SRA:tbl:sra_nopos #1.0.3 = INSDC:SRA:tbl:sra #1.0.3, NCBI:SRA:tbl:spotdesc_nocol #1.0.2 +{ + // v1 declares the POSITION column for all tables + // but leaves all physical columns unstated + + /* POSITION + * 1-based coordinates + * describes a base's position on signal + */ + column INSDC:position:one POSITION = out_position; + readonly column NCBI:SRA:pos16 POSITION = out_position16; + + // zero-based coordinates available upon request + readonly column INSDC:position:zero POSITION + = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position ); + + // statistics + U64 base_count + = < U64 > meta:value < "BASE_COUNT" > (); + U64 spot_count + = < U64 > meta:value < ".seq/spot" > () + | < U64 > meta:value < ".seq" > () ; + + + /* INSDC:tbl:sequence inherited 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 + */ + + /* INSDC:SRA:tbl:spotname inherited productions + * out_x_coord + * out_y_coord + * out_name_fmt + * out_spot_name + * spot_ids_found + */ + + /* INSDC:SRA:tbl:spotdesc inherited productions + * trim_len + * out_label + * out_nreads + * trim_start + * out_read_len + * out_label_len + * out_rd_filter + * out_read_type + * out_read_start + * out_label_start + * static_fixed_spot_len + */ + + /* INSDC:SRA:tbl:stats inherited productions + * max_spot_id + * min_spot_id + * in_stats_bin + * bio_base_count + */ + + /* INSDC:SRA:tbl:sra inherited productions + * out_platform + * platform_name + */ + + /* NCBI:SRA:tbl:spotdesc_nocol inherited productions + * out_read_seg + * out_label_seg + * out_read_seg32 + * out_label_seg32 + */ + + /* NCBI:SRA:tbl:sra_nopos productions + * out_position + * out_position16 + */ +}; + +/* history: + * 1.0.1 - base explicitly upon sra #1.0.1 + * 1.0.2 - base explicitly upon sra_nopos #1.0.2, pos #1.0.1 + * 1.0.3 - base explicitly upon sra_nopos #1.0.3 + */ +table NCBI:SRA:tbl:sra #1.0.3 = NCBI:SRA:tbl:sra_nopos #1.0.3, NCBI:SRA:tbl:pos #1.0.1 +{ + // the POSITION column is synthesized for all contemporary platforms but 454 + + /* INSDC:tbl:sequence inherited 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 + */ + + /* INSDC:SRA:tbl:spotname inherited productions + * out_x_coord + * out_y_coord + * out_name_fmt + * out_spot_name + * spot_ids_found + */ + + /* INSDC:SRA:tbl:spotdesc inherited productions + * trim_len + * out_label + * out_nreads + * trim_start + * out_read_len + * out_label_len + * out_rd_filter + * out_read_type + * out_read_start + * out_label_start + * static_fixed_spot_len + */ + + /* INSDC:SRA:tbl:stats inherited productions + * max_spot_id + * min_spot_id + * in_stats_bin + * bio_base_count + */ + + /* INSDC:SRA:tbl:sra inherited productions + * out_platform + * platform_name + */ + + /* NCBI:SRA:tbl:spotdesc_nocol inherited productions + * out_read_seg + * out_label_seg + * out_read_seg32 + * out_label_seg32 + */ +}; + + +/* v2 consolidates many of the auxiliary columns into a single treatment + * left out are reads, qualities and platform-specific columns + * + * history: + * 2.1.2 - base upon sra #1.0.3, spotdesc #1.0.2, stats #1.1.2 + */ +table NCBI:SRA:tbl:sra_nopos #2.1.3 = INSDC:SRA:tbl:sra #1.0.3, + NCBI:SRA:tbl:skeyname #3.0.1, NCBI:SRA:tbl:spotdesc #1.0.2, NCBI:SRA:tbl:stats #1.2.0 +{ + // this is already specified in INSDC:SRA:tbl:sra #1 + // but putting it here will quiet down outputs + INSDC:SRA:platform_id out_platform = .PLATFORM; + + column INSDC:position:one POSITION + = out_position; + readonly column NCBI:SRA:pos16 POSITION + = cast ( _clip_position ); + INSDC:position:one _clip_position + = < INSDC:position:one > clip < 0, 0xFFFF > ( out_position ); + readonly column INSDC:position:zero POSITION + = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position ); + + + /* INSDC:tbl:sequence inherited 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 + */ + + /* INSDC:SRA:tbl:spotdesc inherited productions + * trim_len + * trim_start + * out_read_type + * static_fixed_spot_len + */ + + /* INSDC:SRA:tbl:stats inherited productions + * in_stats_bin + */ + + /* INSDC:SRA:tbl:sra inherited productions + * out_platform + * platform_name + */ + + /* NCBI:SRA:tbl:skeyname inherited productions + * in_spot_name_tok + */ + + /* NCBI:SRA:tbl:spotdesc_nocol inherited productions + * out_read_seg + * out_label_seg + */ + + /* NCBI:SRA:tbl:sra_nopos productions + * out_position + */ +}; + +/* most platforms don't have a native POSITION + * mix in "pos" table to synthesize it + * + * history: + * 2.1.2 - base upon sra#1.0.3, spotdesc #1.0.2, stats #1.1.2 + */ +table NCBI:SRA:tbl:sra #2.1.3 = INSDC:SRA:tbl:sra #1.0.3, + NCBI:SRA:tbl:skeyname #3.0.1, NCBI:SRA:tbl:spotdesc #1.0.2, + NCBI:SRA:tbl:stats #1.2.0, NCBI:SRA:tbl:pos #1.0.1 +{ + readonly column INSDC:position:one POSITION + = out_position; + readonly column NCBI:SRA:pos16 POSITION + = out_position16; + readonly column INSDC:position:zero POSITION + = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position ); + + + /* INSDC:tbl:sequence inherited 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 + */ + + /* INSDC:SRA:tbl:spotdesc inherited productions + * trim_len + * trim_start + * out_read_type + * static_fixed_spot_len + */ + + /* INSDC:SRA:tbl:stats inherited productions + * in_stats_bin + */ + + /* INSDC:SRA:tbl:sra inherited productions + * out_platform + * platform_name + */ + + /* NCBI:SRA:tbl:skeyname inherited productions + * in_spot_name_tok + */ +};