/usr/lib/ncbi/schema/454.vschema is in sra-toolkit 2.1.7a-1ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* 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 454 Sequence Read Archive schema
*/
version 1;
include 'ncbi/sra.vschema';
include 'ncbi/spotname.vschema';
include 'ncbi/clip.vschema';
/*--------------------------------------------------------------------------
* functions
*/
/* dynamic_read_desc
* uses inputs to determine read type and segmentation
*
* "edit_distance" [ CONST, OPTIONAL ] - a tolerance figure for
* linker matching, where 0 requires exact match, 5 is default.
*
* "spot" [ DATA ] - bases for entire spot
*
* "key" [ DATA, CONTROL ] - bases for key sequence. for version 1,
* the first base following key is taken as biological start
*
* "linker" [ DATA, CONTROL, OPTIONAL ] - if present, is used to separate
* all bases following "key" into mate pair biological reads
*
* returns a trio for each identified read, with read type, start and length
*/
typeset NCBI:SRA:_454_:drdparam_set { ascii, U8, INSDC:2na:packed };
extern function
U32 [ 3 ] NCBI:SRA:_454_:dynamic_read_desc #1 < * U32 edit_distance >
( NCBI:SRA:_454_:drdparam_set spot, NCBI:SRA:_454_:drdparam_set key
* NCBI:SRA:_454_:drdparam_set linker );
const U32 NCBI:SRA:_454_:dyn_read_type = 0;
const U32 NCBI:SRA:_454_:dyn_read_start = 1;
const U32 NCBI:SRA:_454_:dyn_read_len = 2;
/* tokenize_spot_name
* scans name on input
* tokenizes into parts
*/
extern function NCBI:SRA:spot_name_token
NCBI:SRA:_454_:tokenize_spot_name #1 ( ascii name );
/*--------------------------------------------------------------------------
* NCBI:SRA:_454_:common
* Roche 454 SRA Platform
*
* history:
* 1.0.1 - explictly base upon sra #1.0.1
* 1.0.2 - bring in clip processing from external table
* 1.0.3 - base explicitly upon sra #1.0.2, clip #1.0.1
* 1.0.4 - base explicitly upon sra #1.0.3, clip #1.0.2
*/
table NCBI:SRA:_454_:common #1.0.4 = INSDC:SRA:tbl:sra #1.0.3, NCBI:SRA:tbl:clip #1.0.2
{
/* PLATFORM
* platform name is always 454
*/
ascii platform_name
= < ascii > echo < "454" > ();
/* 454 TECHNICAL SEQUENCES
*/
column INSDC:dna:text FLOW_CHARS = out_flow_chars;
INSDC:dna:text in_flow_chars
= < INSDC:dna:text, INSDC:dna:text > map < 'acgtn.', 'ACGTNN' > ( FLOW_CHARS );
column INSDC:dna:text KEY_SEQUENCE = out_key_sequence;
INSDC:dna:text in_key_sequence
= < INSDC:dna:text, INSDC:dna:text > map < 'acgtn.', 'ACGTNN' > ( KEY_SEQUENCE );
column INSDC:dna:text LINKER_SEQUENCE = out_linker_sequence;
INSDC:dna:text in_linker_sequence
= < INSDC:dna:text, INSDC:dna:text > map < 'acgtn.', 'ACGTNN' > ( LINKER_SEQUENCE );
// binary technical sequences
INSDC:x2na:bin out_flow_bin
= < INSDC:dna:text, INSDC:x2na:bin > map < INSDC:x2na:map:CHARSET, INSDC:x2na:map:BINSET > ( out_flow_chars );
INSDC:x2na:bin out_key_bin
= < INSDC:dna:text, INSDC:x2na:bin > map < INSDC:x2na:map:CHARSET, INSDC:x2na:map:BINSET > ( out_key_sequence );
INSDC:x2na:bin out_linker_bin
= < INSDC:dna:text, INSDC:x2na:bin > map < INSDC:x2na:map:CHARSET, INSDC:x2na:map:BINSET > ( out_linker_sequence );
/* SIGNAL
* single channel integer
*/
column NCBI:isamp1 SIGNAL = out_signal;
NCBI:isamp1 out_signal = .SIGNAL;
/* INSDC:tbl:sequence inherited productions
* cs_native
* out_cs_key
* in_dna_text
* 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
*/
/* 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
* base_count
* spot_count
* max_spot_id
* min_spot_id
* in_stats_bin
* bio_base_count
*/
/* NCBI:tbl:n_encoding inherited productions
* read_unpack
*/
/* NCBI:SRA:_454_:common productions
* .SIGNAL
* .CLIP_ADAPTER_LEFT
* .CLIP_QUALITY_LEFT
* .CLIP_ADAPTER_RIGHT
* .CLIP_QUALITY_RIGHT
* out_flow_chars
* out_key_sequence
* out_linker_sequence
*/
};
/*--------------------------------------------------------------------------
* NCBI:SRA:_454_:tbl:v2
* Roche 454 SRA Platform
*
* history:
* 1.0.1 - explictly base upon sra #1.0.1 and related changes
* 1.0.2 - respond to change to 454:common base table #1.0.2
*/
// encodings are declared to have their own version
// so that they may be changed over time independently
physical INSDC:coord:one NCBI:SRA:_454_:encoding:CLIP #2
{
decode { return ( INSDC:coord:one ) iunzip ( @ ); }
encode { return izip ( @ ); }
}
physical NCBI:isamp1 NCBI:SRA:_454_:encoding:SIGNAL #2
{
decode { return ( NCBI:isamp1 ) iunzip ( @ ); }
encode { return izip ( @ ); }
}
physical INSDC:position:one NCBI:SRA:_454_:encoding:POSITION #2
{
decode
{
I32 pos_1st_deriv = iunzip ( @ );
return ( INSDC:position:one ) < I32 > integral ( pos_1st_deriv );
}
encode
{
I32 pos_1st_deriv = < I32 > deriv ( @ );
return izip ( pos_1st_deriv );
}
}
/* normalized v2 table
*
* history:
* 1.0.6 - base upon updated ancestry
* 1.0.7 - base upon updated ancestry
*/
table NCBI:SRA:_454_:tbl:v2 #1.0.7
= NCBI:SRA:tbl:sra_nopos #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:phred_quality #2.0.3
, NCBI:SRA:_454_:common #1.0.4
{
/* NAME tokenizing and coordinates
* most work happens in skeyname table
* we still obtain REGION from name
*/
readonly column INSDC:coord:val REGION = ( INSDC:coord:val )
NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( _out_name, out_spot_name_tok );
NCBI:SRA:spot_name_token out_spot_name_tok
= NCBI:SRA:_454_:tokenize_spot_name ( _out_name );
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:_454_:tokenize_spot_name ( NAME );
// special sequences
INSDC:dna:text out_flow_chars
= .FLOW_CHARS
| < INSDC:dna:text > echo < 'TACG' > ( .SIGNAL )
| < INSDC:dna:text > echo < 'TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG' > ();
physical column < INSDC:dna:text > zip_encoding
.FLOW_CHARS = in_flow_chars;
INSDC:dna:text out_key_sequence
= .KEY_SEQUENCE
| < INSDC:dna:text > echo < 'TCAG' > ();
physical column < INSDC:dna:text > zip_encoding
.KEY_SEQUENCE = in_key_sequence;
INSDC:dna:text out_linker_sequence = .LINKER_SEQUENCE;
physical column < INSDC:dna:text > zip_encoding
.LINKER_SEQUENCE = in_linker_sequence;
// linker needs to be representable by its own table
// either in metadata or somewhere else
// position stored as normal 1-based coordinate
INSDC:position:one out_position = .POSITION;
physical column NCBI:SRA:_454_:encoding:POSITION #2
.POSITION = POSITION;
// clips
physical column NCBI:SRA:_454_:encoding:CLIP #2
.CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
physical column NCBI:SRA:_454_:encoding:CLIP #2
.CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
physical column NCBI:SRA:_454_:encoding:CLIP #2
.CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
physical column NCBI:SRA:_454_:encoding:CLIP #2
.CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
// signal
physical column NCBI:SRA:_454_:encoding:SIGNAL #2
.SIGNAL = SIGNAL;
};
|