Mercurial > repos > charles_s_test > seqsero2
diff libs/sratoolkit.2.8.0-centos_linux64/schema/sra/generic-fastq.vschema @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
| author | charles_s_test |
|---|---|
| date | Mon, 27 Nov 2017 11:21:07 -0500 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/libs/sratoolkit.2.8.0-centos_linux64/schema/sra/generic-fastq.vschema Mon Nov 27 11:21:07 2017 -0500 @@ -0,0 +1,265 @@ +/*=========================================================================== + * + * 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 Generic Fastq Sequence Read Archive schema + */ +version 1; + +include 'insdc/sra.vschema'; +include 'ncbi/sra.vschema'; +include 'ncbi/clip.vschema'; +include 'ncbi/spotname.vschema'; + +/* tokenize_spot_name - currently ascii only capability */ + +extern function NCBI:SRA:spot_name_token + NCBI:SRA:GenericFastq:tokenize_spot_name #1 ( ascii name ); + +/*-------------------------------------------------------------------------- + * NCBI:SRA:GenericFastq:sequence + * Generic Fastq SRA Platform + */ +table NCBI:SRA:GenericFastq:sequence #1 + = NCBI:SRA:tbl:sra #2.1.3 + , NCBI:tbl:base_space #2.0.3 + , NCBI:tbl:phred_quality #2.0.4 + , NCBI:SRA:tbl:clip #1.0.2 +{ + ascii platform_name + = < ascii > echo < "UNDEFINED" > (); + + INSDC:SRA:platform_id out_platform + = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > (); + + /* ascii only spot name tokenizer */ + + NCBI:SRA:spot_name_token out_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name ); + + NCBI:SRA:spot_name_token in_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME ); + + /* clips */ + + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT; +} + +database NCBI:SRA:GenericFastq:db #1 +{ + table NCBI:SRA:GenericFastq:sequence #1.0 SEQUENCE; +}; + +/*-------------------------------------------------------------------------- + * NCBI:SRA:GenericFastq:sequence_no_name + * Generic Fastq SRA Platform (without name) + */ +table NCBI:SRA:GenericFastq:sequence_no_name #1 + = NCBI:SRA:tbl:sra #2.1.3 + , NCBI:tbl:base_space #2.0.3 + , NCBI:tbl:phred_quality #2.0.4 + , NCBI:SRA:tbl:clip #1.0.2 +{ + ascii platform_name + = < ascii > echo < "UNDEFINED" > (); + + INSDC:SRA:platform_id out_platform + = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > (); + + /* clips */ + + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT; +} + +database NCBI:SRA:GenericFastqNoNames:db #1 +{ + table NCBI:SRA:GenericFastq:sequence_no_name #1.0 SEQUENCE; +}; + +/*-------------------------------------------------------------------------- + * NCBI:SRA:GenericFastq:sequence_log_odds + * Generic Fastq SRA Platform (for log_odds) + */ +table NCBI:SRA:GenericFastq:sequence_log_odds #1 + = NCBI:SRA:tbl:sra #2.1.3 + , NCBI:tbl:base_space #2.0.3 + , NCBI:tbl:log_odds_quality #2.1.0 + , NCBI:SRA:tbl:clip #1.0.2 +{ + ascii platform_name + = < ascii > echo < "UNDEFINED" > (); + + INSDC:SRA:platform_id out_platform + = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > (); + + /* ascii only spot name tokenizer */ + + NCBI:SRA:spot_name_token out_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name ); + + NCBI:SRA:spot_name_token in_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME ); + + /* clips */ + + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT; +} + +database NCBI:SRA:GenericFastqLogOdds:db #1 +{ + table NCBI:SRA:GenericFastq:sequence_log_odds #1.0 SEQUENCE; +}; + +/*-------------------------------------------------------------------------- + * NCBI:SRA:GenericFastq:sequence_nanopore + * Oxford Nanopore SRA Platform + */ +table NCBI:SRA:GenericFastq:sequence_nanopore #1 + = NCBI:SRA:tbl:sra #2.1.3 + , NCBI:tbl:base_space #2.0.3 + , NCBI:tbl:phred_quality #2.0.4 +{ + ascii platform_name + = < ascii > echo < "OXFORD_NANOPORE" > (); + + INSDC:SRA:platform_id out_platform + = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > (); + + /* ascii only spot name tokenizer */ + + NCBI:SRA:spot_name_token out_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name ); + + NCBI:SRA:spot_name_token in_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME ); + + /* channel and read number columns */ + + extern column < U32 > izip_encoding #1 CHANNEL; + extern column < U32 > izip_encoding #1 READ_NUMBER; +} + +/*-------------------------------------------------------------------------- + * NCBI:SRA:GenericFastq:consensus_nanopore + * Oxford Nanopore SRA Platform + */ +table NCBI:SRA:GenericFastq:consensus_nanopore #1 + = NCBI:SRA:tbl:sra #2.1.3 + , NCBI:tbl:base_space #2.0.3 + , NCBI:tbl:phred_quality #2.0.4 +{ + ascii platform_name + = < ascii > echo < "OXFORD_NANOPORE" > (); + + INSDC:SRA:platform_id out_platform + = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > (); + + /* ascii only spot name tokenizer */ + + NCBI:SRA:spot_name_token out_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name ); + + NCBI:SRA:spot_name_token in_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME ); + + /* channel and read number columns */ + + extern column < U32 > izip_encoding #1 CHANNEL; + extern column < U32 > izip_encoding #1 READ_NUMBER; +} + +database NCBI:SRA:GenericFastqNanopore:db #1 +{ + table NCBI:SRA:GenericFastq:sequence_nanopore #1.0 SEQUENCE; + table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS; +}; + +database NCBI:SRA:GenericFastqNanoporeConsensusOnly:db #1 +{ + table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS; +}; + +/*-------------------------------------------------------------------------- + * NCBI:SRA:GenericFastq:absolid + * Generic fastq for AB Solid platform + */ +table NCBI:SRA:GenericFastq:absolid #1 + = NCBI:SRA:tbl:sra #2.1.3 + , NCBI:tbl:color_space #2.1.0 + , NCBI:tbl:phred_quality #2.0.4 + , NCBI:SRA:tbl:clip #1.0.2 +{ + ascii platform_name + = < ascii > echo < "UNDEFINED" > (); + + INSDC:SRA:platform_id out_platform + = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > (); + + /* ascii only spot name tokenizer */ + + NCBI:SRA:spot_name_token out_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name ); + + NCBI:SRA:spot_name_token in_spot_name_tok + = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME ); + + /* clips */ + + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT; + physical column < INSDC:coord:one > izip_encoding + .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT; +} + +database NCBI:SRA:GenericFastqAbsolid:db #1 +{ + table NCBI:SRA:GenericFastq:absolid #1.0 SEQUENCE; +};