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TRANSMUTE(1) | NCBI Entrez Direct User's Manual | TRANSMUTE(1) |
NAME¶
align-columns, gbf2xml, transmute - transform (NCBI Entrez Direct) data
SYNOPSIS¶
transmute -x2p|-j2p
transmute -align [-a codes] [-g N] [-h N]
transmute -j2x [-set tag] [-rec tag] [-nest flat|recurse|plural|depth]
transmute -a2x [-set tag] [-rec tag]
transmute -t2x|-c2x [-set tag] [-rec tag] [-skip N] [-header] [-lower|-upper] [-indent|-flush] columnName1 ...
transmute -g2x (gbf2xml
transmute -diff
transmute -revcomp
transmute -remove [-first N] [-last N]
transmute -retain -leading N-trailing N
transmute -replace -offset N|-column N [-delete N] [-insert seq]
transmute -extract feat_loc
transmute -cds2prot [-code N] [-frame N] [-stop] [-trim] [-part5] [-part3] [-every]
transmute -molwt [-met]
transmute -hgvs
transmute -encodeXML|-decodeXML|-plainXML
transmute -encodeURL|-decodeURL
transmute -encode64|-decode64
transmute -aa1to3|-aa3to1
transmute -format fmt [-xml declaration] [-doctype declaration] [-comment] [-cdata] [-separate] [-self] [-unicode style] [-script style] [-mathml terse]
transmute -filter element action target
transmute -normalize database
DESCRIPTION¶
transmute reads data from standard input, transforms it according to the specified mode, and writes the transformed data to standard output.
align-columns aligns the columns of tab-delimited input, and is roughly equivalent to transmute -align, but accepts - as shorthand for -h 2 -g 4 -a l.
gbf2xml converts from GenBank flatfile format to INSDSeq XML, and is equivalent to transmute -g2x.
OPTIONS¶
Pretty-Printing¶
Data Conversion¶
- -j2x
- Convert JSON stream to XML suitable for -path navigation.
- -set tag
- Replace set wrapper tag.
- -rec tag
- Replace record wrapper tag.
- -nest flat|recurse|plural|depth
- Nested array naming policy.
- -a2x
- Convert text ASN.1 stream to XML suitable for -path navigation.
- -t2x, -c2x
- Convert tab-delimited table or comma-separated values file, respectively, to XML.
- -set tag
- Replace set wrapper tag.
- -rec tag
- Replace record wrapper tag.
- -skip N
- Skip the first N lines.
- -header
- Use fields from first row for column names.
- -lower
- Convert text to lowercase.
- -upper
- Convert text to uppercase.
- -indent
- Indent XML output.
- -flush
- Do not indent XML output.
- columnName1 ...
- XML object names per column.
- -g2x
- Convert GenBank flatfile format to INSDSeq XML.
Sequence Comparison¶
- -diff
- Compare two aligned files for point differences.
Sequence Editing¶
- -retain
- Save either end of sequence.
- -leading N
- Keep first N bases or residues.
- -trailing N
- Keep last N bases or residues.
- -replace
- Apply base or residue substition.
- -offset N
- Skip ahead by 0-based count (SPDI), or
- -column N
- Move just before 1-based position (HGVS).
- -delete N
- Delete N bases or residues.
- -insert seq
- Insert given sequence.
- -extract feat_loc
- Use xtract -insd ... feat_location instructions.
Sequence Processing¶
- -cds2prot
- Translate coding region into protein.
- -molwt
- Calculate molecular weight of peptide.
- -met
- Do not cleave leading methionine.
Variation Processing¶
- -hgvs
- Convert Human Genome Variation Society variation format to XML.
String Transformations¶
- -encodeXML
- XML-encode <, >, &, ", and ' characters.
- -decodeXML
- Decode XML entity references.
- -plainXML
- Remove embedded mixed-content tags and compress runs of spaces.
- -encodeURL
- Compress runs of spaces, and URI-escape the result.
- -decodeURL
- URI-unescape the input.
- -encode64
- Base64-encode the input.
- -decode64
- Base64-decode the input.
Protein¶
Customized XML Reformatting¶
- copy
- Fast block copy (still applies processing flags).
- compact
- Compress runs of spaces.
- flush
- Suppress line indentation.
- indent
- Indent according to nesting depth.
- expand
- Place each attribute on a separate line.
- -xml declaration
- Use the given XML declaration.
- -doctype declaration
- Use the given document type declaration.
- -comment
- Preserve comments.
- -cdata
- Preserve cdata blocks.
- -separate
- If the input contains multiple top-level documents, keep them separate.
- -self
- Keep empty self-closing tags.
- -unicode style
- How to handle Unicode superscript and subscript digits (first converted to ASCII form in all cases).
- fuse
- Run them all together, with no additional markup.
- space
- Add spaces between digits in different positions.
- period
- Add periods between digits in different positions.
- brackets
- Surround superscripts by square brackets and subscripts by parentheses.
- markdown
- Surround superscripts with carets and subscripts with tildes.
- slash
- Add backslashes when going up in height and forward slashes when going down.
- tag
- Put superscripts in XML sup elements and subscripts in sub elements.
- -script style
- How to handle XML sup and sub elements (denoting superscripts and subscripts, respectively).
- -mathml terse
- Flatten MathML markup tersely.
XML Modification¶
- -filter element action target
- Actions:
EFetch XML Normalization¶
- -normalize database
- Adjust XML fields to conform to common conventions.
SEE ALSO¶
2021-02-12 | NCBI |