align-columns, gbf2xml, transmute - transform (NCBI Entrez Direct)
data
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
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.
- -x2p
- Reformat XML
- -j2p
- Reformat JSON
- -align
- Table column alignment
- -a codes
- Column alignment codes:
- l
- left
- c
- center
- r
- right
- n
- numeric align on decimal point
- N
- trailing zero-pad decimals
- z
- leading zero-pad integers
- -g N
- Spacing between columns
- -h N
- Indentation before columns
- -j2x
- Convert JSON stream to XML suitable for -path navigation.
- -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.
- 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.
- -diff
- Compare two aligned files for point differences.
- -revcomp
- Reverse complement nucleotide sequence.
- -remove
- Trim at ends of sequence.
- -first N
- Delete first N bases or residues.
- -last N
- Delete last N bases or residues.
- -retain
- Save either end of sequence.
- -replace
- Apply base or residue substition.
- Use xtract -insd ... feat_location instructions.
- -cds2prot
- Translate coding region into protein.
- -code N
- Use genetic code N (1 by default).
- -frame N
- Offset in sequence.
- -stop
- Include stop residue.
- -trim
- Remove trailing Xs.
- -part5
- CDS partial at 5' end.
- -part3
- CDS extends past 3' end.
- -every
- Translate all codons.
- -molwt
- Calculate molecular weight of peptide.
- -met
- Do not cleave leading methionine.
- -hgvs
- Convert Human Genome Variation Society variation format to XML.
- -aa1to3
- Convert amino acids from 1-character to 3-character format.
- -aa3to1
- Convert amino acids from 3-character to 1-character format.
- -format fmt
- 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.
- 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).
- brackets
- Surround superscripts by square brackets and subscripts by
parentheses.
- markdown
- Surround superscripts with carets and subscripts with tildes.
- -mathml terse
- Flatten MathML markup tersely.