transmute - transform data, particularly within NCBI Entrez
Direct
transmute -x2p|-j2p
transmute -align
[-a codes]
[-g N]
[-h N]
[-w N]
transmute -j2x (json2xml)
[-set tag] [-rec tag]
[-nest flat|recurse|plural|singular|depth|element]
transmute -a2x [-set tag]
[-rec tag]
transmute -t2x|-c2x|-s2x
(tbl2xml / csv2xml / scn2xml)
[-set tag] [-rec tag]
[-skip N] [-header]
[-lower|-upper] [-indent|-flush]
columnName1 ...
transmute -g2x (gbf2xml)
transmute -g2r (gbf2ref)
transmute -r2p (ref2pmid) [-options
confirm|verbose|fast|slow|exact ...]
transmute -revcomp
transmute -remove [-first N]
[-last N]
transmute -retain
-leading N-trailing N
transmute -replace
-offset N|-column N
[-delete N] [-insert seq]
[-lower]
transmute -extract [-1-based]
[-0-based] [-lower] feat_loc
transmute -cds2prot [-code N]
[-frame N] [-stop] [-trim]
[-part5] [-part3] [-every]
transmute -molwt [-met]
transmute -hgvs
transmute -counts
transmute -diff
transmute -codons -nuc seq
-prot seq [-frame N]
[-three]
transmute -search [-protein]
[-circular] [-top] pattern ...
transmute -find [-relaxed]
[-sensitive] [-whole] pattern ...
transmute
-encodeXML|-decodeXML|-plainXML
transmute -encodeURL|-decodeURL
transmute -encode64|-decode64
transmute -plain
transmute -upper|-lower
transmute -aa1to3|-aa3to1
transmute -relax
transmute -format [fmt]
[-xml declaration]
[-doctype declaration] [-comment]
[-cdata] [-combine] [-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.
- -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.
- m
- Commas to group by 3 digits.
- M
- Commas plus zero-pad decimals.
- -g N
- Spacing between columns.
- -h N
- Indentation before columns.
- -w N
- Minimum column width.
- -j2x
- Convert JSON stream to XML suitable for -path navigation.
- -a2x
- Convert text ASN.1 stream to XML suitable for -path
navigation.
- -t2x, -c2x,
-s2x
- Convert tab-delimited table, comma-separated values file, or
semicolon-delimited table, 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/GenPept flatfile format to INSDSeq XML.
- -g2r
- Convert GenBank/GenPept flatfile format to Reference XML.
- -r2p [-options
option ...]
- Reference Index XML lookup to find PMIDs. Supported option
values:
- confirm
- Recheck existing PMID claims.
- verbose
- Add NOTE nodes explaining reasoning.
- fast
- Prefilter candidates relatively heavily (default).
- slow
- Prefilter candidates less heavily.
- exact
- Require exact, unique title matches.
- -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.
- -1-based
- GenBank feat_location convention.
- -0-based
- Alignment, or -insd feat_intervals.
- -lower
- Lower-case extracted sequence.
- -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 and *s.
- -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.
- -counts
- Print summary of base or residue counts.
- -diff
- Compare two aligned files for point differences.
- -codons
- Display nucleotide codons above amino acid residues.
- -nuc seq
- Nucleotide sequence.
- -prot seq
- Protein sequence.
- [-frame N]
- Offset in nucleotide sequence.
- [-three]
- Use three-letter residue abbreviations.
- -search
- Search for one or more patterns in a sequence, skipping any FASTA
definition line (with a leading >). Each pattern can have an
optional alias, e.g., GGATCC:BamHI.
- -protein
- Do not expand nucleotide ambiguity characters.
- -circular
- Match patterns spanning the origin of a circular molecule.
- -top
- Do not search reverse complements of non-palindromic patterns.
- pattern
- Pattern to search for.
- -find
- Find one or more patterns in text, allowing digits, spaces, punctuation,
and phrases, e.g., "double, double toil and
trouble".
- -relaxed
- Match on words with letters and digits, ignoring spacing and
punctuation.
- -sensitive
- Case-sensitive match, distinguishing upper-case and lower-case
letters.
- -whole
- Match on whole words or multi-word phrases; implies -relaxed.
- pattern
- Pattern to search for.
- -encodeXML
- XML-encode <, >, &, ", and
' characters.
- -decodeXML
- Decode XML entity references.
- -plainXML
- Remove embedded mixed-content tags and compress runs of spaces.
- -plain
- Strip accents from the input.
- -upper
- Convert the input to uppercase.
- -lower
- Convert the input to lowercase.
- -aa1to3
- Convert amino acids from 1-character to 3-character format.
- -aa3to1
- Convert amino acids from 3-character to 1-character format.
- -relax
- Remove all punctuation and compress whitespace.
- -format [fmt]
- 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.
- -combine
- If the input contains multiple top-level documents, combine them.
- -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.
align-columns(1), blst2tkns(1), cit2pmid(1),
csv2xml(1), disambiguate-nucleotides(1),
download-pubmed(1), ds2pme(1), efetch(1),
pma2pme(1), ref2pmid(1), tbl2prod(1),
uniq-table(1), xml2fsa(1), xml2tbl(1),
xtract(1).