Provided by: ncbi-entrez-direct_24.0.20250523+dfsg-1_amd64 
NAME
transmute - transform data, particularly within NCBI Entrez Direct
SYNOPSIS
transmute -x2p|-j2p|-f2p
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 -i2x (ini2xml)
transmute -m2x (toml2xml)
transmute -y2x (yaml2xml)
transmute -txf (filter-record) [-pattern str] [-exclude str] [-require str] [-min N] [-max N]
transmute -f2x (fsa2xml)
transmute -g2x (gbf2xml)
transmute -g2r (gbf2ref)
transmute -r2p (ref2pmid) [-options confirm|verbose|fast|slow|exact ...]
transmute -gbf (filter-genbank) [-accession acc|-accessions file] [-taxid id|-taxids file]
[-organism name] [-exclude str] [-require str] [-truncate]
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 [-gcode N] [-frame N|-all] [-stop] [-trim] [-part5] [-part3] [-every] [-between str]
[-circular] [-orf] [-max N]
transmute -molwt [-met|-fmet]
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
DESCRIPTION
transmute reads data from standard input, transforms it according to the specified mode, and writes the
transformed data to standard output.
OPTIONS
Pretty-Printing
-x2p Reformat XML.
-j2p Reformat JSON.
-f2p Reformat FASTA.
-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.
w Just print colum widths.
-g N Spacing between columns.
-h N Indentation before columns.
-w N Minimum column width.
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|singular|depth|element
Nested array naming policy.
-a2x Convert text ASN.1 stream to XML suitable for -path navigation.
-set tag Replace set wrapper tag.
-rec tag Replace record wrapper tag.
-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.
-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.
-i2x Convert .ini configuration file format to XML.
-m2x Convert TOML configuration file format to XML.
-y2x Convert YAML configuration file format to XML.
-txf Text file filtering.
-pattern str Pattern at start of record.
-exclude str Reject if string is present.
-require str Require presence of string.
-min N Minimum record number.
-max N Maximum record number.
-f2x Convert a FASTA stream to corresponding XML.
-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.
-gbf GenBank/GenPept filtering.
-accession acc Single accession.
-accessions file File of accessions.
-taxid id Single taxon identifier.
-taxids file File of taxon identifiers.
-organism name Organism scientific name.
-exclude str Reject if string is present.
-require str Require presence of string.
-truncate Remove features and sequence.
Sequence Editing
-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.
-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.
-lower Lower-case original sequence.
-extract Use xtract -insd ... feat_location instructions.
-1-based GenBank feat_location convention.
-0-based Alignment, or -insd feat_intervals.
-lower Lower-case extracted sequence.
feat_loc Feature location.
Sequence Processing
-cds2prot Translate coding region into protein.
-gcode N Genetic code (1 by default).
-frame N Offset in sequence (0-based).
-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.
-between str Optional string between residues.
-all Simultaneous six-frame translations.
-circular Reprocess first two priming bases at end.
-orf Only capitalize residues at start states.
-max N Number of residues per line.
-molwt Calculate molecular weight of peptide.
-met Do not cleave leading methionine.
-fmet Retain leading formyl-methionine.
Variation Processing
-hgvs Convert Human Genome Variation Society variation format to XML.
Sequence Comparison
-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.
Sequence Searching
-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.
Text Searching
-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.
String Transformations
XML
-encodeXML XML-encode <, >, &, ", and ' characters.
-decodeXML Decode XML entity references.
-plainXML Remove embedded mixed-content tags and compress runs of spaces.
URL
-encodeURL Compress runs of spaces, and URI-escape the result.
-decodeURL URI-unescape the input.
Base64
-encode64 Base64-encode the input.
-decode64 Base64-decode the input.
Accent
-plain Strip accents from the input.
Case
-upper Convert the input to uppercase.
-lower Convert the input to lowercase.
Protein
-aa1to3 Convert amino acids from 1-character to 3-character format.
-aa3to1 Convert amino acids from 3-character to 1-character format.
Letters plus Digits
-relax Remove all punctuation and compress whitespace.
Customized XML Reformatting
-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.
-comment 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.
XML Modification
-filter element action target
Actions:
retain Keep matching elements (no-op).
remove Remove matching elements.
encode HTML-escape special characters.
decode Decode HTML escapes.
shrink Compress runs of spaces.
expand Place each attribute on a separate line.
accent Strip off Unicode accents.
Targets:
content Plain-text content.
cdata CDATA blocks.
comment Comments.
object The whole object.
attributes Attributes.
container Start and end tags.
EFetch XML Normalization
-normalize database
Adjust XML fields to conform to common conventions.
SEE ALSO
align-columns(1), blst2tkns(1), bsmp2info(1), cit2pmid(1), csv2xml(1), disambiguate-nucleotides(1),
download-flatfile(1), download-pubmed(1), ds2pme(1), efetch(1), filter-columns(1), filter-genbank(1),
gbf2info(1), gbf2tbl(1), gff2xml(1), gff-sort(1), jsonl2xml(1), pma2apa(1), pma2pme(1), pmc2bioc(1),
pmc2info(1), print-columns(1), ref2pmid(1), snp2tbl(1), sort-table(1), spdi2tbl(1),
systematic-mutations(1), tbl2prod(1), uniq-table(1), xml2fsa(1), xml2tbl(1), xfetch(1), xtract(1).
NCBI 2025-05-26 TRANSMUTE(1)