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TRANSMUTE(1) NCBI Entrez Direct User's Manual TRANSMUTE(1)

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

Reformat XML.
Reformat JSON.
Reformat FASTA.
Table column alignment.
Column alignment codes:
Left.
Center.
Right.
Numeric align on decimal point.
Trailing zero-pad decimals.
Leading zero-pad integers.
Commas to group by 3 digits.
Commas plus zero-pad decimals.
Just print colum widths.
Spacing between columns.
Indentation before columns.
Minimum column width.

Data Conversion

Convert JSON stream to XML suitable for -path navigation.
Replace set wrapper tag.
Replace record wrapper tag.
Nested array naming policy.
Convert text ASN.1 stream to XML suitable for -path navigation.
Replace set wrapper tag.
Replace record wrapper tag.
Convert tab-delimited table, comma-separated values file, or semicolon-delimited table, respectively, to XML.
Replace set wrapper tag.
Replace record wrapper tag.
Skip the first N lines.
Use fields from first row for column names.
Convert text to lowercase.
Convert text to uppercase.
Indent XML output.
Do not indent XML output.
XML object names per column.
Convert .ini configuration file format to XML.
Convert TOML configuration file format to XML.
Convert YAML configuration file format to XML.
Text file filtering.
Pattern at start of record.
Reject if string is present.
Require presence of string.
Minimum record number.
Maximum record number.
Convert a FASTA stream to corresponding XML.
Convert GenBank/GenPept flatfile format to INSDSeq XML.
Convert GenBank/GenPept flatfile format to Reference XML.
Reference Index XML lookup to find PMIDs. Supported option values:
Recheck existing PMID claims.
Add NOTE nodes explaining reasoning.
Prefilter candidates relatively heavily (default).
Prefilter candidates less heavily.
Require exact, unique title matches.
GenBank/GenPept filtering.
Single accession.
File of accessions.
Single taxon identifier.
File of taxon identifiers.
Organism scientific name.
Reject if string is present.
Require presence of string.
Remove features and sequence.

Sequence Editing

Reverse complement nucleotide sequence.
Trim at ends of sequence.
Delete first N bases or residues.
Delete last N bases or residues.
Save either end of sequence.
Keep first N bases or residues.
Keep last N bases or residues.
Apply base or residue substition.
Skip ahead by 0-based count (SPDI), or
Move just before 1-based position (HGVS).
Delete N bases or residues.
Insert given sequence.
Lower-case original sequence.
Use xtract -insd ... feat_location instructions.
-1-based
GenBank feat_location convention.
-0-based
Alignment, or -insd feat_intervals.
Lower-case extracted sequence.
Feature location.

Sequence Processing

Translate coding region into protein.
Genetic code (1 by default).
Offset in sequence (0-based).
Include stop residue.
Remove trailing Xs and *s.
CDS partial at 5' end.
CDS extends past 3' end.
Translate all codons.
Optional string between residues.
Simultaneous six-frame translations.
Reprocess first two priming bases at end.
Only capitalize residues at start states.
Number of residues per line.
Calculate molecular weight of peptide.
Do not cleave leading methionine.
Retain leading formyl-methionine.

Variation Processing

Convert Human Genome Variation Society variation format to XML.

Sequence Comparison

Print summary of base or residue counts.
Compare two aligned files for point differences.
Display nucleotide codons above amino acid residues.
Nucleotide sequence.
Protein sequence.
[-frame N]
Offset in nucleotide sequence.
[-three]
Use three-letter residue abbreviations.

Sequence Searching

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.
Do not expand nucleotide ambiguity characters.
Match patterns spanning the origin of a circular molecule.
Do not search reverse complements of non-palindromic patterns.
Pattern to search for.

Text Searching

Find one or more patterns in text, allowing digits, spaces, punctuation, and phrases, e.g., "double, double toil and trouble".
Match on words with letters and digits, ignoring spacing and punctuation.
Case-sensitive match, distinguishing upper-case and lower-case letters.
Match on whole words or multi-word phrases; implies -relaxed.
Pattern to search for.

String Transformations

XML

XML-encode <, >, &, ", and ' characters.
Decode XML entity references.
Remove embedded mixed-content tags and compress runs of spaces.

URL

Compress runs of spaces, and URI-escape the result.
URI-unescape the input.

Base64

Base64-encode the input.
Base64-decode the input.

Accent

Strip accents from the input.

Case

Convert the input to uppercase.
Convert the input to lowercase.

Protein

Convert amino acids from 1-character to 3-character format.
Convert amino acids from 3-character to 1-character format.

Letters plus Digits

Remove all punctuation and compress whitespace.

Customized XML Reformatting

Compress runs of spaces.
Suppress line indentation.
Indent according to nesting depth.
Place each attribute on a separate line.

Use the given XML declaration.
Use the given document type declaration.
Preserve comments.
Preserve cdata blocks.
If the input contains multiple top-level documents, combine them.
Keep empty self-closing tags.
How to handle Unicode superscript and subscript digits (first converted to ASCII form in all cases).
Run them all together, with no additional markup.
Add spaces between digits in different positions.
Add periods between digits in different positions.
Surround superscripts by square brackets and subscripts by parentheses.
Surround superscripts with carets and subscripts with tildes.
Add backslashes when going up in height and forward slashes when going down.
Put superscripts in XML sup elements and subscripts in sub elements.
How to handle XML sup and sub elements (denoting superscripts and subscripts, respectively).
Surround superscripts by square brackets and subscripts by parentheses.
Surround superscripts with carets and subscripts with tildes.
Flatten MathML markup tersely.

XML Modification

Actions:
Keep matching elements (no-op).
Remove matching elements.
HTML-escape special characters.
Decode HTML escapes.
Compress runs of spaces.
Place each attribute on a separate line.
Strip off Unicode accents.

Targets:

Plain-text content.
CDATA blocks.
Comments.
The whole object.
Attributes.
Start and end tags.

EFetch XML Normalization

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).

2025-05-26 NCBI