---
name: "transmute"
section: "1"
platform: "linux"
package: "ncbi-entrez-direct"
version: "24.0.20250523+dfsg-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/transmute"
---

# transmute(1)

transform data, particularly within NCBI Entrez Direct

## 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)](/align-columns/1.md), [**blst2tkns**(1)](/blst2tkns/1.md), [**bsmp2info**(1)](/bsmp2info/1.md), [**cit2pmid**(1)](/cit2pmid/1.md), [**csv2xml**(1)](/csv2xml/1.md), [**disambiguate-nucleotides**(1)](/disambiguate-nucleotides/1.md), [**download-flatfile**(1)](/download-flatfile/1.md), [**download-pubmed**(1)](/download-pubmed/1.md), [**ds2pme**(1)](/ds2pme/1.md), [**efetch**(1)](/efetch/1.md), [**filter-columns**(1)](/filter-columns/1.md), [**filter-genbank**(1)](/filter-genbank/1.md), [**gbf2info**(1)](/gbf2info/1.md), [**gbf2tbl**(1)](/gbf2tbl/1.md), [**gff2xml**(1)](/gff2xml/1.md), [**gff-sort**(1)](/gff-sort/1.md), [**jsonl2xml**(1)](/jsonl2xml/1.md), [**pma2apa**(1)](/pma2apa/1.md), [**pma2pme**(1)](/pma2pme/1.md), [**pmc2bioc**(1)](/pmc2bioc/1.md), [**pmc2info**(1)](/pmc2info/1.md), [**print-columns**(1)](/print-columns/1.md), [**ref2pmid**(1)](/ref2pmid/1.md), [**snp2tbl**(1)](/snp2tbl/1.md), [**sort-table**(1)](/sort-table/1.md), [**spdi2tbl**(1)](/spdi2tbl/1.md), [**systematic-mutations**(1)](/systematic-mutations/1.md), [**tbl2prod**(1)](/tbl2prod/1.md), [**uniq-table**(1)](/uniq-table/1.md), [**xml2fsa**(1)](/xml2fsa/1.md), [**xml2tbl**(1)](/xml2tbl/1.md), [**xfetch**(1)](/xfetch/1.md), [**xtract**(1)](/xtract/1.md).