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

NAME

align-columns, gbf2xml, transmute - transform (NCBI Entrez Direct) data

SYNOPSIS

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

DESCRIPTION

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.

OPTIONS

Pretty-Printing

Reformat XML
Reformat JSON
Table column alignment
Column alignment codes:
left
center
right
numeric align on decimal point
trailing zero-pad decimals
leading zero-pad integers
Spacing between columns
Indentation before columns

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 or comma-separated values file, 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 GenBank flatfile format to INSDSeq XML.

Sequence Comparison

Compare two aligned files for point differences.

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.
Use xtract -insd ... feat_location instructions.

Sequence Processing

Translate coding region into protein.
Use genetic code N (1 by default).
Offset in sequence.
Include stop residue.
Remove trailing Xs.
CDS partial at 5' end.
CDS extends past 3' end.
Translate all codons.
Calculate molecular weight of peptide.
Do not cleave leading methionine.

Variation Processing

Convert Human Genome Variation Society variation format to XML.

String Transformations

XML-encode <, >, &, ", and ' characters.
Decode XML entity references.
Remove embedded mixed-content tags and compress runs of spaces.
Compress runs of spaces, and URI-escape the result.
URI-unescape the input.
Base64-encode the input.
Base64-decode the input.

Protein

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

Customized XML Reformatting

Fast block copy (still applies processing flags).
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, keep them separate.
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

download-pubmed(1), edirect(1), efetch(1), xtract(1).

2021-02-12 NCBI