.TH TRANSMUTE 1 2021-02-12 NCBI "NCBI Entrez Direct User's Manual"
.SH NAME
align\-columns, gbf2xml, transmute \- transform (NCBI Entrez Direct) data
.SH SYNOPSIS
\fBtransmute\fP \fB\-x2p\fP|\fB\-j2p\fP

\fBtransmute\fP \fB\-align\fP
[\|\fB\-a\ \fIcodes\fP\|]
[\|\fB\-g\ \fIN\fP\|]
[\|\fB\-h\ \fIN\fP\|]

\fBtransmute\fP \fB\-j2x\fP
[\|\fB\-set\fP\ \fItag\fP\|]
[\|\fB\-rec\fP\ \fItag\fP\|]
[\|\fB\-nest\fP\ \fBflat\fP|\fBrecurse\fP|\fBplural\fP|\fBdepth\fP\|]

\fBtransmute\fP \fB\-a2x\fP
[\|\fB\-set\fP\ \fItag\fP\|]
[\|\fB\-rec\fP\ \fItag\fP\|]

\fBtransmute\fP \fB\-t2x\fP|\fB-c2x\fP
[\|\fB\-set\fP\ \fItag\fP\|]
[\|\fB\-rec\fP\ \fItag\fP\|]
[\|\fB\-skip\fP\ \fIN\fP\|]
[\|\fB\-header\fP]
[\|\fB\-lower\fP|\fB\-upper\fP\|]
[\|\fB\-indent\fP|\fB\-flush\fP\|]
\fIcolumnName1\fP\ ...

\fBtransmute\fP \fB\-g2x\fP (\fBgbf2xml\fP\)

\fBtransmute\fP \fB\-diff\fP

\fBtransmute\fP \fB\-revcomp\fP

\fBtransmute\fP \fB\-remove\fP
[\|\fB\-first\fP\ \fIN\fP\|]
[\|\fB\-last\fP\ \fIN\fP\|]

\fBtransmute\fP \fB\-retain\fP
\fB\-leading\fP\ \fIN\fP\|\fB\-trailing\fP\ \fIN\fP

\fBtransmute\fP \fB\-replace\fP
\fB\-offset\fP\ \fIN\fP|\fB\-column\fP\ \fIN\fP
[\|\fB\-delete\fP\ \fIN\fP\|]
[\|\fB\-insert\fP\ \fIseq\fP\|]

\fBtransmute\fP \fB\-extract\fP\ \fIfeat_loc\fP

\fBtransmute\fP \fB\-cds2prot\fP
[\|\fB\-code\fP\ \fIN\fP\|]
[\|\fB\-frame\fP\ \fIN\fP\|]
[\|\fB\-stop\fP\|]
[\|\fB\-trim\fP\|]
[\|\fB\-part5\fP\|]
[\|\fB\-part3\fP\|]
[\|\fB\-every\fP\|]

\fBtransmute\fP \fB\-molwt\fP
[\|\fB\-met\fP\|]

\fBtransmute\fP \fB\-hgvs\fP

\fBtransmute\fP \fB\-encodeXML\fP|\fB\-decodeXML\fP|\fB\-plainXML\fP

\fBtransmute\fP \fB\-encodeURL\fP|\fB\-decodeURL\fP

\fBtransmute\fP \fB\-encode64\fP|\fB\-decode64\fP

\fBtransmute\fP \fB\-aa1to3\fP|\fB\-aa3to1\fP

\fBtransmute\fP \fB\-format\fP\ \fIfmt\fP
[\|\fB\-xml\fP\ \fIdeclaration\fP\|]
[\|\fB\-doctype\fP\ \fIdeclaration\fP\|]
[\|\fB\-comment\fP\|]
[\|\fB\-cdata\fP\|]
[\|\fB\-separate\fP\|]
[\|\fB\-self\fP\|]
[\|\fB\-unicode\fP\ \fIstyle\fP\|]
[\|\fB\-script\fP\ \fIstyle\fP\|]
[\|\fB\-mathml\ terse\fP\|]

\fBtransmute\fP \fB\-filter\fP \fIelement\fP \fIaction\fP \fItarget\fP

\fBtransmute\fP \fB\-normalize\fP \fIdatabase\fP
.SH DESCRIPTION
\fBtransmute\fP reads data from standard input,
transforms it according to the specified mode,
and writes the transformed data to standard output.

\fBalign\-columns\fP aligns the columns of tab\-delimited input,
and is roughly equivalent to \fBtransmute \-align\fP,
but accepts \fB\-\fP as shorthand for \fB\-h 2 \-g 4 \-a l\fP.

\fBgbf2xml\fP converts from GenBank flatfile format to INSDSeq XML,
and is equivalent to \fBtransmute \-g2x\fP.
.SH OPTIONS
.SS Pretty\-Printing
.TP
\fB\-x2p\fP
Reformat XML
.TP
\fB\-j2p\fP
Reformat JSON
.TP
\fB\-align\fP
Table column alignment
.PD 0
.RS
.IP "\fB\-a\fP \fIcodes\fP" 9
Column alignment codes:
.RS
.IP \fBl\fP
left
.IP \fBc\fP
center
.IP \fBr\fP
right
.IP \fBn\fP
numeric align on decimal point
.IP \fBN\fP
trailing zero\-pad decimals
.IP \fBz\fP
leading zero\-pad integers
.RE
.IP "\fB-g\fP \fIN\fP" 9
Spacing between columns
.IP "\fB-h\fP \fIN\fP" 9
Indentation before columns
.RE
.PD
.SS Data Conversion
.TP
\fB\-j2x\fP
Convert JSON stream to XML suitable for \fB\-path\fP navigation.
.PD 0
.RS
.TP
\fB\-set\fP\ \fItag\fP
Replace set wrapper tag.
.TP
\fB\-rec\fP\ \fItag\fP
Replace record wrapper tag.
.TP
\fB\-nest\fP\ \fBflat\fP|\fBrecurse\fP|\fBplural\fP|\fBdepth\fP
Nested array naming policy.
.RE
.PD
.TP
\fB\-a2x\fP
Convert text ASN.1 stream to XML suitable for \fB\-path\fP navigation.
.PD 0
.RS
.IP \fB\-set\fP\ \fItag\fP 10
Replace set wrapper tag.
.IP \fB\-rec\fP\ \fItag\fP 10
Replace record wrapper tag.
.RE
.PD
.TP
\fB\-t2x\fP, \fB\-c2x\fP
Convert tab\-delimited table or comma\-separated values file,
respectively, to XML.
.PD 0
.RS
.IP \fB\-set\fP\ \fItag\fP 16
Replace set wrapper tag.
.IP \fB\-rec\fP\ \fItag\fP 16
Replace record wrapper tag.
.IP \fB\-skip\fP\ \fIN\fP 16
Skip the first \fIN\fP lines.
.IP \fB\-header\fP 16
Use fields from first row for column names.
.IP \fB\-lower\fP 16
Convert text to lowercase.
.IP \fB\-upper\fP 16
Convert text to uppercase.
.IP \fB\-indent\fP 16
Indent XML output.
.IP \fB\-flush\fP 16
Do not indent XML output.
.IP \fIcolumnName1\fP\ ... 16
XML object names per column.
.RE
.PD
.TP
\fB\-g2x\fP
Convert GenBank flatfile format to INSDSeq XML.
.SS Sequence Comparison
.TP
\fB\-diff\fP
Compare two aligned files for point differences.
.SS Sequence Editing
.TP 10
\fB\-revcomp\fP
Reverse complement nucleotide sequence.
.TP 10
\fB\-remove\fP
Trim at ends of sequence.
.PD 0
.RS
.TP 15
\fB\-first\fP\ \fIN\fP
Delete first \fIN\fP bases or residues.
.TP 15
\fB\-last\fP\ \fIN\fP
Delete last \fIN\fP bases or residues.
.RE
.PD
.TP 10
\fB\-retain\fP
Save either end of sequence.
.PD 0
.RS
.TP 15
\fB\-leading\fP\ \fIN\fP
Keep first \fIN\fP bases or residues.
.TP 15
\fB\-trailing\fP\ \fIN\fP
Keep last \fIN\fP bases or residues.
.RE
.PD
.TP 10
\fB\-replace\fP
Apply base or residue substition.
.PD 0
.RS
.TP 15
\fB\-offset\fP\ \fIN\fP
Skip ahead by 0\-based count (SPDI), or
.TP 15
\fB\-column\fP\ \fIN\fP
Move just before 1\-based position (HGVS).
.TP 15
\fB\-delete\fP\ \fIN\fP
Delete \fIN\fP bases or residues.
.TP
\fB\-insert\fP\ \fIseq\fP
Insert given sequence.
.RE
.PD
.TP 10
\fB\-extract\fP\ \fIfeat_loc\fP
Use \fBxtract \-insd\fP ... \fBfeat_location\fP instructions.
.SS Sequence Processing
.TP 10
\fB\-cds2prot\fP
Translate coding region into protein.
.PD 0
.RS
.TP 15
\fB\-code\fP\ \fIN\fP
Use genetic code \fIN\fP (\fB1\fP by default).
.TP 15
\fB\-frame\fP\ \fIN\fP
Offset in sequence.
.TP 15
\fB\-stop\fP
Include stop residue.
.TP 15
\fB\-trim\fP
Remove trailing \fBX\fPs.
.TP 15
\fB\-part5\fP
CDS partial at 5' end.
.TP 15
\fB\-part3\fP
CDS extends past 3' end.
.TP
\fB\-every\fP
Translate all codons.
.RE
.PD
.TP 10
\fB\-molwt\fP
Calculate molecular weight of peptide.
.PD 0
.RS
.TP 15
\fB\-met\fP
Do not cleave leading methionine.
.RE
.PD
.SS Variation Processing
.TP
\fB\-hgvs\fP
Convert Human Genome Variation Society variation format to XML.
.SS String Transformations
.TP 12
\fB\-encodeXML\fP
XML\-encode \fB<\fP, \fB>\fP, \fB&\fP,
\fB\(dq\fP, and \fB\[aq]\fP characters.
.TP 12
\fB\-decodeXML\fP
Decode XML entity references.
.TP 12
\fB\-plainXML\fP
Remove embedded mixed\-content tags and compress runs of spaces.
.TP 12
\fB\-encodeURL\fP
Compress runs of spaces, and URI\-escape the result.
.TP 12
\fB\-decodeURL\fP
URI\-unescape the input.
.TP 12
\fB\-encode64\fP
Base64-encode the input.
.TP 12
\fB\-decode64\fP
Base64-decode the input.
.SS Protein
.TP 9
\fB\-aa1to3\fP
Convert amino acids from 1\-character to 3\-character format.
.TP 9
\fB\-aa3to1\fP
Convert amino acids from 3\-character to 1\-character format.
.SS Customized XML Reformatting
.TP
\fB\-format\fP\ \fIfmt\fP
.PD 0
.RS
.IP \fBcopy\fP 9
Fast block copy (still applies processing flags).
.IP \fBcompact\fP 9
Compress runs of spaces.
.IP \fBflush\fP 9
Suppress line indentation.
.IP \fBindent\fP 9
Indent according to nesting depth.
.IP \fBexpand\fP 9
Place each attribute on a separate line.

.TP
\fB\-xml\fP\ \fIdeclaration\fP
Use the given XML declaration.
.TP
\fB\-doctype\fP\ \fIdeclaration\fP
Use the given document type declaration.
.TP
\fB\-comment\fP
Preserve comments.
.TP
\fB\-cdata\fP
Preserve \fBcdata\fP blocks.
.TP
\fB\-separate\fP
If the input contains multiple top\-level documents,
keep them separate.
.TP
\fB\-self\fP
Keep empty self\-closing tags.
.TP
\fB\-unicode\fP\ \fIstyle\fP
How to handle Unicode superscript and subscript digits
(first converted to ASCII form in all cases).
.\".PD 0
.RS
.IP \fBfuse\fP 9
Run them all together, with no additional markup.
.IP \fBspace\fP 9
Add spaces between digits in different positions.
.IP \fBperiod\fP 9
Add periods between digits in different positions.
.IP \fBbrackets\fP 9
Surround superscripts by square brackets and subscripts by parentheses.
.IP \fBmarkdown\fP 9
Surround superscripts with carets and subscripts with tildes.
.IP \fBslash\fP 9
Add backslashes when going up in height
and forward slashes when going down.
.IP \fBtag\fP 9
Put superscripts in XML \fBsup\fP elements
and subscripts in \fBsub\fP elements.
.RE
.\".PD
.TP
\fB\-script\fP\ \fIstyle\fP
How to handle XML \fBsup\fP and \fBsub\fP elements
(denoting superscripts and subscripts, respectively).
.\".PD 0
.RS
.IP \fBbrackets\fP 9
Surround superscripts by square brackets and subscripts by parentheses.
.IP \fBmarkdown\fP 9
Surround superscripts with carets and subscripts with tildes.
.RE
.\".PD
.TP
\fB\-mathml\ terse\fP
Flatten MathML markup tersely.
.RE
.PD
.SS XML Modification
.TP
\fB\-filter\fP\ \fIelement\fP \fIaction\fP\ \fItarget\fP
Actions:
.PD 0
.RS
.IP \fBretain\fP 12
Keep matching elements (no\-op).
.IP \fBremove\fP 12
Remove matching elements.
.IP \fBencode\fP 12
HTML\-escape special characters.
.IP \fBdecode\fP 12
Decode HTML escapes.
.IP \fBshrink\fP 12
Compress runs of spaces.
.IP \fBexpand\fP 12
Place each attribute on a separate line.
.IP \fBaccent\fP 12
Strip off Unicode accents.
.PD
.P
Targets:
.PD 0
.IP \fBcontent\fP 12
Plain\-text content.
.IP \fBcdata\fP 12
\fBCDATA\fP blocks.
.IP \fBcomment\fP 12
Comments.
.IP \fBobject\fP 12
The whole object.
.IP \fBattributes\fP 12
Attributes.
.IP \fBcontainer\fP 12
Start and end tags.
.RE
.PD
.SS EFetch XML Normalization
.TP
\fB\-normalize\fP\ \fIdatabase\fP
Adjust XML fields to conform to common conventions.
.SH SEE ALSO
.BR download\-pubmed (1),
.BR edirect (1),
.BR efetch (1),
.BR xtract (1).