NAME

transmute - transform data, particularly within NCBI Entrez Direct

SYNOPSIS

transmute -x2p|-j2p
 
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 -g2x (gbf2xml)
 
transmute -g2r (gbf2ref)
 
transmute -r2p (ref2pmid) [ -options confirm|verbose|fast|slow|exact ...]
 
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 [ -code N] [ -frame  N] [ -stop] [ -trim] [ -part5] [ -part3] [ -every]
 
transmute -molwt [ -met]
 
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.
-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.
-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.
-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.

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 [-lower] feat_loc
Use xtract -insd ... feat_location instructions.
-1-based
GenBank feat_location convention.
-0-based
Alignment, or -insd feat_intervals.
-lower
Lower-case extracted sequence.

Sequence Processing

-cds2prot
Translate coding region into protein.
-code N
Use genetic code N (1 by default).
-frame N
Offset in sequence.
-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.
-molwt
Calculate molecular weight of peptide.
-met
Do not cleave leading 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), cit2pmid(1), csv2xml(1), disambiguate-nucleotides(1), download-pubmed(1), ds2pme(1), efetch(1), pma2pme(1), ref2pmid(1), tbl2prod(1), uniq-table(1), xml2fsa(1), xml2tbl(1), xtract(1).