transmute - transform data, particularly within NCBI Entrez Direct

transmute  reads  data from standard input, transforms it according to the specified mode, and writes the
       transformed data to standard output.

       transmute - transform data, particularly within NCBI Entrez Direct

Pretty-Printing-x2p   Reformat XML.

       -j2p   Reformat JSON.

       -align Table column alignment.
              -acodes 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.
              -gN     Spacing between columns.
              -hN     Indentation before columns.
              -wN     Minimum column width.

   DataConversion-j2x   Convert JSON stream to XML suitable for -path navigation.
              -settag
                     Replace set wrapper tag.
              -rectag
                     Replace record wrapper tag.
              -nestflat|recurse|plural|singular|depth|element
                     Nested array naming policy.

       -a2x   Convert text ASN.1 stream to XML suitable for -path navigation.
              -settag  Replace set wrapper tag.
              -rectag  Replace record wrapper tag.

       -t2x, -c2x, -s2x
              Convert  tab-delimited  table,  comma-separated  values  file,   or   semicolon-delimited   table,
              respectively, to XML.
              -settag        Replace set wrapper tag.
              -rectag        Replace record wrapper tag.
              -skipN         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 [-optionsoption ...]
              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.

   SequenceEditing-revcomp  Reverse complement nucleotide sequence.

       -remove   Trim at ends of sequence.
                 -firstN       Delete first N bases or residues.
                 -lastN        Delete last N bases or residues.

       -retain   Save either end of sequence.
                 -leadingN     Keep first N bases or residues.
                 -trailingN    Keep last N bases or residues.

       -replace  Apply base or residue substition.
                 -offsetN      Skip ahead by 0-based count (SPDI), or
                 -columnN      Move just before 1-based position (HGVS).
                 -deleteN      Delete N bases or residues.
                 -insertseq    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.

   SequenceProcessing-cds2prot Translate coding region into protein.
                 -codeN        Use genetic code N (1 by default).
                 -frameN       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.

   VariationProcessing-hgvs  Convert Human Genome Variation Society variation format to XML.

   SequenceComparison-counts   Print summary of base or residue counts.

       -diff     Compare two aligned files for point differences.

       -codons   Display nucleotide codons above amino acid residues.
                 -nucseq       Nucleotide sequence.
                 -protseq      Protein sequence.
                 [-frameN]     Offset in nucleotide sequence.
                 [-three]       Use three-letter residue abbreviations.

   SequenceSearching-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.

   TextSearching-find     Find one or more patterns in text, allowing digits, spaces,  punctuation,  and  phrases,  e.g.,
                 "double,doubletoilandtrouble".
                 -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.

   StringTransformationsXML-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.

   LettersplusDigits-relax Remove all punctuation and compress whitespace.

   CustomizedXMLReformatting-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.

              -xmldeclaration
                       Use the given XML declaration.
              -doctypedeclaration
                       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.
              -unicodestyle
                       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.
              -scriptstyle
                       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.
              -mathmlterse
                       Flatten MathML markup tersely.

   XMLModification-filterelementactiontarget
              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.
              cdataCDATA blocks.
              comment     Comments.
              object      The whole object.
              attributes  Attributes.
              container   Start and end tags.

   EFetchXMLNormalization-normalizedatabase
              Adjust XML fields to conform to common conventions.

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).

NCBI                                               2023-02-21                                       TRANSMUTE(1)

transmute-x2p|-j2ptransmute-align [-acodes][-gN][-hN][-wN]transmute-j2x(json2xml)[-settag][-rectag][-nestflat|recurse|plural|singular|depth|element]transmute-a2x[-settag][-rectag]transmute-t2x|-c2x|-s2x(tbl2xml/csv2xml/scn2xml)[-settag][-rectag][-skipN][-header][-lower|-upper][-indent|-flush]columnName1...transmute-g2x(gbf2xml)transmute-g2r(gbf2ref)transmute-r2p(ref2pmid)[-optionsconfirm|verbose|fast|slow|exact...]transmute-revcomptransmute-remove[-firstN][-lastN]transmute-retain-leadingN-trailingNtransmute-replace-offsetN|-columnN[-deleteN][-insertseq][-lower]transmute-extract[-1-based][-0-based][-lower]feat_loctransmute-cds2prot[-codeN][-frameN][-stop][-trim][-part5][-part3][-every]transmute-molwt[-met]transmute-hgvstransmute-countstransmute-difftransmute-codons-nucseq-protseq[-frameN][-three]transmute-search[-protein][-circular][-top]pattern...transmute-find[-relaxed][-sensitive][-whole]pattern...transmute-encodeXML|-decodeXML|-plainXMLtransmute-encodeURL|-decodeURLtransmute-encode64|-decode64transmute-plaintransmute-upper|-lowertransmute-aa1to3|-aa3to1transmute-relaxtransmute-format[fmt][-xmldeclaration][-doctypedeclaration][-comment][-cdata][-combine][-self][-unicodestyle][-scriptstyle][-mathmlterse]transmute-filterelementactiontargettransmute-normalizedatabase