Provided by: ncbi-entrez-direct_19.0.20230216+dfsg-2_amd64 bug

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).