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
       -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
              -g N     Spacing between columns
              -h N     Indentation before columns

   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|depth
                     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
              Convert tab-delimited table or comma-separated values file, 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 flatfile format to INSDSeq XML.

   Sequence Comparison
       -diff  Compare two aligned files for point differences.

   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.

       -extract feat_loc
                 Use xtract -insd ... feat_location instructions.

   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.
                 -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.

   String Transformations
       -encodeXML  XML-encode <, >, &, ", and ' characters.

       -decodeXML  Decode XML entity references.

       -plainXML   Remove embedded mixed-content tags and compress runs of spaces.

       -encodeURL  Compress runs of spaces, and URI-escape the result.

       -decodeURL  URI-unescape the input.

       -encode64   Base64-encode the input.

       -decode64   Base64-decode the input.

   Protein
       -aa1to3  Convert amino acids from 1-character to 3-character format.

       -aa3to1  Convert amino acids from 3-character to 1-character format.

   Customized XML Reformatting
       -format fmt
              copy     Fast block copy (still applies processing flags).
              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.
              -separate
                       If the input contains multiple top-level documents, keep them separate.
              -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

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