NAME

       xtract - convert XML into a table of data values

SYNOPSIS

       xtract    [-help]    [-strict]   [-mixed]   [-accent]   [-ascii]   [-compress]   [-spaces]
       [-input filename]    [-pattern expr]    [-group expr]     [-block expr]     [-subset expr]
       [-if expr [constraint]]   [-unless expr [constraint]]   [-and condition]   [-or condition]
       [-else] [-position pos] [-equals str] [-contains str] [-starts-with str]  [-ends-with str]
       [-is-not str]  [-gt N]  [-ge N]  [-lt N]  [-le N]  [-eq N]  [-ne N]  [-ret str] [-tab str]
       [-sep str]  [-pfx str]  [-sfx str]  [-clr]   [-pfc str]   [-rst]   [-def str]   [-lbl str]
       [-element element]  [-first element] [-last element] [-NAME] [-num element] [-len element]
       [-sum element] [-min element] [-max element] [-inc element] [-dec element]  [-sub element]
       [-avg element]    [-dev element]   [-encode element]   [-upper element]   [-lower element]
       [-title element]  [-terms element]  [-words element]  [-pairs element]  [-letters element]
       [-indices element]        [-phrase str]        [-0-based element]       [-1-based element]
       [-ucsc-based element]  [-insd arg ...]   [-head str]   [-tail str]   [-hd str]   [-tl str]
       [-format fmt]    [-filter element    action target]   [-verify]   [-outline]   [-synopsis]
       [-archive directory]   [-index element]    [-flag strict|mixed|none]    [-gzip]    [-hash]
       [-skip filename] [-examples] [-extras] [-version]

DESCRIPTION

       xtract  converts  an  XML document into a table of data values according to user-specified
       rules.

OPTIONS

   Processing Flags
       -strict
              Remove HTML highlight tags.

       -mixed Allow PubMed mixed content.

       -accent
              Delete Unicode accents.

       -ascii Convert Unicode to numeric character references.

       -compress
              Compress runs of spaces.

       -spaces
              Fix non-ASCII spaces.

       -input filename
              Read XML from file instead of standard input.

   Exploration Argument Hierarchy
       -pattern expr
       -group expr
       -block expr
       -subset expr
              Name of record within set.  Use of different  argument  names  allows  command-line
              control of nested looping.

   Exploration Constructs
       Object         DateCreated
       Parent/Child   Book/AuthorList
       Heterogeneous  "PubmedArticleSet/*"
       Nested         "*/Taxon"
       Recursive      "**/Gene-commentary"

   Conditional Execution
       -if expr [constraint]
              Element (or @attribute) must exist and satisfy any specified constraint.

       -unless expr [constraint]
              Skip if element matches.

       -and condition
              Preceding and following tests must both pass.

       -or condition
              Any passing test suffices.

       -else  Execute if conditional test failed.

       -position pos
              Must be at first/last location in list.

   String Constraints
       -equals str
              String must match exactly.

       -contains str
              Substring must be present.

       -starts-with str
              Substring must be at beginning.

       -ends-with str
              Substring must be at end.

       -is-not str
              String must not match.

   Numeric Constraints
       -gt N  Greater than.

       -ge N  Greater than or equal to.

       -lt N  Less than to.

       -le N  Less than or equal to.

       -eq N  Equal to.

       -ne N  Not equal to.

   Format Customization
       -ret str
              Override line break between patterns.

       -tab str
              Replace tab character between fields.

       -sep str
              Separator between group members.

       -pfx str
              Prefix to print before group.

       -sfx str
              Suffix to print after group.

       -clr   Clear queued tab separator.

       -pfc str
              Preface combines -clr and -pfx.

       -rst   Reset -sep, -pfx, and -sfx.

       -def str
              Default placeholder for missing fields.

       -lbl str
              Insert arbitrary text.

   Element Selection
       -element element
              Print all items that match tag name.

       -first element
              Only print value of first item.

       -last element
              Only print value of last item.

       -NAME  Record value in named variable.

   -element Constructs
       Tag            Caption
       Group          Initials,LastName
       Attribute      DescriptorName@MajorTopicYN
       Recursive      "**/Gene-commentary_accession"
       Object Count   "#Author"
       Item Length    "%Title"
       Element Depth  "^PMID"
       Variable       "&NAME"

   Special -element Operations
       Parent Index   "+"
       XML Subtree    "*"
       Children       "$"
       Attributes     "@"

   Numeric Processing
       -num element
              Count.

       -len element
              Length.

       -sum element
              Sum.

       -min element
              Minimum.

       -max element
              Maximum.

       -inc element
              Increment.

       -dec element
              Decrement.

       -sub element
              Difference.

       -avg element
              Average.

       -dev element
              Deviation.

   String Processing
       -encode element
              URL-encode <, >, &, ", and ' characters.

       -upper element
              Convert text to uppercase.

       -lower element
              Convert text to lowercase.

       -title element
              Capitalize initial letters of words.

   Phrase Processing
       -terms element
              Partition phrase at spaces.

       -words element
              Split at punctuation marks.

       -pairs element
              Adjacent informative words.

       -letters element
              Separate individual letters.

       -indices element
              Experimental index generation.

   Phrase Filtering
       -phrase str
              Keep records that contain a given phrase.

   Sequence Coordinates
       -0-based element
              Zero-based.

       -1-based element
              One-based.

       -ucsc-based element
              Half-open.

   Command Generator
       -insd arg ...
              Generate  INSDSeq  extraction commands.  Print them if invoked standalone; run them
              if invoked as part of a pipeline.  Requires one or more arguments, which may appear
              in the following order:

              Descriptor(s)  INSDSeq_sequence/INSDSeq_definition/INSDSeq_division/... [...]

              Completeness   complete/partial

              Feature(s)     CDS/mRNA/...[,...]

              Qualifier(s)   INSDFeature_key/"#INSDInterval"/gene/product/... [...]

   Miscellaneous
       -head str
              Print before everything else.

       -tail str
              Print after everything else.

       -hd str
              Print before each record.

       -tl str
              Print after each record.

   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.

   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.

   Summary
       -outline
              Display outline of XML structure.

       -synopsis
              Display count of unique XML paths.

   Local Record Indexing
       -archive directory
              Base path for individual XML files.

       -index element
              Name of element to use for identifier.

       -flag strict|mixed|none

       -gzip  Use compression for local XML files.

       -hash  Print UIDs and checksum values to standard output.

       -skip filename
              File of UIDs to skip.

   Documentation
       -help  Print usage information and some example argument combinations.

       -examples
              Complete examples of edirect(1) and xtract usage.

       -extras
              Batch  and local processing examples, and a summary of specialized options the main
              -help text doesn't cover.

       -version
              Print version number.

NOTES

       String constraints use case-insensitive comparisons.

       Numeric constraints and selection arguments use integer values.

       -num and -len selections are synonyms for Object Count (#) and Item Length (%).

       -words, -pairs, and -indices convert to lower case.

SEE ALSO

       edirect(1), xy-plot(1).