Provided by: ncbi-entrez-direct_7.40.20170928+ds-1_amd64 
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).