Provided by: ncbi-entrez-direct_14.6.20210224+dfsg-5ubuntu0.3_amd64 
NAME
xtract - NCBI Entrez Direct XML conversion and transformation tool
SYNOPSIS
xtract [-help] [-strict] [-mixed] [-accent] [-ascii] [-compress] [-stops]
[-input filename] [-transform filename] [-pattern expr] [-group expr] [-block expr]
[-subset expr] [-path path] [-if expr [constraint]] [-unless expr [constraint]]
[-and condition] [-or condition] [-else] [-position pos] [-equals str] [-contains str]
[-is-within str] [-starts-with str] [-ends-with str] [-is-not str] [-is-before str]
[-is-after str] [-matches str] [-resembles str] [-is-equal-to expr] [-differs-from expr]
[-gt N] [-ge N] [-lt N] [-le N] [-eq N] [-ne N] [-ret str] [-tab str] [-sep str]
[-pfx str] [-sfx str] [-rst] [-clr] [-pfc str] [-deq str] [-def str] [-lbl str] [-set tag]
[-rec tag] [-wrp tag] [-enc tag] [-plg str] [-elg str] [-pkg tag] [-fwd str] [-awd str]
[-element element] [-first element] [-last element] [-NAME] [--STATS] [-num element]
[-len element] [-sum element] [-min element] [-max element] [-inc element] [-dec element]
[-sub element] [-avg element] [-dev element] [-med element] [-mul element] [-div element]
[-mod element] [-bin element] [-bit element] [-encode element] [-plain element]
[-upper element] [-lower element] [-chain element] [-title element] [-year element]
[-doi element] [-translate element] [-terms element] [-words element] [-pairs element]
[-order element] [-reverse element] [-letters element] [-clauses element] [-replace
-reg target -exp replacement] [-revcomp] [-nucleic] [-fasta] [-ncbi2na] [-ncbi4na]
[-molwt] [-0-based element] [-1-based element] [-ucsc-based element] [-insd arg ...]
[-histogram] [-e2index] [-indices element] [-head str] [-tail str] [-hd str] [-tl str]
[-select condition] [-in filename] [-sort element] [-format fmt [-unicode style]]
[-verify] [-outline] [-synopsis] [-contour [delimiter]] [-examples] [-unix] [-version]
DESCRIPTION
xtract converts an XML document into a table of data values according to user-specified
rules.
OPTIONS
Processing Flags
-strict
Remove HTML and MathML tags.
-mixed Allow mixed content XML.
-accent
Delete Unicode accents and diacritical marks.
-ascii Convert Unicode to numeric HTML character entities.
-compress
Compress runs of spaces.
-stops Retain stop words in selected phrases.
Data Source
-input filename
Read XML from file instead of standard input.
-transform filename
File of substitutions for -translate.
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.
Path Navigation
-path path
Explore by list of adjacent object names.
Exploration Constructs
Object DateRevised
Parent/Child Book/AuthorList
Path MedlineCitation/Article/Journal/JournalIssue/PubDate
Heterogeneous "PubmedArticleSet/*"
Exhaustive "History/**"
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
first/last/outer/inner/even/odd/all.
String Constraints
-equals str
String must match exactly.
-contains str
Substring must be present.
-is-within str
String 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.
-is-before str
First string < second string.
-is-after str
First string > second string.
-matches str
Matches without commas or semicolons.
-resembles str
Requires all words, but in any order.
Object Constraints
-is-equal-to expr
Object values must match.
-differs-from expr
Object values must differ.
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.
-rst Reset -sep through -elg.
-clr Clear queued tab separator.
-pfc str
Preface combines -clr and -pfx.
-deq str
Delete and replace queued tab separator.
-def str
Default placeholder for missing fields.
-lbl str
Insert arbitrary text.
XML Generation
-set tag
XML tag for entire set.
-rec tag
XML tag for each record.
-wrp tag
Wrap elements in XML object.
-enc tag
Encase instance in XML object.
-plg str
Prologue to print before instance.
-elg str
Epilogue to print after instance.
-pkg tag
Package subset in XML object.
-fwd str
Foreword to print before subset.
-awd str
Afterword to print after subset.
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.
--STATS
Accumulate values into variable.
-element Constructs
Tag Caption
Group Initials,LastName
Parent/Child MedlineCitation/PMID
Recursive "**/Gene-commentary_accession"
Unrestricted PubDate/*
Attribute DescriptorName@MajorTopicYN
Range MedlineDate[1:4]
Substring "Title[phospholipase | rattlesnake]"
Object Count "#Author"
Item Length "%Title"
Element Depth "^PMID"
Variable "&NAME"
Special -element Operations
Parent Index "+"
Object Name "+"
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.
-med element
Median.
-mul element
Product.
-div element
Quotient.
-mod element
Remainder.
-bin element
Binary.
-bit element
Bit count.
String Processing
-encode element
XML-encode <, >, &, ", and ' characters.
-plain element
Remove embedded mixed-content markup tags.
-upper element
Convert text to uppercase.
-lower element
Convert text to lowercase.
-chain element
Change spaces to underscores.
-title element
Capitalize initial letters of words.
-year element
Extract first 4-digit year from string.
-doi element
Add https://doi.org/ prefix, URL encode.
-translate element
Substitute values with -transform table.
Text Processing
-terms element
Partition text at spaces.
-words element
Split at punctuation marks.
-pairs element
Adjacent informative words.
-order element
Rearrange words in sorted order.
-reverse element
Reverse words in string.
-letters element
Separate individual letters.
-clauses element
Break at phrase separators.
Regular Expression
-replace
Substitute text using regular expressions.
-reg target Target expression.
-exp pattern Replacement pattern.
Sequence Processing
-revcomp
Reverse complement nucleotide sequence.
-nucleic
Subrange determines forward or revcomp.
-fasta Split sequence into blocks of 50 letters.
-ncbi2na
Expand ncbi2na to IUPAC. (May need to truncate result to actual sequence length.)
-ncbi4na
Expand ncbi4na to IUPAC. (May need to truncate result to actual sequence length.)
-molwt Calculate molecular weight of peptide.
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/
feat_location/sub_sequence/... [...]
Frequency Table
-histogram
Collects data for sort-uniq-count(1) on entire set of records.
Entrez Indexing
-e2index
Create Entrez index XML.
-indices element
Index normalized words.
Output Organization
-head str
Print before everything else.
-tail str
Print after everything else.
-hd str
Print before each record.
-tl str
Print after each record.
Record Selection
-select condition
Select record subset by conditions.
-in filename
File of identifiers to use for selection.
Record Rearrangement
-sort element
Element to use as sort key.
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.
Validation
-verify
Report XML data integrity problems.
Summary
-outline
Display outline of XML structure.
-synopsis
Display individual XML paths.
-contour [delimiter]
Display XML paths to leaf nodes (delimited by / by default).
Documentation
-help Print usage information and some example argument combinations.
-examples
Complete examples of edirect(1) and xtract usage.
-unix Illustrate common Unix command arguments.
-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
download-ncbi-data(1), edirect(1), esample(1), index-extras(1), index-pubmed(1),
pm-index(1), pm-invert(1), pm-stash(1), rchive(1), sort-uniq-count(1), transmute(1),
xml2tbl(1), xy-plot(1).