XTRACT(1) NCBI Entrez Direct User's Manual XTRACT(1)

xtract - NCBI Entrez Direct XML conversion and transformation tool

xtract [-help] [-strict] [-mixed] [-self] [-accent] [-ascii] [-compress] [-stops] [-input filename] [-transform filename] [-aliases 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] [-includes 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] [-tag tag] [-att key value] [-cls] [-slf] [-end tag] [-element element] [-first element] [-last element] [-backward element] [-NAME] [--STATS] [-num element] [-len element] [-sum element] [-acc 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] [-oct element] [-hex element] [-bit element] [-pad element] [-encode element] [-upper element] [-lower element] [-chain element] [-title element] [-mirror element] [-alnum element] [-basic element] [-plain element] [-simple element] [-author element] [-prose element] [-terms element] [-words element] [-pairs element] [-order element] [-reverse element] [-letters element] [-clauses element] [-year element] [-month element] [-date element] [-page element] [-auth element] [-initials element] [-jour element] [-trim element] [-wct element] [-doi element] [-translate element] [-classify 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 [extras]] [-indices element] [-article element] [-abstract element] [-paragraph element] [-stemmed element] [-head str] [-tail str] [-hd str] [-tl str] [-select condition] [-in filename] [-sort[-fwd] element] [-sort-rev element] [-format fmt [-unicode style]] [-verify] [-outline] [-synopsis] [-contour [delimiter]] [-examples] [-unix] [-version]

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

Remove HTML and MathML tags.
Allow mixed content XML.
Allow detection of empty self-closing tags.
Delete Unicode accents and diacritical marks.
Convert Unicode to numeric HTML character entities.
Compress runs of spaces.
Retain stop words in selected phrases.

Read XML from file instead of standard input.
File of substitutions for -translate.
Mappings file for -classify operation.

Name of record within set. Use of different argument names allows command-line control of nested looping.

Explore by list of adjacent object names.

DateRevised
Book/AuthorList
MedlineCitation/Article/Journal/JournalIssue/PubDate
"PubmedArticleSet/*"
"History/**"
"*/Taxon"

Element (or @attribute) must exist and satisfy any specified constraint.
Skip if element matches.
Preceding and following tests must both pass.
Any passing test suffices.
Execute if conditional test failed.
first/last/outer/inner/even/odd/all.

String must match exactly.
Substring must be present.
Substring must match at word boundaries.
String must be present.
Substring must be at beginning.
Substring must be at end.
String must not match.
First string < second string.
First string > second string.
Matches without commas or semicolons.
Requires all words, but in any order.

Object values must match.
Object values must differ.

Greater than.
Greater than or equal to.
Less than to.
Less than or equal to.
Equal to.
Not equal to.

Override line break between patterns.
Replace tab character between fields.
Separator between group members.
Prefix to print before group.
Suffix to print after group.
Reset -sep through -elg.
Clear queued tab separator.
Preface combines -clr and -pfx.
Delete and replace queued tab separator.
Default placeholder for missing fields.
Insert arbitrary text.

XML tag for entire set.
XML tag for each record.
Wrap elements in XML object.
Encase instance in XML object.
Prologue to print before instance.
Epilogue to print after instance.
Package subset in XML object.
Foreword to print before subset.
Afterword to print after subset.

Start with <tag.
Attribute key and value.
Close with >.
Self-close with />.
End contents with </tag>.

Print all items that match tag name.
Only print value of first item.
Only print value of last item.
Print values in reverse order.
-NAME
Record value in named variable.
Accumulate values into variable.

-element Constructs

Caption
Initials,LastName
MedlineCitation/PMID
"**/Gene-commentary_accession"
PubDate/*
DescriptorName@MajorTopicYN
MedlineDate[1:4]
"Title[phospholipase | rattlesnake]"
Object Count
"#Author"
"%Title"
"^PMID"
"&NAME"

"+"
Object Name
"?"
Object Value
"~"
"*"
"$"
"@"
"."
"%"

Count.
Length.
Sum.
Accumulator.
Minimum.
Maximum.
Increment.
Decrement.
Difference.
Average.
Deviation.
Median.
Product.
Quotient.
Remainder.
Binary.
Octal.
Hexadecimal.
Bit count.
Zero-pad to eight digits.

XML-encode <, >, &, ", and ' characters.
Convert text to uppercase.
Convert text to lowercase.
Change spaces to underscores.
Capitalize initial letters of words.
Reverse order of letters.
Non-alphanumeric characters to space.

Convert superscripts and subscripts.
Remove embedded mixed-content markup tags.
Normalize accented letters; spell Greek letters.
Multi-step author cleanup.
Text conversion to ASCII.

Partition text at spaces.
Split at punctuation marks.
Adjacent informative words.
Rearrange words in sorted order.
Reverse words in string.
Separate individual letters.
Break at phrase separators.

Extract first 4-digit year from string.
Match first month name and return a corresponding integer.
YYYY/MM/DD from -unit "PubDate" -date "*"
Get digits (and letters) of first page number.
Change GenBank authors to Medline form.
Parse initials from forename or given name.
Clean up journal name punctuation.
Remove extra spaces and leading zeros.
Count number of -words in a string.
Add https://doi.org/ prefix, URL encode.

Substitute values with -transform table.
Substring word or phrase matches to -aliases table.

Substitute text using regular expressions.
Target expression.
Replacement pattern.

Reverse complement nucleotide sequence.
Subrange determines forward or revcomp.
Split sequence into blocks of 70 uppercase letters.
Expand ncbi2na to IUPAC. (May need to truncate result to actual sequence length.)
Expand ncbi4na to IUPAC. (May need to truncate result to actual sequence length.)
Calculate molecular weight of peptide.

-0-based element
Zero-based.
-1-based element
One-based.
Half-open.

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:
INSDSeq_sequence/INSDSeq_definition/INSDSeq_division/... [...]
complete/partial
CDS/mRNA/...[,...]
INSDFeature_key/"#INSDInterval"/gene/product/feat_location/sub_sequence/... [...]

Collects data for sort-uniq-count(1) on entire set of records.

Create Entrez index XML. extras (true or false; false by default) indicates whether to index extra fields.
Index normalized words.
Title positional index.
Abstract positional index.
Index text paragraphs.
Apply Porter2 algorithm.

Print before everything else.
Print after everything else.
Print before each record.
Print after each record.

Select record subset by conditions.
File of identifiers to use for selection.

Element to use as sort key.
Sort records in reverse order.

Fast block copy (still applies processing flags).
Compress runs of spaces.
Suppress line indentation.
Indent according to nesting depth.
Place each attribute on a separate line.

Report XML data integrity problems.

Display outline of XML structure.
Display individual XML paths.
Display XML paths to leaf nodes (delimited by / by default).

Print usage information and some example argument combinations.
Complete usage examples, involving additional Entrez Direct tools.
Illustrate common Unix command arguments.
Print version number.

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.

archive-pmc(1), archive-pubmed(1), custom-index(1), disambiguate-nucleotides(1), download-ncbi-data(1), ds2pme(1), esample(1), fetch-pmc(1), fetch-pubmed(1), find-in-gene(1), fuse-segments(1), gene2range(1), hgvs2spdi(1), index-extras(1), index-pubmed(1), pma2pme(1), rchive(1), snp2hgvs(1), snp2tbl(1), sort-uniq-count(1), spdi2tbl(1), tbl2prod(1), transmute(1), uniq-table(1), xml2fsa(1), xml2tbl(1), xy-plot(1).

2023-03-31 NCBI