transmute1

Pretty-Printing

-x2p

Reformat XML.

-j2p

Reformat JSON.

-f2p

Reformat FASTA.

-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.

m

Commas to group by 3 digits.

M

Commas plus zero-pad decimals.

w

Just print colum widths.

-g N

Spacing between columns.

-h N

Indentation before columns.

-w N

Minimum column width.

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|singular|depth|element

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, -s2x

Convert tab-delimited table, comma-separated values file, or semicolon-delimited table, 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.

-i2x

Convert .ini configuration file format to XML.

-m2x

Convert TOML configuration file format to XML.

-y2x

Convert YAML configuration file format to XML.

-txf

Text file filtering.

-pattern str

Pattern at start of record.

-exclude str

Reject if string is present.

-require str

Require presence of string.

-min N

Minimum record number.

-max N

Maximum record number.

-f2x

Convert a FASTA stream to corresponding XML.

-g2x

Convert GenBank/GenPept flatfile format to INSDSeq XML.

-g2r

Convert GenBank/GenPept flatfile format to Reference XML.

-r2p [-options option ...]

Reference Index XML lookup to find PMIDs. Supported option values:

confirm

Recheck existing PMID claims.

verbose

Add NOTE nodes explaining reasoning.

fast

Prefilter candidates relatively heavily (default).

slow

Prefilter candidates less heavily.

exact

Require exact, unique title matches.

-gbf

GenBank/GenPept filtering.

-accession acc

Single accession.

-accessions file

File of accessions.

-taxid id

Single taxon identifier.

-taxids file

File of taxon identifiers.

-organism name

Organism scientific name.

-exclude str

Reject if string is present.

-require str

Require presence of string.

-truncate

Remove features and sequence.

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.

-lower

Lower-case original sequence.

-extract

Use xtract -insd ... feat_location instructions.

-1-based

GenBank feat_location convention.

-0-based

Alignment, or -insd feat_intervals.

-lower

Lower-case extracted sequence.

feat_loc

Feature location.

Sequence Processing

-cds2prot

Translate coding region into protein.

-gcode N

Genetic code (1 by default).

-frame N

Offset in sequence (0-based).

-stop

Include stop residue.

-trim

Remove trailing Xs and *s.

-part5

CDS partial at 5' end.

-part3

CDS extends past 3' end.

-every

Translate all codons.

-between str

Optional string between residues.

-all

Simultaneous six-frame translations.

-circular

Reprocess first two priming bases at end.

-orf

Only capitalize residues at start states.

-max N

Number of residues per line.

-molwt

Calculate molecular weight of peptide.

-met

Do not cleave leading methionine.

-fmet

Retain leading formyl-methionine.

Variation Processing

-hgvs

Convert Human Genome Variation Society variation format to XML.

Sequence Comparison

-counts

Print summary of base or residue counts.

-diff

Compare two aligned files for point differences.

-codons

Display nucleotide codons above amino acid residues.

-nuc seq

Nucleotide sequence.

-prot seq

Protein sequence.

[-frame N]

Offset in nucleotide sequence.

[-three]

Use three-letter residue abbreviations.

Sequence Searching

-search

Search for one or more patterns in a sequence, skipping any FASTA definition line (with a leading >). Each pattern can have an optional alias, e.g., GGATCC:BamHI.

-protein

Do not expand nucleotide ambiguity characters.

-circular

Match patterns spanning the origin of a circular molecule.

-top

Do not search reverse complements of non-palindromic patterns.

pattern

Pattern to search for.

Text Searching

-find

Find one or more patterns in text, allowing digits, spaces, punctuation, and phrases, e.g., "double, double toil and trouble".

-relaxed

Match on words with letters and digits, ignoring spacing and punctuation.

-sensitive

Case-sensitive match, distinguishing upper-case and lower-case letters.

-whole

Match on whole words or multi-word phrases; implies -relaxed.

pattern

Pattern to search for.

String Transformations

XML

-encodeXML

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

-decodeXML

Decode XML entity references.

-plainXML

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

URL

-encodeURL

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

-decodeURL

URI-unescape the input.

Base64

-encode64

Base64-encode the input.

-decode64

Base64-decode the input.

Accent

-plain

Strip accents from the input.

Case

-upper

Convert the input to uppercase.

-lower

Convert the input to lowercase.

Protein

-aa1to3

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

-aa3to1

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

Letters plus Digits

-relax

Remove all punctuation and compress whitespace.

Customized XML Reformatting

-format [fmt]

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.

-combine

If the input contains multiple top-level documents, combine them.

-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.