Pretty-Printing

 Reformat XML

  -x2p

 Reformat JSON

  -j2p

 Reformat FASTA

  -f2p

 Table column alignment

  -align

    -a    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 column widths

    -g    Spacing between columns
    -h    Indent before columns
    -w    Minimum column width

Data Conversion

 JSON stream to XML

  -j2x

    -set setWrapper
    -rec recordWrapper
    -nest [flat|recurse|plural|singular|depth|element]

 ASN.1 stream to XML

  -a2x

    -set setWrapper
    -rec recordWrapper

 Tab-delimited table to XML

  -t2x

    -set setWrapper
    -rec recordWrapper
    -skip linesToSkip
    -header
    -lower | -upper
    -indent | -flush

      XML object names per column

 Comma-separated values file to XML

  -c2x

    -set setWrapper
    -rec recordWrapper
    -skip linesToSkip
    -header
    -lower | -upper
    -indent | -flush

      XML object names per column

 Configuration files to XML

  -i2x         INI format
  -m2x         TOML format
  -y2x         YAML format

 Text File Filtering

  -txf

    -pattern       Pattern at start of record
    -exclude       Reject if string is present
    -require       Require presence of string
    -min           Minimum record number
    -max           Maximum record number

 FASTA stream to XML

  -f2x

 GenBank/GenPept flatfile to INSDSeq XML

  -g2x

 GenBank/GenPept to Reference Index XML

  -g2r

 Reference Index XML Lookup to Find PMID

  -r2p

    -options [confirm|verbose|fast|slow|exact]

 GenBank/GenPept Filtering

  -gbf         Filter GenBank or GenPept flatfile release records

    -accession     Single accession
    -accessions    File of accessions
    -taxid         Single taxon identifiers
    -taxids        File of taxon identifiers
    -organism      Organism scientific name
    -exclude       Reject if string is present
    -require       Require presence of string
    -truncate      Remove features and sequence

Sequence Editing

  -revcomp     Reverse complement nucleotide sequence

  -remove      Trim at ends of sequence

    -first       Delete first N bases
    -last        Delete last N bases

  -retain      Save either end of sequence

    -leading     Keep first N bases
    -trailing    Keep last N bases

  -replace     Apply base or residue substitution

    -offset      Skip ahead by 0-based count (SPDI), or
    -column      Move just before 1-based position (HGVS)

    -delete      Delete N bases
    -insert      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

Sequence Processing

  -cds2prot    Translate coding region into protein

    -gcode       Genetic code
    -frame       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     Optional string between residues
    -all         Simultaneous 6-frame translations
    -circular    Reprocess first two priming bases at end
    -orf         Only capitalize residues at start states
    -max         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 HGVS 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         Nucleotide sequence
    -prt         Protein sequence
    -frame       Offset in nucleotide sequence
    -three       Use 3 letter residue abbreviations

Sequence Searching

  -search       Search for patterns in sequence, skips FASTA definition line,
                  each pattern can have optional alias, e.g., "GGATCC:BamHI"

    -protein      Do not expand nucleotide ambiguity characters
    -circular     Match patterns spanning origin of circular molecule
    -top          Do not search reverse-complement of non-palindromic patterns

Text Searching

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

    -relaxed      Match on words with letters and digits, ignore spacing, punctuation
    -sensitive    Case-sensitive match distinguishes upper-case and lower-case letters
    -whole        Match on whole words or multi-word phrases, also imposes -relaxed flag

String Transformations

 XML

  -encodeXML
  -decodeXML

  -plainXML

 URL

  -encodeURL
  -decodeURL

 Base64

  -encode64
  -decode64

 Accent

  -plain

 Case

  -upper
  -lower

Protein

  -aa1to3
  -aa3to1

Letters plus Digits

  -relax

Customized XML Reformatting

  -format [compact|flush|indent|expand]

    -xml
    -doctype
    -comment
    -cdata
    -combine
    -self
    -unicode [fuse|space|period|brackets|markdown|slash|tag]
    -script [brackets|markdown]
    -mathml [terse]

XML Modification

  -filter Object
            [retain|remove|encode|decode|shrink|expand|accent]
              [content|cdata|comment|object|attributes|container]

EFetch XML Normalization

  -normalize [database]

Examples

  -j2x -set - -rec GeneRec

  -t2x -set Set -rec Rec -skip 1 Code Name

  -filter ExpXml decode content

  -filter LocationHist remove object

  -normalize pubmed

  -wrp PubmedArticleSet -pattern PubmedArticle -format

Sequence Substitution

  echo ATGAAACCCGGGTTTTAG |
  transmute -replace -offset 5 -delete 1 -insert G

Protein Translation

  echo "CTAAAACCCGGGTTTCAT" |
  transmute -revcomp |
  transmute -cds2prot

Variation Extraction

  echo "NP_000504.1:p.Glu41Lys,NP_000504.1:p.P43Leu,NP_000504.1:p.Trp142Ter" |
  transmute -hgvs | transmute -format

Sequence Comparison

  transmute -diff <( echo "MKPGSQPVIY" ) <( echo "-KPGFQ*VIY" )

Translation of Coding Regions

  efetch -db nuccore -id U54469 -format gb |
  transmute -g2x |
  xtract -insd CDS sub_sequence |
  cut -f 2 |
  while read seq
  do
    echo "$seq" |
    transmute -cds2prot
    echo ""
  done

Codon Translation Reports

  efetch -db nuccore -id U54469 -format gb |
  transmute -g2x |
  xtract -insd CDS sub_sequence |
  cut -f 2 |
  while read nuc
  do
    prt=$( echo "$nuc" | transmute -cds2prot -every )
    transmute -codons -nuc "$nuc" -prt "$prt" -three
    echo ""
  done

Mitochondrial Mistranslation

  efetch -db nuccore -id NC_012920 -format gb |
  transmute -g2x |
  xtract -insd CDS gene product protein_id translation sub_sequence |
  while IFS=$'\t' read acc gene prod prid prot seq
  do
    mito=$( echo "$seq" | transmute -cds2prot -gcode 2 -stop )
    norm=$( echo "$seq" | transmute -cds2prot -gcode 1 -stop )
    if [ "$mito" != "$norm" ]
    then
      echo ">$acc $gene $prid $prod"
      transmute -diff <( echo "$mito" ) <( echo "$norm" )
      echo ""
    fi
  done

Systematic Mutations

  echo ATGAAACCCGGGTTTTAG |
  while read seq
  do
    for (( i=0; i<${#seq}; i++ ))
    do
      ch="${seq:$i:1}"
      for sub in A C G T
      do
        echo "$seq" |
        transmute -replace -offset "$i" -delete "$ch" -insert "$sub"
      done
    done
  done |
  while read seq
  do
    tns=$( echo "$seq" | transmute -cds2prot )
    mwt=$( echo "$tns" | transmute -molwt )
    echo -e "${seq}\t${tns}\t${mwt}"
  done

Sequence Search

  efetch -db nuccore -id J01749 -format fasta |
  transmute -search -circular AAGCTT:HindIII CAGCTG CTGCAG GAATTC:EcoRI GGATCC:BamHI

Nucleotide Expansion

  expanded=$(
    echo GTMKAC | disambiguate-nucleotides |
    tr '\n' ':' | sed -e 's/:/:AccI /g'
  )
  efetch -db nuccore -id J01749 -format fasta |
  transmute -search -circular "$expanded"

Minus-Strand Pattern

  efetch -db nuccore -id U00096 -format fasta |
  transmute -search -circular ATGACCATGATTACGGATT

SNP Table

  efetch -db snp -id 11549407 -format docsum |
  snp2tbl

Matching CDS/Protein Pairs

  efetch -db snp -id 11549407 -format docsum |
  snp2hgvs | hgvs2spdi | spdi2tbl |
  align-columns -g 4 | cut -c 1-78
