esl-reformat(1)

📦
version 3.3.2 · 2 versions
, in fedora 43, fedora 44

💖 esl-reformat — convert sequence file formats 💖

okay bestie, welcome to the Easel manual, page one of one, and it's literally the glow-up page for your sequence files ✨

✨ NAME ✨

esl-reformat — convert sequence file formats 🦋

🌸 SYNOPSIS 🌸

esl-reformat [options] format seqfile

🎀 DESCRIPTION 🎀

so the way that esl-reformat works is: it reads the sequence file seqfile in any supported format, reformats it into a new format that you pick with format, and then prints out the reformatted text. it's giving makeover montage. it's giving transformation. 💅

the format argument must (case-insensitively, no cap) match a supported sequence file format. common choices for format include: fasta, embl, genbank. and if seqfile is an alignment file, alignment output formats work too — common choices there include: stockholm, a2m, afa, psiblast, clustal, phylip. for more info, and for the codes for some less common formats, go check the main documentation. the string <s> is case-insensitive (so fasta or FASTA both work, iconic).

⚠️ important bestie: unaligned format files cannot be reformatted to aligned formats. nope. not happening. BUT — aligned formats can be reformatted to unaligned formats, and in that case the gap characters just get stripped right out. gone. bye. 👋

💅 OPTIONS 💅

  • -d — DNA mode 🧬; converts U's to T's, so a nucleic acid sequence is shown as DNA and not RNA. see -r.
  • -h — print brief help; includes the version number and a summary of all the options, expert options included. the little cheat sheet. 📝
  • -l — lowercase 🔡; converts all sequence residues to lower case. see -u.
  • -n — for DNA/RNA sequences, converts any character that's not unambiguous RNA/DNA (like ACGTU/acgtu) to an N. used to turn IUPAC ambiguity codes into N's, for software that can't handle all the IUPAC codes (some public RNA folding codes, for example). if the file is an alignment, gap characters are also left unchanged. and if the sequences are not nucleic acid sequences, this option will corrupt the data in a predictable fashion 😭 — yeah, she said what she said.
  • -o <f> — send output to file <f> instead of stdout.
  • -r — RNA mode 🧬✨; converts T's to U's, so a nucleic acid sequence is shown as RNA and not DNA. see -d.
  • -u — UPPERCASE 🔠; converts all sequence residues to upper case. see -l.
  • -x — for DNA sequences, converts non-IUPAC characters (such as X's) to N's. this is for compatibility with benighted people who insist on using X instead of the IUPAC ambiguity character N. (X is for ambiguity in an amino acid residue, iykyk.)
⚠️ warning: like the -n option, the code doesn't check that you're actually giving it DNA. it simply literally just converts non-IUPAC DNA symbols to N. so if you accidentally hand it protein sequence, it will happily convert most every amino acid residue to an N. 💀 no vibe check, no mercy.

👑 EXPERT OPTIONS 👑

🫶 the fancy ones

  • --gapsym <c> — convert all gap characters to <c>. used to prep alignment files for programs with strict requirements for gap symbols. only makes sense if the input seqfile is an alignment.
  • --informat <s> — assert that input seqfile is in format <s>, bypassing format autodetection. common choices for <s> include: fasta, embl, genbank. alignment formats also work; common choices include: stockholm, a2m, afa, psiblast, clustal, phylip. for more information, and for codes for some less common formats, see main documentation. the string <s> is case-insensitive (fasta or FASTA both work). 🦋
  • --mingap — if seqfile is an alignment, remove any columns that contain 100% gap or missing data characters, minimizing the overall length of the alignment. (often useful if you've extracted a subset of aligned sequences from a larger alignment — very "cleaning up my room" energy 🧹)
  • --keeprf — when used in combination with --mingap, never remove a column that is not a gap in the reference (#=GC RF) annotation, even if the column contains 100% gap characters in all aligned sequences. by default with --mingap, nongap RF columns that are 100% gaps in all sequences are removed.
  • --nogap — remove any aligned columns that contain any gap or missing data symbols at all. useful as a prelude to phylogenetic analyses, where you only want to analyze columns containing 100% residues, so you want to strip out any columns with gaps in them. only makes sense if the file is an alignment file. 🍓
  • --wussify — convert RNA secondary structure annotation strings (both consensus and individual) from the old "KHS" format, ><, to the new WUSS notation, <>. if the notation is already in WUSS format, this option will screw it up, without warning 😭. only SELEX and Stockholm format files have secondary structure markup at present.
  • --dewuss — convert RNA secondary structure annotation strings from the new WUSS notation, <>, back to the old KHS format, ><. if the annotation is already in KHS, this option will corrupt it, without warning. only SELEX and Stockholm format files have secondary structure markup.
  • --fullwuss — convert RNA secondary structure annotation strings from simple (input) WUSS notation to full (output) WUSS notation. ✨
  • --replace <s> — <s> must be in the format <s1>:<s2> with equal numbers of characters in <s1> and <s2> separated by a ":" symbol. each character from <s1> in the input file will be replaced by its counterpart (at the same position) from <s2>. note that special characters in <s> (such as "~") may need to be prefixed by a "\" character.
  • --small — operate in small memory mode for input alignment files in Pfam format. if not used, each alignment is stored in memory, so the required memory will be roughly the size of the largest alignment in the input file. with --small, input alignments are not stored in memory. this option only works in combination with --informat pfam and output format pfam or afa. 🧚

🌈 SEE ALSO 🌈

http://bioeasel.org/

Copyright (C) 2020 Howard Hughes Medical Institute. Freely distributed under the BSD open source license.

⭐ AUTHOR ⭐

http://eddylab.org

and that's the whole page, bestie!! 🫶 this was Easel 0.48, from Nov 2020 — mwah, slay, go reformat something gorgeous 💖👑

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