READSEQ(1)

💖 NAME 💖

readseq — bestie, this girl reads and writes nucleic/protein sequences in various formats. that's it, that's the whole job, and she does it flawlessly 💅

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✨ SYNOPSIS ✨

readseq [-options] in.seq > out.seq

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🦋 DESCRIPTION 🦋

okay so first thing, this manual page is just a lil brief overview of the readseq command — it got written for the Debian GNU/Linux distribution because the original program literally does not ship a manual page, no cap. instead it has documentation in text form, see below 👇

now the actual tea: readseq reads and writes biosequences (nucleic/protein) in various formats. data files may have multiple sequences in them, and that's fine, she handles it. the reason readseq is so iconic is that she automatically detects a ton of sequence formats and interconverts among them. she just knows. iykyk 🧚

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🌸 FORMATS 🌸

these are the formats readseq currently understands, and yes she understands all of them:

• * IG/Stanford, used by Intelligenetics and others
• * GenBank/GB, genbank flatfile format
• * NBRF format
• * EMBL, EMBL flatfile format
• * GCG, single sequence format of GCG software
• * DNAStrider, for common Mac program
• * Fitch format, limited use
• * Pearson/Fasta, a common format used by Fasta programs and others
• * Zuker format, limited use. Input only.
• * Olsen, format printed by Olsen VMS sequence editor. Input only.
• * Phylip3.2, sequential format for Phylip programs
• * Phylip, interleaved format for Phylip programs (v3.3, v3.4)
• * Plain/Raw, sequence data only (no name, document, numbering)
• + MSF multi sequence format used by GCG software
• + PAUP's multiple sequence (NEXUS) format
• + PIR/CODATA format used by PIR
• + ASN.1 format used by NCBI
• + Pretty print with various options for nice looking output. Output only.
• + LinAll format, limited use (LinAll and ConStruct programs)
• + Vienna format used by ViennaRNA programs

psst — the * ones and the + ones are listed with different markers in the original, and a couple of the * entries are flagged Input only / Output only right in their descriptions. read those flags, they matter 💀

see the included Formats file for detail on file formats. it's giving homework but it's worth it 📚

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👑 OPTIONS 👑

• -help — show summary of options. the "help me bestie" button 🫶
• -a[ll] — Select All sequences
• -c[aselower] — Change to lower case
• -C[ASEUPPER] — Change to UPPER CASE
• -degap[=-] — Remove gap symbols
• -i[tem=2,3,4] — Select Item number(s) from several
• -l[ist] — List sequences only
• -o[utput=]out.seq — Redirect Output
• -p[ipe] — Pipe (command line, <stdin, >stdout)
• -r[everse] — Change to Reverse-complement
• -v[erbose] — Verbose progress
• -f[ormat=]# — Format number for output, or
• -f[ormat=]Name — Format name for output:

 1. IG/Stanford           11. Phylip3.2
 2. GenBank/GB            12. Phylip
 3. NBRF                  13. Plain/Raw
 4. EMBL                  14. PIR/CODATA
 5. GCG                   15. MSF
 6. DNAStrider            16. ASN.1
 7. Fitch                 17. PAUP/NEXUS
 8. Pearson/Fasta         18. Pretty (out-only)
 9. Zuker (in-only)       19. LinAll
10. Olsen (in-only)       20. Vienna

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🎀 Pretty format options 🎀

(yes, only the pretty ones get their own little section, they're the main characters ✨)

• -wid[th]=# — Sequence line width
• -tab=# — Left indent
• -col[space]=# — Column space within sequence line on output
• -gap[count] — Count gap chars in sequence numbers
• -nameleft, -nameright[=#] — Name on left/right side [=max width]
• -nametop — Name at top/bottom
• -numleft, -numright — Seq index on left/right side
• -numtop, -numbot — Index on top/bottom
• -match[=.] — Use match base for 2..n species
• -inter[line=#] — Blank line(s) between sequence blocks

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🔥 EXAMPLES 🔥

the receipts, bestie. watch and learn 👀

readseq

-- for interactive use

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readseq my.1st.seq  my.2nd.seq  -all  -format=genbank  -output=my.gb

-- convert all of two input files to one genbank format output file

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readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match

-- output to standard output a file in a pretty format

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readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev

-- select 4 items from input, degap, reverse, and uppercase them

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cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn

-- pipe a bunch of data thru readseq, converting all to asn

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⭐ SEE ALSO ⭐

The programs are documented fully in text form. See the files in

/usr/share/doc/readseq

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💜 AUTHOR 💜

This manual page was written by Stephane Bortzmeyer <bortzmeyer@debian.org>, for the Debian GNU/Linux system (but may be used by others).

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and that's the whole page bestie — this was readseq(1) from the General Commands Manual, and you're officially in the know now. go forth and convert sequences, you absolute icon 👑💖 bye ✨