readseq1

Reads and writes nucleic/protein sequences in various formats

Usage

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

Overview

This manual page documents briefly the readseq command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has documentation in text form, see below.

readseq reads and writes biosequences (nucleic/protein) in various formats. Data files may have multiple sequences. readseq is particularly useful as it automatically detects many sequence formats, and interconverts among them.

Formats

Formats which readseq currently understands:

* 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

See the included "Formats" file for detail on file formats.

Options

-help: Show summary of options.

-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

Pretty format options:

-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

Examples

`readseq`	-- for interactive use
`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
`readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match`	-- output to standard output a file in a pretty format
`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
`cat *.seq \| readseq -pipe -all -format=asn > bunch-of.asn`	-- pipe a bunch of data thru readseq, converting all to asn

Releases

13 releases since Debian 2.2 (Potato); the text changed 3 times.