--- /dev/null
+
+ * ReadSeq.Help -- 30 Dec 92
+ *
+ * Reads and writes nucleic/protein sequences in various
+ * formats. Data files may have multiple sequences.
+ *
+ * Copyright 1990 by d.g.gilbert
+ * biology dept., indiana university, bloomington, in 47405
+ * e-mail: gilbertd@bio.indiana.edu
+ *
+ * This program may be freely copied and used by anyone.
+ * Developers are encourged to incorporate parts in their
+ * programs, rather than devise their own private sequence
+ * format.
+ *
+ * This should compile and run with any ANSI C compiler.
+ * Please advise me of any bugs, additions or corrections.
+
+Readseq is particularly useful as it automatically detects many
+sequence formats, and interconverts among them.
+
+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.
+
+See the included "Formats" file for detail on file formats.
+
+
+Example usage:
+ 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
+
+
+The brief usage of readseq is as follows. The "[]" denote
+optional parts of the syntax:
+
+readseq -help
+readSeq (27Dec92), multi-format molbio sequence reader.
+usage: readseq [-options] in.seq > out.seq
+ 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 10. Olsen (in-only)
+ 2. GenBank/GB 11. Phylip3.2
+ 3. NBRF 12. Phylip
+ 4. EMBL 13. Plain/Raw
+ 5. GCG 14. PIR/CODATA
+ 6. DNAStrider 15. MSF
+ 7. Fitch 16. ASN.1
+ 8. Pearson/Fasta 17. PAUP
+ 9. Zuker 18. Pretty (out-only)
+
+ 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
+
+
+Notes:
+
+In use, readseq will respond to command line arguments, or to
+interactive use. Command line arguments cannot be combined
+but must each follow a switch character (-). In this release,
+the command line options are now words, with an equals (=)
+to separate parameter(s) fromt he command. You cannot put a
+space between a command and its parameter, as is usual for
+Unix programs (this is to preserve compatibility with VMS).
+The command line syntax of the earlier versions is still
+supported.
+
+See the file Formats for details of the sequence formats which
+are supported by readseq. The auto-detection feature of
+readseq which distinguishes these formats looks for some of the
+unique keywords and symbols that are found in each format. It
+is not infallible at this, though it attempts to exclude unknown
+formats. In general, if you feed to readseq a sequence file that
+you know is one of these common formats, you are okay. If you feed
+it data that might be oddball formats, or non-sequence data,
+you might well get garbage results. Also, different developers
+are always thinking up minor twists on these common formats
+(like PAUP requiring a blank line between blocks of Phylip format,
+or IG adding form feeds between sequences), which may cause hassles.
+
+In general, output supports only minimal subsets of each format
+needed for sequence data exchanges. Features, descriptions
+and other format-unique information is discarded.
+
+The pretty format requires additional options to generate a
+nice output. Try the various pretty options to see what you like.
+Pretty format is OUPUT only, readseq cannot read a Pretty format
+file.
+
+Readseq is NOT optimized for LARGE files. It generally makes several
+reads thru each input file (one per sequence output at present, future
+version may optimize this). It should handle input and output files
+and sequences of any size, but will slow down quite a bit for very large
+(multi megabyte) sized files. It is NOT recommended for converting
+databanks or large subsets there-of. It is primarily directed at the
+small files that researchers use to maintain their personal data, which
+they frequently need to interconvert for the various analysis programs
+which so frequently require a special format.
+
+Users of Olsen multi sequence editor (VMS). The Olsen format
+here is produced with the print command:
+ print/out=some.file
+Use Genbank output from readseq to produce a format that this
+editor can read, and use the command
+ load/genbank some.file
+Dan Davison has a VMS program that will convert to/from the
+Olsen native binary data format. E-mail davison@uh.edu
+
+Warning: Phylip format input is now supported (30Dec92), however the
+auto-detection of Phylip format is very probabilistic and messy,
+especially distinguishing sequential from interleaved versions. It
+is not recommended that one use readseq to convert files from Phylip
+format to others unless essential.
+
+
+This program is available thru Internet gopher, as
+
+ gopher ftp.bio.indiana.edu
+ browse into the IUBio-Software+Data/molbio/readseq/ folder
+ select the readseq.shar document
+
+Or thru anonymous FTP in this manner:
+ my_computer> ftp ftp.bio.indiana.edu (or IP address 129.79.224.25)
+ username: anonymous
+ password: my_username@my_computer
+ ftp> cd molbio/readseq
+ ftp> get readseq.shar
+ ftp> bye
+
+readseq.shar is a Unix shell archive of the readseq files.
+This file can be editted by any text editor to reconstitute the
+original files, for those who do not have a Unix system or an
+Unshar program. Read the top of this .shar file for further
+instructions.
+
+There are also pre-compiled executables for the following computers:
+Silicon Graphics Iris, Sparc (Sun Sparcstation & clones), VMS-Vax,
+Macintosh. Use binary ftp to transfer these, except Macintosh. The
+Mac version is just the command-line program in a window, not very
+handy.
+
+C source files:
+ readseq.c ureadseq.c ureadasn.c ureadseq.h
+
+Document files:
+ Readme (this doc)
+ Formats (description of sequence file formats)
+ add.gdemenu (GDE program users can add this to the .GDEmenu file)
+ Stdfiles -- test sequence files
+ Makefile -- Unix make file
+ Make.com -- VMS make file
+ *.std -- files for testing validity of readseq
+
+
+Recent changes (see also readseq.c for all history of changes):
+
+4 May 92
++ added 32 bit CRC checksum as alternative to GCG 6.5bit checksum
+Aug 92
+= fixed Olsen format input to handle files w/ more sequences,
+ not to mess up when more than one seq has same identifier,
+ and to convert number masks to symbols.
+= IG format fix to understand ^L
+30 Dec 92
+* revised command-line & interactive interface. Suggested form is now
+ readseq infile -format=genbank -output=outfile -item=1,3,4 ...
+ but remains compatible with prior commandlines:
+ readseq infile -f2 -ooutfile -i3 ...
++ added GCG MSF multi sequence file format
++ added PIR/CODATA format
++ added NCBI ASN.1 sequence file format
++ added Pretty, multi sequence pretty output (only)
++ added PAUP multi seq format
++ added degap option
++ added Gary Williams (GWW, G.Williams@CRC.AC.UK) reverse-complement option.
++ added support for reading Phylip formats (interleave & sequential)
+* string fixes, dropped need for compiler flags NOSTR, FIXTOUPPER, NEEDSTRCASECMP
+* changed 32bit checksum to default, -DSMALLCHECKSUM for GCG version
+
+
git://source.jalview.org / jpred.git / blobdiff