4 * Reads and writes nucleic/protein sequences in various
5 * formats. Data files may have multiple sequences.
7 * Copyright 1990 by d.g.gilbert
8 * biology dept., indiana university, bloomington, in 47405
9 * e-mail: gilbertd@bio.indiana.edu
11 * This program may be freely copied and used by anyone.
12 * Developers are encourged to incorporate parts in their
13 * programs, rather than devise their own private sequence
16 * This should compile and run with any ANSI C compiler.
17 * Please advise me of any bugs, additions or corrections.
19 Readseq has been updated. There have been a number of enhancements
20 and a few bug corrections since the previous general release in Nov 91
21 (see below). If you are using earlier versions, I recommend you update to
24 Readseq is particularly useful as it automatically detects many
25 sequence formats, and interconverts among them.
26 Formats added to this release include
27 + MSF multi sequence format used by GCG software
28 + PAUP's multiple sequence (NEXUS) format
29 + PIR/CODATA format used by PIR
30 + ASN.1 format used by NCBI
31 + Pretty print with various options for nice looking output.
33 As well, Phylip format can now be used as input. Options to
34 reverse-compliment and to degap sequences have been added. A menu
35 addition for users of the GDE sequence editor is included.
37 This program is available thru Internet gopher, as
39 gopher ftp.bio.indiana.edu
40 browse into the IUBio-Software+Data/molbio/readseq/ folder
41 select the readseq.shar document
43 Or thru anonymous FTP in this manner:
44 my_computer> ftp ftp.bio.indiana.edu (or IP address 129.79.224.25)
46 password: my_username@my_computer
47 ftp> cd molbio/readseq
51 readseq.shar is a Unix shell archive of the readseq files.
52 This file can be editted by any text editor to reconstitute the
53 original files, for those who do not have a Unix system or an
54 Unshar program. Read the top of this .shar file for further
57 There are also pre-compiled executables for the following computers:
58 Silicon Graphics Iris, Sparc (Sun Sparcstation & clones), VMS-Vax,
59 Macintosh. Use binary ftp to transfer these, except Macintosh. The
60 Mac version is just the command-line program in a window, not very
64 readseq.c ureadseq.c ureadasn.c ureadseq.h
67 Readseq.help (longer than this doc)
68 Formats (description of sequence file formats)
69 add.gdemenu (GDE program users can add this to the .GDEmenu file)
70 Stdfiles -- test sequence files
71 Makefile -- Unix make file
72 Make.com -- VMS make file
73 *.std -- files for testing validity of readseq
78 -- for interactive use
79 readseq my.1st.seq my.2nd.seq -all -format=genbank -output=my.gb
80 -- convert all of two input files to one genbank format output file
81 readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match
82 -- output to standard output a file in a pretty format
83 readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev
84 -- select 4 items from input, degap, reverse, and uppercase them
85 cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn
86 -- pipe a bunch of data thru readseq, converting all to asn
89 The brief usage of readseq is as follows. The "[]" denote
90 optional parts of the syntax:
93 readSeq (27Dec92), multi-format molbio sequence reader.
94 usage: readseq [-options] in.seq > out.seq
96 -a[ll] select All sequences
97 -c[aselower] change to lower case
98 -C[ASEUPPER] change to UPPER CASE
99 -degap[=-] remove gap symbols
100 -i[tem=2,3,4] select Item number(s) from several
101 -l[ist] List sequences only
102 -o[utput=]out.seq redirect Output
103 -p[ipe] Pipe (command line, <stdin, >stdout)
104 -r[everse] change to Reverse-complement
105 -v[erbose] Verbose progress
106 -f[ormat=]# Format number for output, or
107 -f[ormat=]Name Format name for output:
108 1. IG/Stanford 10. Olsen (in-only)
109 2. GenBank/GB 11. Phylip3.2
111 4. EMBL 13. Plain/Raw
112 5. GCG 14. PIR/CODATA
113 6. DNAStrider 15. MSF
115 8. Pearson/Fasta 17. PAUP
116 9. Zuker 18. Pretty (out-only)
118 Pretty format options:
119 -wid[th]=# sequence line width
121 -col[space]=# column space within sequence line on output
122 -gap[count] count gap chars in sequence numbers
123 -nameleft, -nameright[=#] name on left/right side [=max width]
124 -nametop name at top/bottom
125 -numleft, -numright seq index on left/right side
126 -numtop, -numbot index on top/bottom
127 -match[=.] use match base for 2..n species
128 -inter[line=#] blank line(s) between sequence blocks
135 + added 32 bit CRC checksum as alternative to GCG 6.5bit checksum
137 = fixed Olsen format input to handle files w/ more sequences,
138 not to mess up when more than one seq has same identifier,
139 and to convert number masks to symbols.
140 = IG format fix to understand ^L
142 * revised command-line & interactive interface. Suggested form is now
143 readseq infile -format=genbank -output=outfile -item=1,3,4 ...
144 but remains compatible with prior commandlines:
145 readseq infile -f2 -ooutfile -i3 ...
146 + added GCG MSF multi sequence file format
147 + added PIR/CODATA format
148 + added NCBI ASN.1 sequence file format
149 + added Pretty, multi sequence pretty output (only)
150 + added PAUP multi seq format
152 + added Gary Williams (GWW, G.Williams@CRC.AC.UK) reverse-complement option.
153 + added support for reading Phylip formats (interleave & sequential)
154 * string fixes, dropped need for compiler flags NOSTR, FIXTOUPPER, NEEDSTRCASECMP
155 * changed 32bit checksum to default, -DSMALLCHECKSUM for GCG version
158 = reverted Genbank output format to fixed left margin
159 (change in 30 Dec release), so GDE and others relying on fixed margin