1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
|
.TH READSEQ 1
.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
.\" other parms are allowed: see man(7), man(1)
.SH NAME
readseq \- Reads and writes nucleic/protein sequences in various formats
.SH SYNOPSIS
.B readseq
.I "[-options] in.seq > out.seq"
.SH "DESCRIPTION"
This manual page documents briefly the
.BR 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.
.PP
.B readseq
reads and writes biosequences (nucleic/protein) in various formats.
Data files may have multiple sequences.
.B readseq
is particularly useful as it automatically detects many
sequence formats, and interconverts among them.
.SH FORMATS
.TP
Formats which readseq currently understands:
.PD 0
.TP
* IG/Stanford, used by Intelligenetics and others
.TP
* GenBank/GB, genbank flatfile format
.TP
* NBRF format
.TP
* EMBL, EMBL flatfile format
.TP
* GCG, single sequence format of GCG software
.TP
* DNAStrider, for common Mac program
.TP
* Fitch format, limited use
.TP
* Pearson/Fasta, a common format used by Fasta programs and others
.TP
* Zuker format, limited use. Input only.
.TP
* Olsen, format printed by Olsen VMS sequence editor. Input only.
.TP
* Phylip3.2, sequential format for Phylip programs
.TP
* Phylip, interleaved format for Phylip programs (v3.3, v3.4)
.TP
* Plain/Raw, sequence data only (no name, document, numbering)
.TP
+ MSF multi sequence format used by GCG software
.TP
+ PAUP's multiple sequence (NEXUS) format
.TP
+ PIR/CODATA format used by PIR
.TP
+ ASN.1 format used by NCBI
.TP
+ Pretty print with various options for nice looking output. Output only.
.PD 1
.TP
See the included "Formats" file for detail on file formats.
.SH OPTIONS
.PD 0
.TP
.B \-help
Show summary of options.
.TP
.B \-a[ll]
Select All sequences
.TP
.B \-c[aselower]
Change to lower case
.TP
.B \-C[ASEUPPER]
Change to UPPER CASE
.TP
.B \-degap[=-]
Remove gap symbols
.TP
.B \-i[tem=2,3,4]
Select Item number(s) from several
.TP
.B \-l[ist]
List sequences only
.TP
.B \-o[utput=]out.seq
Redirect Output
.TP
.B \-p[ipe]
Pipe (command line, <stdin, >stdout)
.TP
.B \-r[everse]
Change to Reverse-complement
.TP
.B \-v[erbose]
Verbose progress
.TP
.B \-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:
.TP
.B \-wid[th]=#
Sequence line width
.TP
.B \-tab=#
Left indent
.TP
.B \-col[space]=#
Column space within sequence line on output
.TP
.B \-gap[count]
Count gap chars in sequence numbers
.TP
.B \-nameleft, -nameright[=#]
Name on left/right side [=max width]
.TP
.B \-nametop
Name at top/bottom
.TP
.B \-numleft, -numright
Seq index on left/right side
.TP
.B \-numtop, -numbot
Index on top/bottom
.TP
.B \-match[=.]
Use match base for 2..n species
.TP
.B \-inter[line=#]
Blank line(s) between sequence blocks
.PD 1
.SH EXAMPLES
.PD 0
.TP
readseq
-- for interactive use
.TP
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
.TP
readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match
-- output to standard output a file in a pretty format
.TP
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
.TP
cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn
-- pipe a bunch of data thru readseq, converting all to asn
.PD 1
.SH "SEE ALSO"
The programs are documented fully in text form. See the files in
.I /usr/doc/readseq
.SH AUTHOR
This manual page was written by Stephane Bortzmeyer <bortzmeyer@debian.org>,
for the Debian GNU/Linux system (but may be used by others).
|
