Package list tigr-glimmer / d494af1
Moved scripts to debian/bin to avoid name conflict with package target dir, removed redundant index.html which is a copy of tigr-extract(1); enhanced README.Debian Andreas Tille 13 years ago
7 changed file(s) with 51 addition(s) and 213 deletion(s). Raw diff Collapse all Expand all
1010
1111 In version 2.13-1, the binaries and man pages all have a prefix "tigr-"
1212 to avoid conflicts with other programs, with extract in particular.
13 This was changed
13 This was changed in the current packaging of version 3.x in favour of
14 putting the executables under /usr/lib/tigr-glimmer. A wrapper is
15 provided that enables to call the binaries via
16
17 tigr-glimmer <binary>
18
19 (see man tigr-glimmer). Alternatively you might add this directory
20 to your search PATH to call the binaries directly.
1421
1522 -- Steffen Moeller <moeller@debian.org>, Thu, 10 Nov 2004 12:33:46 +0100
0 #!/bin/sh
1
2 BINDIR=/usr/lib/tigr-glimmer
3
4 if [ $# -lt 1 ] ; then
5 echo "Usage: $0 <program>" 1>&2
6 echo " Existing programs are:"
7 ls ${BINDIR}
8 exit 1
9 fi
10
11 WRAPPER=$0
12 PROGRAM=$1
13 shift
14 ARGS=$*
15
16 if [ -x ${BINDIR}/${PROGRAM} ]; then
17 exec ${BINDIR}/${PROGRAM} ${ARGS}
18 else
19 echo "Usage: ${PROGRAM} does not exist in Tigr Glimmer"
20 echo " Existing programs are:"
21 ls ${BINDIR}
22 exit 1
23 fi
0 #!/bin/sh
1 echo "run Glimmer3"
2 clear
3 echo "Genome is " $1
4 echo "Find non-overlapping orfs in tmp.coord"
5 BINDIR="/usr/lib/tigr-glimmer"
6 rm -f tmp.coord
7 ${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord
8 echo "Extract training sequences to tmp.train"
9 rm -f tmp.train
10 ${BINDIR}/extract $1 tmp.coord >tmp.train
11 wc tmp.train
12 echo "Build interpolated context model in tmp.model"
13 rm -f tmp.model
14 ${BINDIR}/build-icm <tmp.train >tmp.model
15 echo "Predict genes with Glimmer3 with coordinates in g3.coord"
16 rm -f g3.coord
17 ${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord
+0
-168
debian/index.html less more
0 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
1 <HTML
2 ><HEAD
3 ><TITLE
4 >EXTRACT</TITLE
5 ><META
6 NAME="GENERATOR"
7 CONTENT="Modular DocBook HTML Stylesheet Version 1.7"></HEAD
8 ><BODY
9 CLASS="REFENTRY"
10 BGCOLOR="#FFFFFF"
11 TEXT="#000000"
12 LINK="#0000FF"
13 VLINK="#840084"
14 ALINK="#0000FF"
15 ><H1
16 ><A
17 NAME="AEN1"
18 ></A
19 >EXTRACT</H1
20 ><DIV
21 CLASS="REFNAMEDIV"
22 ><A
23 NAME="AEN15"
24 ></A
25 ><H2
26 >Name</H2
27 >extract&nbsp;--&nbsp;Fine start/stop positions of genes in genome sequence</DIV
28 ><DIV
29 CLASS="REFSYNOPSISDIV"
30 ><A
31 NAME="AEN18"
32 ></A
33 ><H2
34 >Synopsis</H2
35 ><P
36 ><B
37 CLASS="COMMAND"
38 >long-orgs</B
39 > [genome-file <VAR
40 CLASS="OPTION"
41 ><VAR
42 CLASS="REPLACEABLE"
43 >options</VAR
44 ></VAR
45 >]</P
46 ></DIV
47 ><DIV
48 CLASS="REFSECT1"
49 ><A
50 NAME="AEN24"
51 ></A
52 ><H2
53 >DESCRIPTION</H2
54 ><P
55 >Program extract takes a FASTA format sequence file and a file
56 with a list of start/stop positions in that file (e.g., as produced
57 by the long-orfs program) and extracts and outputs the
58 specified sequences.</P
59 ><P
60 >The first command-line argument is the name of the sequence file,
61 which must be in FASTA format.</P
62 ><P
63 >The second command-line argument is the name of the coordinate file.
64 It must contain a list of pairs of positions in the first file, one
65 per line. The format of each entry is:</P
66 ><P
67 > &lt;IDstring&#62;&gt; &lt;start position&#62; &lt;stop position&gt;</P
68 ><P
69 >This file should contain no other information, so if you're using
70 the output of glimmer or long-orfs , you'll have to cut off
71 header lines.</P
72 ><P
73 >The output of the program goes to the standard output and has one
74 line for each line in the coordinate file. Each line contains
75 the IDstring , followed by white space, followed by the substring
76 of the sequence file specified by the coordinate pair. Specifically,
77 the substring starts at the first position of the pair and ends at
78 the second position (inclusive). If the first position is bigger
79 than the second, then the DNA reverse complement of each position
80 is generated. Start/stop pairs that "wrap around" the end of the
81 genome are allowed.</P
82 ></DIV
83 ><DIV
84 CLASS="REFSECT1"
85 ><A
86 NAME="AEN32"
87 ></A
88 ><H2
89 >OPTIONS</H2
90 ><P
91 ></P
92 ><DIV
93 CLASS="VARIABLELIST"
94 ><DL
95 ><DT
96 ><VAR
97 CLASS="OPTION"
98 >-skip</VAR
99 ></DT
100 ><DD
101 ><P
102 > makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</P
103 ></DD
104 ><DT
105 ><VAR
106 CLASS="OPTION"
107 >-l</VAR
108 ></DT
109 ><DD
110 ><P
111 > makes the output omit an sequences shorter than n characters.
112 n includes the 3 skipped characters if the -skip switch
113 is one.
114 </P
115 ></DD
116 ></DL
117 ></DIV
118 ></DIV
119 ><DIV
120 CLASS="REFSECT1"
121 ><A
122 NAME="AEN45"
123 ></A
124 ><H2
125 >SEE ALSO</H2
126 ><P
127 >glimmer2 (1),
128 long-orfs (1),
129 adjust (1),
130 anomaly (1),
131 build-icm (1),
132 check (1),
133 codon-usage (1),
134 compare-lists (1),
135 extract (1),
136 generate (1),
137 get-len (1),
138 get-putative (1),</P
139 ><P
140 >http://www.tigr.org/software/glimmer/</P
141 ><P
142 >Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</P
143 ></DIV
144 ><DIV
145 CLASS="REFSECT1"
146 ><A
147 NAME="AEN50"
148 ></A
149 ><H2
150 >AUTHOR</H2
151 ><P
152 >This manual page was quickly copied from the glimmer web site by Steffen Moeller <CODE
153 CLASS="EMAIL"
154 >&#60;<A
155 HREF="mailto:moeller@pzr.uni-rostock.de"
156 >moeller@pzr.uni-rostock.de</A
157 >&#62;</CODE
158 > for
159 the <SPAN
160 CLASS="PRODUCTNAME"
161 >Debian</SPAN
162 > system.
163 </P
164 ></DIV
165 ></BODY
166 ></HTML
167 >
00 bin/* usr/lib/tigr-glimmer
1 debian/tigr-run-glimmer3 usr/bin
2 debian/tigr-glimmer usr/bin
1 debian/bin/* usr/bin
+0
-24
debian/tigr-glimmer less more
0 #!/bin/sh
1
2 BINDIR=/usr/lib/tigr-glimmer
3
4 if [ $# -lt 1 ] ; then
5 echo "Usage: $0 <program>" 1>&2
6 echo " Existing programs are:"
7 ls ${BINDIR}
8 exit 1
9 fi
10
11 WRAPPER=$0
12 PROGRAM=$1
13 shift
14 ARGS=$*
15
16 if [ -x ${BINDIR}/${PROGRAM} ]; then
17 exec ${BINDIR}/${PROGRAM} ${ARGS}
18 else
19 echo "Usage: ${PROGRAM} does not exist in Tigr Glimmer"
20 echo " Existing programs are:"
21 ls ${BINDIR}
22 exit 1
23 fi
+0
-18
debian/tigr-run-glimmer3 less more
0 #!/bin/sh
1 echo "run Glimmer3"
2 clear
3 echo "Genome is " $1
4 echo "Find non-overlapping orfs in tmp.coord"
5 BINDIR="/usr/lib/tigr-glimmer"
6 rm -f tmp.coord
7 ${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord
8 echo "Extract training sequences to tmp.train"
9 rm -f tmp.train
10 ${BINDIR}/extract $1 tmp.coord >tmp.train
11 wc tmp.train
12 echo "Build interpolated context model in tmp.model"
13 rm -f tmp.model
14 ${BINDIR}/build-icm <tmp.train >tmp.model
15 echo "Predict genes with Glimmer3 with coordinates in g3.coord"
16 rm -f g3.coord
17 ${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord