Newer
Older
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
#!/bin/sh -
# this script will run a search program on a sequence input file or on each
# file in a file of filenames
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_hth,v 1.1 2004-06-09 10:03:06 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
if [ $# = 4 -a x$1 = x-onefile ]
then
shift
ONEFILE=t
PARAMETERS=$3 export PARAMETERS
else
if [ $# = 2 ]
then
PARAMETERS=$2 export PARAMETERS
else
echo usage: $0 -onefile input_file output_file parameters 1>&2
echo or: $0 file_of_filenames parameters 1>&2
exit 1
fi
fi
# expand any ~ or environment variables
EXPANDED_PARAMETERS=`echo "echo $PARAMETERS" | /bin/csh -f`
### change this function to suit your site:
run_one_prog () {
INPUT_FILE=$1
OUTPUT_FILE=$2
PARAMETERS=$3
### change these lines:
EXEC=helixturnhelix
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE using database $PARAMETERS" 1>&2
echo "command line: $EXEC $PARAMETERS $INPUT_FILE" 1>&2
$EXEC $INPUT_FILE $OUTPUT_FILE $PARAMETERS 2> hth_errors.new
# add/change the flags to suit your site:
$EXEC $INPUT_FILE -outfile $OUTPUT_FILE $PARAMETERS 2>&1 |
tee ${PROG}_errors.new 1>&2
#### end of changes
if [ -s ${PROG}_errors.new ]
then
( echo ERROR running $PROG: ; echo;
echo ===================================================
cat ${PROG}_errors.new ) >> $OUTPUT_FILE
cat ${PROG}_errors.new >> ${PROG}_errors
fi
}
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
if [ x$ONEFILE = x ]
then
for i in `cat $1`
do
run_one_prog $i $i.out $EXPANDED_PARAMETERS
done
else
run_one_prog $1 $2 $EXPANDED_PARAMETERS
fi
if [ x$ONEFILE = x ]
then
PEPFILES=`cat $1`
else
PEPFILES=$1
fi
if [ -e hth/hth.tab ]
then
mv -f hth/hth.tab hth/hth.tab.old
fi
for i in $PEPFILES
do
# write a tab file containing a feature for each hth
perl -e '
open PEPFILE, "$ARGV[0]" or die "$0: cannot open $ARGV[0]\n";
my $first_line = <PEPFILE>;
close PEPFILE;
if ($first_line !~ m/^>(.*?), (.*) (\d+):(\d+)\s+(\S+)/) {
die "first line of $ARGV[0] is badly formatted\n";
}
my ($gene_name, $description, $pep_first_base,
$pep_last_base, $forward_or_back) = ($1, $2, $3, $4, $5);
open HTHFILE, "$ARGV[1]" or die "$0: cannot open $ARGV[1]\n";
my $score;
my $first_match_base;
while (<HTHFILE>) {
if (m/^Score (\d+) .* in .* at residue (\d+)/) {
$score = $1;
$first_match_base = $2;
}
if (m/^\s+Sequence:\s+(\S+)/ &&
defined ($score) && defined ($pep_first_base)) {
if ($forward_or_back eq "forward") {
my $start_base = $pep_first_base + ($first_match_base - 1) * 3;
my $end_base = $start_base + (length $1) * 3 - 1;
print <<EOF;
FT CDS_motif $start_base..$end_base
FT /note="Helix-turn-helix from $gene_name score $score"
FT /label=hth
EOF
} else {
my $end_base = $pep_last_base - ($first_match_base - 1) * 3;
my $start_base = $end_base - ((length $1) * 3 - 1);
print <<EOF;
FT CDS_motif complement($start_base..$end_base)
FT /note="Helix-turn-helix from $gene_name score $score"
FT /label=hth
EOF
}
}
}
' $i $i.out >> hth/hth.tab
done
exit 0