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
|
#!/bin/bash -e
PROGNAME=`basename $0`
function usage {
echo "usage: remove_short_seqs.sh [[-i input] [-l length] | [-h]]"
echo "-i DIRECTORY the input directory of GenBank files with .gbk extensions"
echo "-l INTEGER remove GenBank files that describe sequences shorter than this length"
echo "
USAGE:
remove_short_seqs.sh -i DIR -l INTEGER
DESCRIPTION:
Removes GenBank files that are shorter than the specified length from the
provided directory.
REQUIRED ARGUMENTS:
-i, --input DIR
Input directory of GenBank files with .gbk extensions.
-l, --length INTEGER
Remove GenBank files that describe sequences shorter than this length.
OPTIONAL ARGUMENTS:
-h, --help
Show this message
EXAMPLE:
remove_short_seqs.sh -i my_project/comparison_genomes -l 100000
"
}
function error_exit {
echo "${PROGNAME}: ${1:-"Unknown Error"}" 1>&2
exit 1
}
function remove_trailing_slash {
string="$1"
new_string=`echo "$string" | perl -nl -e 's/\/+$//;' -e 'print $_'`
echo $new_string
}
function get_sequence_length {
file="$1"
seq_length=`head -n 1 "$file" | perl -nl -e 'm/(\d+)\sbp/;' -e 'print $1'`
echo $seq_length
}
while [ "$1" != "" ]; do
case $1 in
-i | --input ) shift
input=$1
;;
-l | --length ) shift
min_length=$1
;;
-h | --help ) usage
exit
;;
* ) usage
exit 1
esac
shift
done
if [ -z $input ]; then
error_exit "Please use '-i' to specify an input directory of GenBank files with .gbk extensions. Use '-h' for help."
fi
if [ -z $min_length ]; then
error_exit "Please use '-l' to specify a minimum sequence length to keep. Use '-h' for help."
fi
cct_home=$CCT_HOME
input=`remove_trailing_slash "$input"`
# save and change IFS to avoid problems with filesnames with spaces
OLDIFS=$IFS
IFS=$'\n'
#find all GenBank files in the directory
files=($( find "$input" -maxdepth 1 -type f -name "*.gbk" ))
# restore IFS
IFS=$OLDIFS
length=${#files[@]}
for (( i=0; i<$length; i++ ));
do
gbk_file=${files[$i]}
seq_length=`get_sequence_length "$gbk_file"`
if [ -z $seq_length ]; then
error_exit "Unable to determine length of sequence '$gbk_file'"
fi
if [ "$seq_length" -lt "$min_length" ]; then
echo "Removing file '$gbk_file' because sequence length is $seq_length"
rm -f "$gbk_file"
else
echo "Keeping file '$gbk_file' because sequence length is $seq_length"
fi
done
|
