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
|
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 11 Feb 2014 10:02:25 +0100
Bug-Debian: http://bugs.debian.org/737913
Description: Set explicit PATH for fastasort to /usr/lib/dnaclust to avoid
name space conflict with exonerate.
.
Besides the reported name space conflict there ase also a conflict
with mira-assembler detected which is also featuring a file
/usr/bin/fastaselect
This executable from dnaclust was moved as well to /usr/lib/dnaclust.
--- a/dnaclust-abun.sh
+++ b/dnaclust-abun.sh
@@ -67,8 +67,8 @@ trap "rm -fr $tempdir" EXIT
db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
# Reads the sequences from STDIN.
print_message "Reading and sorting the database sequences: $tempdir/${db_sorted}"
-#"$dnaclust_path/fastasort" --random-shuffle > $sequences_sorted
-cat $cluster_centers | "$dnaclust_path/fastasort" > $tempdir/${db_sorted}
+#"/usr/lib/dnaclust/fastasort" --random-shuffle > $sequences_sorted
+cat $cluster_centers | "/usr/lib/dnaclust/fastasort" > $tempdir/${db_sorted}
print_message "Recruiting from the sequences, using database."
-"$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $input -p $tempdir/${db_sorted} -r | awk '{if (NF > 1) print $0}' > $input.db.clusters
\ No newline at end of file
+"$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $input -p $tempdir/${db_sorted} -r | awk '{if (NF > 1) print $0}' > $input.db.clusters
--- a/dnaclust-ref
+++ b/dnaclust-ref
@@ -74,8 +74,8 @@ trap "rm -fr $tempdir" EXIT
db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
# Reads the sequences from STDIN.
print_message "Reading and sorting the database sequences: $tempdir/${db_sorted}"
-#"$dnaclust_path/fastasort" --random-shuffle > $sequences_sorted
-cat $cluster_centers | "$dnaclust_path/fastasort" > $tempdir/${db_sorted}
+#"/usr/lib/dnaclust/fastasort" --random-shuffle > $sequences_sorted
+cat $cluster_centers | "/usr/lib/dnaclust/fastasort" > $tempdir/${db_sorted}
print_message "Recruiting from the sequences, using database."
"$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $input -p $tempdir/${db_sorted} -r | awk '{if (NF > 1) print $0}' > $input.db.clusters
@@ -87,7 +87,7 @@ then
unclustered_seq=`basename $input .fasta`.unclustered.fasta
awk '{ for (i = 1; i <= NF; i++) print $i}' $input.db.clusters > $tempdir/clustered_seqs
- "$dnaclust_path/fastaselect" --everything-except -f ${input} < $tempdir/clustered_seqs > $tempdir/${unclustered_seq}
+ "/usr/lib/dnaclust/fastaselect" --everything-except -f ${input} < $tempdir/clustered_seqs > $tempdir/${unclustered_seq}
if [[ -s $tempdir/${unclustered_seq} ]] ; then
"$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $tempdir/${unclustered_seq} > $input.denovo.clusters
print_message "Writing de novo clusters to: $input.denovo.clusters"
--- a/find-large-clusters
+++ b/find-large-clusters
@@ -54,7 +54,7 @@ tempdir=`mktemp -d -p .`
sequences_sorted=`mktemp -p $tempdir`
# Reads the sequences from STDIN.
print_message "Reading and sorting the input sequences."
-"$dnaclust_path/fastasort" --random-shuffle > $sequences_sorted
+"/usr/lib/dnaclust/fastasort" --random-shuffle > $sequences_sorted
input_count=`grep -c '^>' $sequences_sorted`
if [ $input_count -le 1 ]
@@ -82,10 +82,10 @@ print_message "Clustering the set of sam
| awk --assign=minimum=$minimum_cluster_size '{if (NF >= minimum) print $0}' > $large_clusters
sequences_sorted_head_large_centers=`mktemp -p $tempdir`
-"$dnaclust_path/fastaselect" -c -f $sequences_sorted_head < $large_clusters > $sequences_sorted_head_large_centers
+"/usr/lib/dnaclust/fastaselect" -c -f $sequences_sorted_head < $large_clusters > $sequences_sorted_head_large_centers
sequences_minus_centers=`mktemp -p $tempdir`
-"$dnaclust_path/fastaselect" --everything-except -f $sequences_sorted < $large_clusters > $sequences_minus_centers
+"/usr/lib/dnaclust/fastaselect" --everything-except -f $sequences_sorted < $large_clusters > $sequences_minus_centers
centers_count=`grep -c '^>' $sequences_sorted_head_large_centers`
print_message "Recruiting from the rest of the sequences, using $centers_count centers."
--- a/star-align
+++ b/star-align
@@ -38,7 +38,7 @@ sequences_fasta=`mktemp -p $tempdir`
while read line
do
- echo $line | "$dnaclust_path/fastaselect" -f $input_fasta --cluster-centers > $center_fasta
- echo $line | "$dnaclust_path/fastaselect" -f $input_fasta --cluster-sequences > $sequences_fasta
+ echo $line | "/usr/lib/dnaclust/fastaselect" -f $input_fasta --cluster-centers > $center_fasta
+ echo $line | "/usr/lib/dnaclust/fastaselect" -f $input_fasta --cluster-sequences > $sequences_fasta
"$dnaclust_path/dnaclust" -s $similarity --multiple-alignment --no-k-mer-filter -i $sequences_fasta -p $center_fasta -r
-done
\ No newline at end of file
+done
|
