Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
edna
benchmark_pipelines
Commits
eeb23f20
Commit
eeb23f20
authored
Dec 09, 2019
by
root
Browse files
assign threshold
parent
9406e8a0
Changes
2
Hide whitespace changes
Inline
Side-by-side
07_assignation/Assign_sintax.sh
View file @
eeb23f20
...
...
@@ -111,7 +111,7 @@ all_sample_sequences_sort_uppercase="${all_sample_sequences_sort/.fasta/.upperca
awk
'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $0}}'
$all_sample_sequences_sort
>
$all_sample_sequences_sort_uppercase
## Taxonomic assignation
all_sample_sequences_sintax_ann
=
"
${
all_sample_sequences_sort
/.fasta/.sintax_ann.csv
}
"
$usearch
-sintax
$all_sample_sequences_sort_uppercase
-db
$refdb_dir
-sintax_cutoff
0.8
-strand
plus
-tabbedout
$all_sample_sequences_sintax_ann
$usearch
-sintax
$all_sample_sequences_sort_uppercase
-db
$refdb_dir
-sintax_cutoff
0.
9
8
-strand
plus
-tabbedout
$all_sample_sequences_sintax_ann
## convert usearch output to obifasta
all_sample_sequences_sintax_ann_fas
=
"
${
all_sample_sequences_sintax_ann
/.csv/.fasta
}
"
$container_python2
07_assignation/convert_assign_sintax_2_obifasta.py
-f
$all_sample_sequences_sort
-s
$all_sample_sequences_sintax_ann
-o
$all_sample_sequences_sintax_ann_fas
...
...
07_assignation/Assign_vsearch.sh
View file @
eeb23f20
...
...
@@ -110,7 +110,7 @@ all_sample_sequences_sort="${all_sample_sequences_ann/.fasta/.sort.fasta}"
$obisort
-k
count
-r
$all_sample_sequences_ann
>
$all_sample_sequences_sort
# Taxonomic assignation
all_sample_sequences_vsearch_tag
=
"
${
all_sample_sequences_sort
/.fasta/.tag.vsearch
}
"
$vsearch
--usearch_global
$all_sample_sequences_sort
--db
$refdb_dir
--notrunclabels
--id
0.8
--fasta_width
0
--top_hits_only
--blast6out
$all_sample_sequences_vsearch_tag
$vsearch
--usearch_global
$all_sample_sequences_sort
--db
$refdb_dir
--notrunclabels
--id
0.
9
8
--fasta_width
0
--top_hits_only
--blast6out
$all_sample_sequences_vsearch_tag
## convert vsearch assignation file into obifasta
all_sample_sequences_vsearch_tag_obifasta
=
"
${
all_sample_sequences_vsearch_tag
/.vsearch/.vsearch.fasta
}
"
$container_python2
07_assignation/convert_assign_vsearch_2_obifasta.py
-f
$all_sample_sequences_sort
-a
$all_sample_sequences_vsearch_tag
-o
$all_sample_sequences_vsearch_tag_obifasta
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment