Commit eeb23f20 authored by root's avatar root
Browse files

assign threshold

parent 9406e8a0
......@@ -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 0.98 -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 $all_sample_sequences_sintax_ann_fas
......
......@@ -110,7 +110,7 @@ all_sample_sequences_sort="${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 0.98 --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
......
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