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Michael BarnettMichael Barnett
Michael Barnett
authored and
Michael Barnett
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Fixed isses with carrying over category into domain text for functional test.
1 parent 0986750 commit 7c22acf

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-40
lines changed

2 files changed

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-40
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‎commec/tests/screen_factory.py‎

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Original file line numberDiff line numberDiff line change
@@ -164,6 +164,7 @@ def add_hit(self,
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"name": title,
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"tax_id": taxid,
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"list_acronym": "DTL",
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"category" : superkingdom,
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},
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]))
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‎commec/tests/test_data/functional.json‎

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@@ -3,7 +3,7 @@
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"commec_version": "1.0.1",
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"json_output_version": "0.4",
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"time_taken": "00:00:05",
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"date_run": "2025-11-13 19:54:00",
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"date_run": "2025-11-17 18:06:57",
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"search_tool_info": {
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"biorisk_search_info": {
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"tool_info": "# HMMER 3.4 (Aug 2023); http://hmmer.org/",
@@ -41,7 +41,7 @@
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]
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},
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"query_info": {
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"file": "/tmp/pytest-of-root/pytest-55/test_functional_screen0/functional.fasta",
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"file": "/tmp/pytest-of-root/pytest-62/test_functional_screen0/functional.fasta",
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"number_of_queries": 1,
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"total_query_length": 600
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},
@@ -64,7 +64,7 @@
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"from_step": "Nucleotide Taxonomy Search"
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},
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"name": "NT_HIT_MIXED",
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"description": "Mix of 1 regulated None and 1 non-regulated None",
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"description": "Mix of 1 controlled sequence and 1 non-regulated sequence",
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"ranges": [
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{
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"e_value": 0.16,
@@ -76,15 +76,15 @@
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "1",
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"number_of_unregulated_taxids": "1",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "1",
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"regulated_taxa": [
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{
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"evalue": 0.16,
@@ -94,7 +94,7 @@
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"control_list": [
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{
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"name": "ShouldntClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -118,7 +118,7 @@
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"from_step": "Nucleotide Taxonomy Search"
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},
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"name": "NT_HIT_FLAG3",
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"description": "Regulated None - SUBJECT",
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"description": "Regulated sequence - SUBJECT",
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"ranges": [
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{
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"e_value": 0.15,
@@ -130,15 +130,15 @@
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "2",
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"number_of_unregulated_taxids": "0",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "2",
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"regulated_taxa": [
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{
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"evalue": 0.14,
@@ -148,7 +148,7 @@
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"control_list": [
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{
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"name": "ShouldntClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -161,7 +161,7 @@
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"control_list": [
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{
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"name": "SUBJECT",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -178,7 +178,7 @@
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"from_step": "Nucleotide Taxonomy Search"
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},
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"name": "NT_HIT_FLAG2",
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"description": "Regulated None - SUBJECT",
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"description": "Regulated sequence - SUBJECT",
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"ranges": [
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{
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"e_value": 0.14,
@@ -190,15 +190,15 @@
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "2",
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"number_of_unregulated_taxids": "0",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "2",
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"regulated_taxa": [
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{
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"evalue": 0.14,
@@ -208,7 +208,7 @@
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"control_list": [
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{
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"name": "ShouldntClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -221,7 +221,7 @@
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"control_list": [
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{
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"name": "SUBJECT",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -238,7 +238,7 @@
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"from_step": "Nucleotide Taxonomy Search"
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},
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"name": "NT_HIT_FLAG1",
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"description": "Regulated None - SUBJECT",
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"description": "Regulated sequence - SUBJECT",
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"ranges": [
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{
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"e_value": 0.13,
@@ -250,15 +250,15 @@
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "1",
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"number_of_unregulated_taxids": "0",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "1",
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"regulated_taxa": [
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{
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"evalue": 0.13,
@@ -268,7 +268,7 @@
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"control_list": [
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{
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"name": "ShouldntClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -285,7 +285,7 @@
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"from_step": "Protein Taxonomy Search"
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},
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"name": "NR_HIT_MIXED1",
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"description": "Mix of 1 regulated None and 2 non-regulated None",
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"description": "Mix of 1 controlled sequence and 2 non-regulated sequence",
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"ranges": [
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{
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"e_value": 0.1,
@@ -297,15 +297,15 @@
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "1",
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"number_of_unregulated_taxids": "2",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "1",
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"regulated_taxa": [
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{
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"evalue": 0.1,
@@ -315,7 +315,7 @@
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"control_list": [
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{
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"name": "ShouldMixedReg",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -345,7 +345,7 @@
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"from_step": "Protein Taxonomy Search"
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},
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"name": "NR_HIT_FLAG4",
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"description": "Regulated None - ShouldClear",
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"description": "Regulated sequence - ShouldClear",
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"ranges": [
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{
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"e_value": 0.09,
@@ -357,15 +357,15 @@
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "1",
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"number_of_unregulated_taxids": "0",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "1",
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"regulated_taxa": [
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{
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"evalue": 0.09,
@@ -375,7 +375,7 @@
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"control_list": [
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{
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"name": "ShouldClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -392,7 +392,7 @@
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"from_step": "Protein Taxonomy Search"
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},
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"name": "NR_HIT_FLAG3",
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"description": "Regulated None - ShouldntClear",
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"description": "Regulated sequence - ShouldntClear",
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"ranges": [
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{
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"e_value": 0.08,
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "1",
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"number_of_unregulated_taxids": "0",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "1",
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"regulated_taxa": [
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{
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"evalue": 0.07,
@@ -422,7 +422,7 @@
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"control_list": [
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{
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"name": "ShouldntClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -439,7 +439,7 @@
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"from_step": "Protein Taxonomy Search"
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},
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"name": "NR_HIT_FLAG2",
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"description": "Regulated None - ShouldClearBySynBio",
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"description": "Regulated sequence - ShouldClearBySynBio",
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"ranges": [
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{
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"e_value": 0.07,
@@ -451,15 +451,15 @@
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "1",
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"number_of_unregulated_taxids": "0",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "1",
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"regulated_taxa": [
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{
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"evalue": 0.07,
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"control_list": [
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{
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"name": "ShouldntClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]
@@ -486,7 +486,7 @@
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"from_step": "Protein Taxonomy Search"
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},
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"name": "NR_HIT_FLAG1",
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"description": "Regulated None - ShouldntClear",
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"description": "Regulated sequence - ShouldntClear",
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"ranges": [
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{
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"e_value": 0.06,
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],
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"annotations": {
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"domain": [
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"None"
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"Viruses"
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],
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"regulated_taxonomy": [
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{
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"number_of_regulated_taxids": "1",
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"number_of_unregulated_taxids": "0",
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"regulated_eukaryotes": "0",
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"regulated_bacteria": "0",
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"regulated_viruses": "0",
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"regulated_viruses": "1",
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"regulated_taxa": [
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{
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"evalue": 0.06,
@@ -516,7 +516,7 @@
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"control_list": [
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{
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"name": "ShouldntClear",
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"category": "None",
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"category": "Viruses",
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"list": "DTL"
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}
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]

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