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Add bad genomes to score ortho evo test #263

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Merged
crockettz merged 1 commit into from
Oct 21, 2025
Merged

Add bad genomes to score ortho evo test #263

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1 change: 1 addition & 0 deletions lib/kb_phylogenomics/kb_phylogenomicsImpl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
import random
import subprocess
from Bio import SeqIO
from Bio.Seq import Seq

from datetime import datetime
from pprint import pformat,pprint
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17 changes: 13 additions & 4 deletions test/kb_phylogenomics_server_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
from kb_phylogenomics.kb_phylogenomicsImpl import kb_phylogenomics
from kb_phylogenomics.kb_phylogenomicsServer import MethodContext
from kb_phylogenomics.authclient import KBaseAuth as _KBaseAuth

ws = workspaceService("https://appdev.kbase.us/services/ws")

class kb_phylogenomicsTest(unittest.TestCase):

Expand Down Expand Up @@ -1100,18 +1100,26 @@ def test_score_ortho_evo_rates_01(self):

print ("\n\nRUNNING: test_"+method+"_01()")
print ("==================================================\n\n")

# input_data
genomeInfo_0 = self.getGenomeInfo('GCF_000287295.1_ASM28729v1_genomic', 0) # Candidatus Carsonella ruddii HT isolate Thao2000
genomeInfo_1 = self.getGenomeInfo('GCF_000306885.1_ASM30688v1_genomic', 1) # Wolbachia endosymbiont of Onchocerca ochengi
genomeInfo_2 = self.getGenomeInfo('GCF_001439985.1_wTPRE_1.0_genomic', 2) # Wolbachia endosymbiont of Trichogramma pretiosum
genomeInfo_3 = self.getGenomeInfo('GCF_000022285.1_ASM2228v1_genomic', 3) # Wolbachia sp. wRi

#genomeInfo_4 = ws.copy_object({
# "from":{'ref':'76694/103/1'},
# "to":{"workspace":os.environ['KB_WORKSPACE_ID'],'name':'additional_genome'}
# })
#genomeInfo_4 = ws.get_objects2({'objects':[{'ref':'76694/103/1'}]})['data'][0]['data']
genomeInfo_4 = next((obj for obj in ws.list_objects(params={'ids':['76694']}) if str(obj[0]) == '103'), None)
print ("==================================================\n\n*3")
print(genomeInfo_4)
print ("==================================================\n\n*3")
[OBJID_I, NAME_I, TYPE_I, SAVE_DATE_I, VERSION_I, SAVED_BY_I, WSID_I, WORKSPACE_I, CHSUM_I, SIZE_I, META_I] = range(11) # object_info tuple
genome_ref_0 = str(genomeInfo_0[WSID_I]) + '/' + str(genomeInfo_0[OBJID_I]) + '/' + str(genomeInfo_0[VERSION_I])
genome_ref_1 = str(genomeInfo_1[WSID_I]) + '/' + str(genomeInfo_1[OBJID_I]) + '/' + str(genomeInfo_1[VERSION_I])
genome_ref_2 = str(genomeInfo_2[WSID_I]) + '/' + str(genomeInfo_2[OBJID_I]) + '/' + str(genomeInfo_2[VERSION_I])
genome_ref_3 = str(genomeInfo_3[WSID_I]) + '/' + str(genomeInfo_3[OBJID_I]) + '/' + str(genomeInfo_3[VERSION_I])
genome_ref_4 = str(genomeInfo_4[WSID_I]) + '/' + str(genomeInfo_4[OBJID_I]) + '/' + str(genomeInfo_4[VERSION_I])

#feature_id_0 = 'A355_RS00030' # F0F1 ATP Synthase subunit B
#feature_id_1 = 'WOO_RS00195' # F0 ATP Synthase subunit B
Expand All @@ -1122,7 +1130,8 @@ def test_score_ortho_evo_rates_01(self):
genome_refs_map = { '23880/3/1': genome_ref_0,
'23880/4/1': genome_ref_1,
'23880/5/1': genome_ref_2,
'23880/6/1': genome_ref_3
'23880/6/1': genome_ref_3,
'23880/7/1': genome_ref_4
}
obj_info = self.getPangenomeInfo('Tiny_things.OrthoMCL_pangenome', 0, genome_refs_map)
[OBJID_I, NAME_I, TYPE_I, SAVE_DATE_I, VERSION_I, SAVED_BY_I, WSID_I, WORKSPACE_I, CHSUM_I, SIZE_I, META_I] = range(11) # object_info tuple
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