diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/.DS_Store differ diff --git a/lib/kb_phylogenomics/kb_phylogenomicsImpl.py b/lib/kb_phylogenomics/kb_phylogenomicsImpl.py index 6f77306..2df881f 100644 --- a/lib/kb_phylogenomics/kb_phylogenomicsImpl.py +++ b/lib/kb_phylogenomics/kb_phylogenomicsImpl.py @@ -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 diff --git a/test/kb_phylogenomics_server_test.py b/test/kb_phylogenomics_server_test.py index 75a496e..e08c39a 100644 --- a/test/kb_phylogenomics_server_test.py +++ b/test/kb_phylogenomics_server_test.py @@ -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): @@ -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 @@ -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