release.

.gitignore

@@ -6,24 +6,6 @@ __pycache__/
 # C extensions
 *.so
 
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

KPHMMER.egg-info/PKG-INFO

@@ -0,0 +1,16 @@
+Metadata-Version: 1.1
+Name: KPHMMER
+Version: 1.0.2
+Summary: KPHMMER: Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes
+Home-page: UNKNOWN
+Author: Hirotaka Suetake
+Author-email: [email protected]
+License: MIT
+Description: UNKNOWN
+Keywords: Life Science,Bioinfomatics,HMMER,KEGG
+Platform: UNKNOWN
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

KPHMMER.egg-info/SOURCES.txt

@@ -0,0 +1,328 @@
+LICENSE
+MANIFEST.in
+README.md
+setup.cfg
+setup.py
+KPHMMER/__init__.py
+KPHMMER/analysis.py
+KPHMMER/argument_parser.py
+KPHMMER/config.py
+KPHMMER/config_file_manager.py
+KPHMMER/convert.py
+KPHMMER/query.py
+KPHMMER/search.py
+KPHMMER/util.py
+KPHMMER.egg-info/PKG-INFO
+KPHMMER.egg-info/SOURCES.txt
+KPHMMER.egg-info/dependency_links.txt
+KPHMMER.egg-info/not-zip-safe
+KPHMMER.egg-info/requires.txt
+KPHMMER.egg-info/top_level.txt
+KPHMMER/config_files/config.yml
+KPHMMER/config_files/config.yml-dist
+KPHMMER/config_files/help_message.yml
+bin/kphmmer
+data/2ndfind/.DS_Store
+data/2ndfind/2ndfind.hmm
+data/2ndfind/2ndfind.hmm.h3f
+data/2ndfind/domains/AATase.hmm
+data/2ndfind/domains/AATase_new.hmm
+data/2ndfind/domains/ACP_syn_III_C.hmm
+data/2ndfind/domains/ACP_syn_III_C_new.hmm
+data/2ndfind/domains/AMP-binding.hmm
+data/2ndfind/domains/ATP-grasp_3_new.hmm
+data/2ndfind/domains/Abhydrolase_2.hmm
+data/2ndfind/domains/Abhydrolase_2_new.hmm
+data/2ndfind/domains/Acyl_transf_1.hmm
+data/2ndfind/domains/Alk_phosphatase_new.hmm
+data/2ndfind/domains/Aminotran_1_2.hmm
+data/2ndfind/domains/BTAD.hmm
+data/2ndfind/domains/BTAD_new.hmm
+data/2ndfind/domains/CP_ATPgrasp_2.hmm
+data/2ndfind/domains/CP_ATPgrasp_2_new.hmm
+data/2ndfind/domains/Chal_sti_synt_C.hmm
+data/2ndfind/domains/Chal_sti_synt_C_new.hmm
+data/2ndfind/domains/Chal_sti_synt_N.hmm
+data/2ndfind/domains/CheR.hmm
+data/2ndfind/domains/Condensation_new.hmm
+data/2ndfind/domains/Cyclase_polyket.hmm
+data/2ndfind/domains/DHQS.hmm
+data/2ndfind/domains/DHQS_new.hmm
+data/2ndfind/domains/DUF1295.hmm
+data/2ndfind/domains/DUF1295_new.hmm
+data/2ndfind/domains/DUF1702.hmm
+data/2ndfind/domains/DUF1702_new.hmm
+data/2ndfind/domains/DUF2172_new.hmm
+data/2ndfind/domains/DUF3463.hmm
+data/2ndfind/domains/Docking.hmm
+data/2ndfind/domains/ERG4_ERG24.hmm
+data/2ndfind/domains/ERG4_ERG24_new.hmm
+data/2ndfind/domains/Eno-Rase_FAD_bd_new.hmm
+data/2ndfind/domains/Enoyl_reductase.hmm
+data/2ndfind/domains/Enoyl_reductase_new.hmm
+data/2ndfind/domains/FabA.hmm
+data/2ndfind/domains/FabA_new.hmm
+data/2ndfind/domains/FcoT_new.hmm
+data/2ndfind/domains/Glyco_trans_4_4_new.hmm
+data/2ndfind/domains/HMG-CoA_red.hmm
+data/2ndfind/domains/HMG-CoA_red_new.hmm
+data/2ndfind/domains/HMG_CoA_synt_N.hmm
+data/2ndfind/domains/HMG_CoA_synt_N_new.hmm
+data/2ndfind/domains/Hexose_dehydrat.hmm
+data/2ndfind/domains/ICMT_new.hmm
+data/2ndfind/domains/IucA_IucC.hmm
+data/2ndfind/domains/KR.hmm
+data/2ndfind/domains/KR_new.hmm
+data/2ndfind/domains/Ketoacyl-synt_C.hmm
+data/2ndfind/domains/Ketoacyl-synt_C_new.hmm
+data/2ndfind/domains/Lant_dehyd_C.hmm
+data/2ndfind/domains/Lant_dehydr_N.hmm
+data/2ndfind/domains/Lant_dehydr_N_new.hmm
+data/2ndfind/domains/LuxC.hmm
+data/2ndfind/domains/Lycopene_cycl.hmm
+data/2ndfind/domains/Lycopene_cycl_new.hmm
+data/2ndfind/domains/MbtH_new.hmm
+data/2ndfind/domains/MelC1.hmm
+data/2ndfind/domains/MelC1_new.hmm
+data/2ndfind/domains/Methyltransf_13_new.hmm
+data/2ndfind/domains/Methyltransf_14_new.hmm
+data/2ndfind/domains/NTF2.hmm
+data/2ndfind/domains/OCD_Mu_crystall.hmm
+data/2ndfind/domains/PEMT.hmm
+data/2ndfind/domains/PEMT_new.hmm
+data/2ndfind/domains/ParBc.hmm
+data/2ndfind/domains/Peptidase_M42.hmm
+data/2ndfind/domains/Peptidase_M42_new.hmm
+data/2ndfind/domains/Polyketide_cyc.hmm
+data/2ndfind/domains/Polyketide_cyc2.hmm
+data/2ndfind/domains/Polyketide_cyc2_new.hmm
+data/2ndfind/domains/PqqD.hmm
+data/2ndfind/domains/PqqD_new.hmm
+data/2ndfind/domains/Prenyltrans.hmm
+data/2ndfind/domains/Prenyltrans_new.hmm
+data/2ndfind/domains/Regulator_TrmB.hmm
+data/2ndfind/domains/Regulator_TrmB_new.hmm
+data/2ndfind/domains/Ring_hydroxyl_A.hmm
+data/2ndfind/domains/Ring_hydroxyl_A_new.hmm
+data/2ndfind/domains/SAF_new.hmm
+data/2ndfind/domains/SLA_LP_auto_ag.hmm
+data/2ndfind/domains/SLA_LP_auto_ag_new.hmm
+data/2ndfind/domains/SQS_PSY.hmm
+data/2ndfind/domains/SQS_PSY_new.hmm
+data/2ndfind/domains/Steroid_dh.hmm
+data/2ndfind/domains/Terpene_synth_C.hmm
+data/2ndfind/domains/Terpene_synth_C_new.hmm
+data/2ndfind/domains/Thioesterase.hmm
+data/2ndfind/domains/Thioesterase_new.hmm
+data/2ndfind/domains/Transglut_core3.hmm
+data/2ndfind/domains/Transglut_core3_new.hmm
+data/2ndfind/domains/TylF.hmm
+data/2ndfind/domains/TylF_new.hmm
+data/2ndfind/domains/Tyrosinase.hmm
+data/2ndfind/domains/Tyrosinase_new.hmm
+data/2ndfind/domains/UnbV_ASPIC.hmm
+data/2ndfind/domains/YcaO.hmm
+data/2ndfind/domains/YcaO_new.hmm
+data/2ndfind/domains/dTDP_sugar_isom_new.hmm
+data/2ndfind/domains/ketoacyl-synt.hmm
+data/2ndfind/domains/p450.hmm
+data/2ndfind/domains/p450_new.hmm
+data/2ndfind/domains/peroxidase.hmm
+data/2ndfind/domains/peroxidase_new.hmm
+data/2ndfind/domains/polyprenyl_synt_new.hmm
+data/scb/scb.yml
+data/scb/scb_1st.fasta
+data/scb/scb_2nd.fasta
+data/scb/scb_all.fasta
+data/scb/scb_analysis_2ndfind.txt
+data/scb/scb_analysis_KPHMMER.txt
+data/scb/scb_domain_2ndfind.tsv
+data/scb/scb_domain_KPHMMER.tsv
+data/sco_sma_sgr_sen/sco.yml
+data/sco_sma_sgr_sen/sco_1st.fasta
+data/sco_sma_sgr_sen/sco_2nd.fasta
+data/sco_sma_sgr_sen/sco_all.fasta
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st.tsv
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd.tsv
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_all.tsv
+data/sco_sma_sgr_sen/sen.yml
+data/sco_sma_sgr_sen/sen_1st.fasta
+data/sco_sma_sgr_sen/sen_2nd.fasta
+data/sco_sma_sgr_sen/sen_all.fasta
+data/sco_sma_sgr_sen/sgr.yml
+data/sco_sma_sgr_sen/sgr_1st.fasta
+data/sco_sma_sgr_sen/sgr_2nd.fasta
+data/sco_sma_sgr_sen/sgr_all.fasta
+data/sco_sma_sgr_sen/sma.yml
+data/sco_sma_sgr_sen/sma_1st.fasta
+data/sco_sma_sgr_sen/sma_2nd.fasta
+data/sco_sma_sgr_sen/sma_all.fasta
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/AAA_16.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/AAA_22.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/AAA_33.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/ATP-grasp.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/Alpha-amylase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/Amidohydro_1.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/Amidohydro_3.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/Aminotran_3.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/Biotin_lipoyl.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/CPSase_L_D2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/His_biosynth.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/IlvN.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/K_oxygenase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_1st/TPP_enzyme_N.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/3Beta_HSD.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/3HCDH.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/A2M_comp.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/AAT.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/AA_kinase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/ACP_syn_III.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/ACT_7.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/ATP_bind_3.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/AXE1.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Abhydrolase_3.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Acyl_transf_1.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Aldedh.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Alliinase_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Amino_oxidase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Aminotran_1_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Anth_synt_I_N.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/BcrAD_BadFG.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Beta-lactamase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Beta-lactamase2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/CMAS.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Chorismate_bind.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Condensation.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DAO.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DEDD_Tnp_IS110.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DHDPS.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DUF1205.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DUF1487.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DUF1702.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DUF5423.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DXPR_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DXP_redisom_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DXP_reductoisom.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DXP_synthase_N.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DapB_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/DapB_N.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Dimerisation.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Dimerisation2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Diphthami_syn_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Docking.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/ECH_1.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/ECH_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/EHN.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Epimerase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Erythro-docking.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/FAD_binding_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/FAD_binding_3.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Flavin_Reduct.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/GDP_Man_Dehyd.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/GFO_IDH_MocA.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/GFO_IDH_MocA_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/GH3.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/GTP_EFTU.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/GTP_EFTU_D2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/GcpE.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Glucokinase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Glyco_tran_28_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/HI0933_like.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/HTH_21.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/HTH_Crp_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Herpes_BBRF1.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Hexose_dehydrat.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Hydant_A_N.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Inos-1-P_synth.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Inositol_P.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/IspD.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/KAsynt_C_assoc.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/KR.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Ketoacyl-synt_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/LYTB.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Lactamase_B.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Lactamase_B_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/MCRA.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Mago-bind.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/MbtH.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Methyltransf_12.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Methyltransf_13.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Methyltransf_14.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Methyltransf_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Methyltransf_23.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Methyltransf_32.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Methyltransf_9.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NAD_binding_10.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NAD_binding_4.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NAD_binding_5.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NAD_binding_8.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NAD_binding_9.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NTP_transf_3.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NUDIX.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NmrA.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/NodS.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/OmdA.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/PAPS_reduct.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/PCMT.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/PP-binding.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/PS-DH.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/PUA.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Penicil_amidase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Peptidase_M22.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Peptidase_S9.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Polyketide_cyc.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Polyketide_cyc2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Polysacc_synt_2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Prenyltrans.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Prenyltransf.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Pyr_redox.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/QueC.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/ROK.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Ribosomal_L50.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/RmlD_sub_bind.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/S4.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/SQHop_cyclase_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/SQHop_cyclase_N.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/SQS_PSY.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/SRP72.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Sacchrp_dh_NADP.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Semialdhyde_dh.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Semialdhyde_dhC.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/SpoVAD.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Terpene_synth_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Thi4.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Thiolase_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Thiolase_N.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Transket_pyr.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Transketolase_C.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Trp_halogenase.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/TylF.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/UDPGT.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/Ubie_methyltran.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/YgbB.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/adh_short.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/adh_short_C2.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/dTDP_sugar_isom.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/ketoacyl-synt.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/p450.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/polyprenyl_synt.hmm
+data/sco_sma_sgr_sen/sco_sma_sgr_sen_2nd/zf-RING_7.hmm
+data/sve/sve.yml
+data/sve/sve_1st.fasta
+data/sve/sve_2nd.fasta
+data/sve/sve_all.fasta
+data/sve/sve_analysis_2ndfind.txt
+data/sve/sve_analysis_KPHMMER.txt
+data/sve/sve_domain_2ndfind.tsv
+data/sve/sve_domain_KPHMMER.tsv
+script/KPHMMER_API_access.py
+script/KPHMMER_stat.py
+script/README.txt
+script/calc_pvalue.py
+script/domain_text.py
+script/dup.py
+script/make_ensemble_tsv.py
+script/tsv.py
+script/tsv2txt.py
+script/txt2hmm_domain_changer.py
+script/yaml_gene_count_getter.py

KPHMMER.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

KPHMMER.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

KPHMMER.egg-info/requires.txt

@@ -0,0 +1,4 @@
+numpy
+PyYAML
+scipy
+requests

KPHMMER.egg-info/top_level.txt

@@ -0,0 +1 @@
+KPHMMER

build/lib/KPHMMER/__init__.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+# coding: utf-8
+"""
+KPHMMER: Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes
+"""
+from .analysis import Analysis
+from .argument_parser import determine_submethod, get_args
+from .config import Config
+from .config_file_manager import ConfigFileManager
+from .convert import Convert
+from .query import Query
+from .search import Search
+from .util import check_status_code, dump_log, get_kegg, get_pfam