added compila_conda.pl to bin/COGsoft to export it as a conda recipe

CHANGES.txt

@@ -383,6 +383,8 @@
 21042022: transcripts2cdsCPP.pl not tested by default with make test, as bioconda lacks Inline::CPP
 21042022: if bin/ not in place phyTools::set_phyTools_env assumes binary dependencies in PATH
 21042022: updated install.pl so that it copes with binary dependencies in PATH
-21042022: added install_cogs, which only gets/compiles COGS, so that other binaries can be taken from PATH
-22042022: make install_cogs (install.pl) does "make clean; make"
+21042022: install.pl no_databases COGS only gets/compiles COGS, so that other binaries can be taken from PATH ()
 22042022: added CODE_OF_CONDUCT
+28042022: added test_swiss to Makefile
+28042022: added compila_conda.pl to bin/COGsoft to export it as a conda recipe (macosx-intel copy still the same)
+28042022: COGsoft source released as https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.4.6/COGsoft.tgz

sample_intersection/intersection_t0.cluster_list

@@ -3,184 +3,184 @@
 # -o sample_intersection
 # -I 
 # -r 0
-608_tetB.faa
-382_conserved_hypothetic...faa
-644_ardR.faa
-605_hypothetical_protein.faa
-302_conserved_hypothetic...faa
-173_arsR.faa
-353_S-formylglutathione_...faa
-245_dfrA14.faa
-640_ardA.faa
-304_transposase-_IS4_fam...faa
-286_streptomycin_phospho...faa
-289_beta-lactamase.faa
-296_hypothetical_protein.faa
-634_stbA.faa
-241_PilT.faa
-635_stbB.faa
-643_ccgEIII.faa
+637_hypothetical_protein.faa
+391_hypothetical_protein.faa
+420_hypothetical_protein.faa
+280_transposase.faa
+228_truncated_TnpA.faa
 10_mrx.faa
-627_traF.faa
-301_putative_transposase.faa
-255_hypothetical_protein.faa
-602_resP.faa
-200_AacA4.faa
-744_tnp.faa
-73_mph2.faa
-616_traL.faa
-448_hypothetical_protein.faa
-232_hypothetical_protein.faa
-61_linF.faa
-352_resolvase.faa
-231_hypothetical_protein.faa
-607_tetC.faa
-168_unknown.faa
-495_MAK2.05.faa
-366_excinuclease_ABC-_A_...faa
+349_transposase_InsF.faa
+229_QnrS1.faa
+7_transposase_A.faa
 175_arsA.faa
-384_hypothetical_protein.faa
-250_putative_mobilizatio...faa
-171_unknown.faa
-413_TraA.faa
+383_hypothetical_protein.faa
+318_TraB.faa
+390_hypothetical_protein.faa
+73_mph2.faa
+70_tnpD.faa
+13_hypothetical_protein.faa
 288_resolvase.faa
-471_putative_relaxase-he...faa
-743_putative_IS91_ORF2.faa
+286_streptomycin_phospho...faa
 638_ccgAII.faa
-642_ccgD.faa
-282_hypothetical_protein.faa
-74_hypothetical_protein.faa
-65_sul1.faa
-363_putative_transposase...faa
-368_hypothetical_protein.faa
-383_hypothetical_protein.faa
-293_hypothetical_protein.faa
-362_group_II_intron-enco...faa
+608_tetB.faa
+384_hypothetical_protein.faa
+163_unknown.faa
+294_hypothetical_protein.faa
+629_nuc.faa
+630_fipA.faa
 435_ampR.faa
-307_hypothetical_protein.faa
-548_insB.faa
-246_hypothetical_protein.faa
-606_type_IV_restriction_...faa
 625_traE.faa
-498_sph.faa
-648_mpr.faa
-604_dcm.faa
-166_unknown.faa
-350_transposase.faa
-402_conserved_hypothetic...faa
-230_hypothetical_protein.faa
-380_hypothetical_protein.faa
-8_tnpA.faa
-299_site-specific_recomb...faa
-391_hypothetical_protein.faa
-226_TnpA.faa
-647_mucB.faa
-639_ccgAI.faa
+413_TraA.faa
+321_arsenical_pump-drivi...faa
+603_ecoRII.faa
+471_putative_relaxase-he...faa
+225_delta-FipA.faa
+416_TraL.faa
+633_traK.faa
 174_arsD.faa
-557_insF.faa
+444_FosA.faa
 341_hypothetical_protein.faa
-318_TraB.faa
-13_hypothetical_protein.faa
-72_mph1.faa
-71_mel.faa
-351_putative_transposase...faa
-620_traB.faa
-364_conserved_hypothetic...faa
-614_hypothetical_protein.faa
-198_TnpA.faa
-390_hypothetical_protein.faa
-264_hypothetical_protein.faa
-9_mphA.faa
-338_InsB.faa
-354_glyoxalase-bleomycin...faa
+744_tnp.faa
+34_methyl-accepting_che...faa
+60_ant3-9.faa
+240_putative_invertase-r...faa
+602_resP.faa
+246_hypothetical_protein.faa
+230_hypothetical_protein.faa
+382_conserved_hypothetic...faa
+353_S-formylglutathione_...faa
+501_yahA.faa
+644_ardR.faa
+226_TnpA.faa
+643_ccgEIII.faa
+238_TnpA.faa
+621_traC.faa
+743_putative_IS91_ORF2.faa
 613_kikA.faa
-630_fipA.faa
-611_strB.faa
+635_stbB.faa
+302_conserved_hypothetic...faa
 348_group_II_intron-enco...faa
-619_traA.faa
-381_hypothetical_protein.faa
-615_korB.faa
-416_TraL.faa
-621_traC.faa
-34_methyl-accepting_che...faa
-7_transposase_A.faa
-438_unknown.faa
-163_unknown.faa
-396_TraK.faa
-401_protein_of_unknown_f...faa
-497_ble.faa
-445_tnpA.faa
-528_MAK2.40.faa
-225_delta-FipA.faa
-400_DNA_polymerase-_beta...faa
+264_hypothetical_protein.faa
+298_conserved_hypothetic...faa
 295_hypothetical_protein.faa
+628_traG.faa
 236_putative_DeoR-type_t...faa
-172_unknown.faa
-60_ant3-9.faa
-268_hypothetical_protein.faa
-601_repA.faa
+548_insB.faa
+61_linF.faa
+634_stbA.faa
+243_TnpM.faa
+611_strB.faa
+297_hypothetical_protein.faa
+241_PilT.faa
 176_arsB.faa
-327_TraB.faa
+605_hypothetical_protein.faa
+159_intI1.faa
+497_ble.faa
+523_pecM.faa
+71_mel.faa
+200_AacA4.faa
+35_tnpA.faa
+380_hypothetical_protein.faa
+160_oxa2.faa
+376_hypothetical_protein.faa
+289_beta-lactamase.faa
+381_hypothetical_protein.faa
+402_conserved_hypothetic...faa
 234_hypothetical_protein.faa
+601_repA.faa
+36_beta-lactamase_CTX-M...faa
+308_conserved_hypothetic...faa
+72_mph1.faa
+327_TraB.faa
+171_unknown.faa
+615_korB.faa
+352_resolvase.faa
+304_transposase-_IS4_fam...faa
+646_mucA.faa
+648_mpr.faa
+232_hypothetical_protein.faa
+401_protein_of_unknown_f...faa
 641_ccgC.faa
+338_InsB.faa
+231_hypothetical_protein.faa
+396_TraK.faa
+166_unknown.faa
+8_tnpA.faa
+362_group_II_intron-enco...faa
+250_putative_mobilizatio...faa
+65_sul1.faa
+68_armA.faa
+642_ccgD.faa
+623_traD.faa
+367_ISEc8_transposase.faa
 355_S--hydroxymethyl-glu...faa
-379_hypothetical_protein.faa
+268_hypothetical_protein.faa
+299_site-specific_recomb...faa
+301_putative_transposase.faa
+11_blaCTX-M-1.faa
+647_mucB.faa
+618_traM.faa
+636_stbC.faa
+609_tetR.faa
 645_ardB.faa
-159_intI1.faa
-626_traO.faa
+640_ardA.faa
+448_hypothetical_protein.faa
+627_traF.faa
+622_eex.faa
+368_hypothetical_protein.faa
+366_excinuclease_ABC-_A_...faa
+9_mphA.faa
+351_putative_transposase...faa
+616_traL.faa
+614_hypothetical_protein.faa
+282_hypothetical_protein.faa
+604_dcm.faa
+379_hypothetical_protein.faa
+74_hypothetical_protein.faa
+198_TnpA.faa
+365_NADH_dehydrogenase-_...faa
+66_hypothetical_protein.faa
+281_phage_integrase_fami...faa
+173_arsR.faa
 624_traN.faa
-523_pecM.faa
-87_traA.faa
-367_ISEc8_transposase.faa
-243_TnpM.faa
-444_FosA.faa
-349_transposase_InsF.faa
-233_YdaA.faa
+350_transposase.faa
+364_conserved_hypothetic...faa
+417_hypothetical_protein.faa
+619_traA.faa
+363_putative_transposase...faa
+528_MAK2.40.faa
+296_hypothetical_protein.faa
 631_traI.faa
-238_TnpA.faa
-636_stbC.faa
-617_korA.faa
-11_blaCTX-M-1.faa
-35_tnpA.faa
-408_hypothetical_protein.faa
-160_oxa2.faa
-321_arsenical_pump-drivi...faa
-609_tetR.faa
-637_hypothetical_protein.faa
+168_unknown.faa
+69_hypothetical_protein.faa
+64_qacEdelta1.faa
 547_insA.faa
-629_nuc.faa
-618_traM.faa
-365_NADH_dehydrogenase-_...faa
+233_YdaA.faa
+498_sph.faa
 201_VIM-1.faa
-294_hypothetical_protein.faa
-603_ecoRII.faa
-240_putative_invertase-r...faa
+639_ccgAI.faa
+649_ardK.faa
+87_traA.faa
+408_hypothetical_protein.faa
+438_unknown.faa
+307_hypothetical_protein.faa
+177_arsC.faa
+400_DNA_polymerase-_beta...faa
+607_tetC.faa
+495_MAK2.05.faa
+245_dfrA14.faa
+632_traJ.faa
+626_traO.faa
 253_transposition_modula...faa
-308_conserved_hypothetic...faa
-229_QnrS1.faa
-623_traD.faa
-70_tnpD.faa
-297_hypothetical_protein.faa
-64_qacEdelta1.faa
-628_traG.faa
+172_unknown.faa
+293_hypothetical_protein.faa
 242_TnpA.faa
-622_eex.faa
-298_conserved_hypothetic...faa
-177_arsC.faa
-281_phage_integrase_fami...faa
-649_ardK.faa
-376_hypothetical_protein.faa
-501_yahA.faa
-69_hypothetical_protein.faa
-36_beta-lactamase_CTX-M...faa
-228_truncated_TnpA.faa
-420_hypothetical_protein.faa
-66_hypothetical_protein.faa
-646_mucA.faa
+606_type_IV_restriction_...faa
+617_korA.faa
+445_tnpA.faa
+255_hypothetical_protein.faa
 235_hypothetical_protein.faa
-417_hypothetical_protein.faa
-633_traK.faa
-632_traJ.faa
-280_transposase.faa
-68_armA.faa
+557_insF.faa
+354_glyoxalase-bleomycin...faa
+620_traB.faa
 # intersection size = 180 clusters

sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algCOG_e0_.venn_t0.txt

@@ -1,16 +1,16 @@
-496_aph.faa
 247_TnpA.faa
-612_hypothetical_protein.faa
-335_conserved_hypothetic...faa
-305_transposase.faa
-377_hypothetical_protein.faa
-214_hypothetical_protein.faa
 204_hypothetical_protein.faa
 33_tnpA.faa
+496_aph.faa
+526_tnpA.faa
+335_conserved_hypothetic...faa
+527_tnpR.faa
 178_recombinase.faa
+300_transposase.faa
 279_transposase.faa
 57_transposase.faa
+214_hypothetical_protein.faa
+305_transposase.faa
+377_hypothetical_protein.faa
+612_hypothetical_protein.faa
 610_strA.faa
-526_tnpA.faa
-300_transposase.faa
-527_tnpR.faa

sample_intersection/unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algOMCL_e0_.venn_t0.txt

@@ -1,13 +1,13 @@
+300_transposase.faa
+450_tnpA.faa
+319_transposase.faa
+279_transposase.faa
 204_hypothetical_protein.faa
-610_strA.faa
+612_hypothetical_protein.faa
+205_hypothetical_protein.faa
 33_tnpA.faa
-450_tnpA.faa
+610_strA.faa
 385_hypothetical_protein.faa
-279_transposase.faa
-305_transposase.faa
 214_hypothetical_protein.faa
 178_recombinase.faa
-319_transposase.faa
-300_transposase.faa
-205_hypothetical_protein.faa
-612_hypothetical_protein.faa
+305_transposase.faa