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added compila_conda.pl to bin/COGsoft to export it as a conda recipe
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eead-csic-compbio committed Apr 28, 2022
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6 changes: 4 additions & 2 deletions CHANGES.txt
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Expand Up @@ -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
312 changes: 156 additions & 156 deletions sample_intersection/intersection_t0.cluster_list
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Expand Up @@ -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
Binary file modified sample_intersection/pangenome_matrix_t0__shell.pdf
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Binary file modified sample_intersection/pangenome_matrix_t0__shell_circle.pdf
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Original file line number Diff line number Diff line change
@@ -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
Original file line number Diff line number Diff line change
@@ -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
Binary file modified sample_intersection/venn_t0.pdf
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