Generate build instructions

basicsynbio/utils/seva.py

@@ -8,7 +8,7 @@
     "1": "Ampicillin",
     "2": "Kanamycin",
     "3": "Chloramphenicol",
-    "4": "Streptomycin",
+    "4": "Streptomycin/Spectinomycin",
     "5": "Tetracycline",
     "6": "Gentamicin",
 }

csv_xlsx_files/AbR_marker_clip_masses.csv

@@ -0,0 +1,7 @@
+Marker ID,mass (ng)
+BS_1xx,191
+BS_2xx,186
+BS_3xx,179
+BS_4xx,189
+BS_5axx,202
+BS_6xx,180

csv_xlsx_files/BASIC_SEVA_10_abbreviations.csv

@@ -0,0 +1,31 @@
+Abbreviations
+15a
+16
+17
+19
+17_pKD46
+25a
+26
+27
+29
+27_pKD46
+35a
+36
+37
+39
+37_pKD46
+45a
+46
+47
+49
+47_pKD46
+5a5a
+5a6
+5a7
+5a9
+5a7_pKD46
+65a
+66
+67
+69
+67_pKD46

csv_xlsx_files/BASIC_SEVA_10_bsaI_digest.csv

@@ -0,0 +1,31 @@
+Assembly ID,Fragment 1 Length (bp),Fragment 2 Length (bp)
+BASIC_SEVA_15a.10,878,5055
+BASIC_SEVA_16.10,878,2113
+BASIC_SEVA_17.10,1074,2841
+BASIC_SEVA_19.10,878,2766
+BASIC_SEVA_17_pKD46.10,1074,2910
+BASIC_SEVA_25a.10,878,4943
+BASIC_SEVA_26.10,878,2001
+BASIC_SEVA_27.10,1074,2729
+BASIC_SEVA_29.10,878,2654
+BASIC_SEVA_27_pKD46.10,1074,2798
+BASIC_SEVA_35a.10,878,4799
+BASIC_SEVA_36.10,878,1857
+BASIC_SEVA_37.10,1074,2585
+BASIC_SEVA_39.10,878,2510
+BASIC_SEVA_37_pKD46.10,1074,2654
+BASIC_SEVA_45a.10,878,5013
+BASIC_SEVA_46.10,878,2071
+BASIC_SEVA_47.10,1074,2799
+BASIC_SEVA_49.10,878,2724
+BASIC_SEVA_47_pKD46.10,1074,2868
+BASIC_SEVA_5a5a.10,878,5291
+BASIC_SEVA_5a6.10,878,2349
+BASIC_SEVA_5a7.10,1074,3077
+BASIC_SEVA_5a9.10,878,3002
+BASIC_SEVA_5a7_pKD46.10,1074,3146
+BASIC_SEVA_65a.10,878,4821
+BASIC_SEVA_66.10,878,1879
+BASIC_SEVA_67.10,1074,2607
+BASIC_SEVA_69.10,878,2532
+BASIC_SEVA_67_pKD46.10,1074,2676

csv_xlsx_files/BASIC_SEVA_10_overnights.csv

@@ -0,0 +1,97 @@
+Overnight Well,Transformation Well,Marker,Name
+A1,A1,Ampicillin,BASIC_SEVA_15a.10
+B1,A1,Ampicillin,BASIC_SEVA_15a.10
+C1,A1,Ampicillin,BASIC_SEVA_15a.10
+D1,A1,Ampicillin,BASIC_SEVA_15a.10
+E1,B1,Ampicillin,BASIC_SEVA_16.10
+F1,B1,Ampicillin,BASIC_SEVA_16.10
+G1,B1,Ampicillin,BASIC_SEVA_16.10
+H1,B1,Ampicillin,BASIC_SEVA_16.10
+A2,C1,Ampicillin,BASIC_SEVA_17.10
+B2,C1,Ampicillin,BASIC_SEVA_17.10
+C2,C1,Ampicillin,BASIC_SEVA_17.10
+D2,C1,Ampicillin,BASIC_SEVA_17.10
+E2,D1,Ampicillin,BASIC_SEVA_19.10
+F2,D1,Ampicillin,BASIC_SEVA_19.10
+G2,D1,Ampicillin,BASIC_SEVA_19.10
+H2,D1,Ampicillin,BASIC_SEVA_19.10
+A3,F1,Kanamycin,BASIC_SEVA_25a.10
+B3,F1,Kanamycin,BASIC_SEVA_25a.10
+C3,F1,Kanamycin,BASIC_SEVA_25a.10
+D3,F1,Kanamycin,BASIC_SEVA_25a.10
+E3,G1,Kanamycin,BASIC_SEVA_26.10
+F3,G1,Kanamycin,BASIC_SEVA_26.10
+G3,G1,Kanamycin,BASIC_SEVA_26.10
+H3,G1,Kanamycin,BASIC_SEVA_26.10
+A4,H1,Kanamycin,BASIC_SEVA_27.10
+B4,H1,Kanamycin,BASIC_SEVA_27.10
+C4,H1,Kanamycin,BASIC_SEVA_27.10
+D4,H1,Kanamycin,BASIC_SEVA_27.10
+E4,A2,Kanamycin,BASIC_SEVA_29.10
+F4,A2,Kanamycin,BASIC_SEVA_29.10
+G4,A2,Kanamycin,BASIC_SEVA_29.10
+H4,A2,Kanamycin,BASIC_SEVA_29.10
+A5,C2,Chloramphenicol,BASIC_SEVA_35a.10
+B5,C2,Chloramphenicol,BASIC_SEVA_35a.10
+C5,C2,Chloramphenicol,BASIC_SEVA_35a.10
+D5,C2,Chloramphenicol,BASIC_SEVA_35a.10
+E5,D2,Chloramphenicol,BASIC_SEVA_36.10
+F5,D2,Chloramphenicol,BASIC_SEVA_36.10
+G5,D2,Chloramphenicol,BASIC_SEVA_36.10
+H5,D2,Chloramphenicol,BASIC_SEVA_36.10
+A6,E2,Chloramphenicol,BASIC_SEVA_37.10
+B6,E2,Chloramphenicol,BASIC_SEVA_37.10
+C6,E2,Chloramphenicol,BASIC_SEVA_37.10
+D6,E2,Chloramphenicol,BASIC_SEVA_37.10
+E6,F2,Chloramphenicol,BASIC_SEVA_39.10
+F6,F2,Chloramphenicol,BASIC_SEVA_39.10
+G6,F2,Chloramphenicol,BASIC_SEVA_39.10
+H6,F2,Chloramphenicol,BASIC_SEVA_39.10
+A7,H2,Streptomycin/Spectinomycin,BASIC_SEVA_45a.10
+B7,H2,Streptomycin/Spectinomycin,BASIC_SEVA_45a.10
+C7,H2,Streptomycin/Spectinomycin,BASIC_SEVA_45a.10
+D7,H2,Streptomycin/Spectinomycin,BASIC_SEVA_45a.10
+E7,A3,Streptomycin/Spectinomycin,BASIC_SEVA_46.10
+F7,A3,Streptomycin/Spectinomycin,BASIC_SEVA_46.10
+G7,A3,Streptomycin/Spectinomycin,BASIC_SEVA_46.10
+H7,A3,Streptomycin/Spectinomycin,BASIC_SEVA_46.10
+A8,B3,Streptomycin/Spectinomycin,BASIC_SEVA_47.10
+B8,B3,Streptomycin/Spectinomycin,BASIC_SEVA_47.10
+C8,B3,Streptomycin/Spectinomycin,BASIC_SEVA_47.10
+D8,B3,Streptomycin/Spectinomycin,BASIC_SEVA_47.10
+E8,C3,Streptomycin/Spectinomycin,BASIC_SEVA_49.10
+F8,C3,Streptomycin/Spectinomycin,BASIC_SEVA_49.10
+G8,C3,Streptomycin/Spectinomycin,BASIC_SEVA_49.10
+H8,C3,Streptomycin/Spectinomycin,BASIC_SEVA_49.10
+A9,E3,Tetracycline,BASIC_SEVA_5a5a.10
+B9,E3,Tetracycline,BASIC_SEVA_5a5a.10
+C9,E3,Tetracycline,BASIC_SEVA_5a5a.10
+D9,E3,Tetracycline,BASIC_SEVA_5a5a.10
+E9,F3,Tetracycline,BASIC_SEVA_5a6.10
+F9,F3,Tetracycline,BASIC_SEVA_5a6.10
+G9,F3,Tetracycline,BASIC_SEVA_5a6.10
+H9,F3,Tetracycline,BASIC_SEVA_5a6.10
+A10,G3,Tetracycline,BASIC_SEVA_5a7.10
+B10,G3,Tetracycline,BASIC_SEVA_5a7.10
+C10,G3,Tetracycline,BASIC_SEVA_5a7.10
+D10,G3,Tetracycline,BASIC_SEVA_5a7.10
+E10,H3,Tetracycline,BASIC_SEVA_5a9.10
+F10,H3,Tetracycline,BASIC_SEVA_5a9.10
+G10,H3,Tetracycline,BASIC_SEVA_5a9.10
+H10,H3,Tetracycline,BASIC_SEVA_5a9.10
+A11,B4,Gentamicin,BASIC_SEVA_65a.10
+B11,B4,Gentamicin,BASIC_SEVA_65a.10
+C11,B4,Gentamicin,BASIC_SEVA_65a.10
+D11,B4,Gentamicin,BASIC_SEVA_65a.10
+E11,C4,Gentamicin,BASIC_SEVA_66.10
+F11,C4,Gentamicin,BASIC_SEVA_66.10
+G11,C4,Gentamicin,BASIC_SEVA_66.10
+H11,C4,Gentamicin,BASIC_SEVA_66.10
+A12,D4,Gentamicin,BASIC_SEVA_67.10
+B12,D4,Gentamicin,BASIC_SEVA_67.10
+C12,D4,Gentamicin,BASIC_SEVA_67.10
+D12,D4,Gentamicin,BASIC_SEVA_67.10
+E12,E4,Gentamicin,BASIC_SEVA_69.10
+F12,E4,Gentamicin,BASIC_SEVA_69.10
+G12,E4,Gentamicin,BASIC_SEVA_69.10
+H12,E4,Gentamicin,BASIC_SEVA_69.10