almacenado y renombrado en Nuevo-Dropbox

@@ -299,7 +299,7 @@ if __name__ == "__main__":
 
     # Original: labels = list(crf.classes_)
     # Original: labels.remove('O')
-    labels = list(['Air', 'Gtype', 'Gversion', 'Med', 'Phase', 'Sample', 'Serie', 'Strain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Vess'])
+    labels = list(['Air', 'Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Vess'])
 
     # use the same metric for evaluation
     f1_scorer = make_scorer(metrics.flat_f1_score,

-!Sample_characteristics_ch1	!Sample_characteristics_ch2	!Sample_data_processing	!Sample_extract_protocol_ch1	!Sample_growth_protocol_ch1	!Sample_growth_protocol_ch2	!Sample_library_strategy	!Sample_organism_ch1	!Sample_organism_ch2	!Sample_source_name_ch1	!Sample_source_name_ch2	!Sample_title	!Sample_treatment_protocol_ch1
-Med	Substrain	Technique	Phase	Med	Med	Technique	Substrain	Orgn	Supp	Name	Name	Supp
-Orgn	Med	Gversion		Vess	Agit	Gversion	Strain		Gtype			Phase
-Strain	Gtype			Temp	Temp		Orgn		Name			OD
-Supp	Supp			Supp	Air		Name		Air			Temp
-Air	Air			OD								Med
-Substrain				Air								
-Anti				Phase								
-Phase				Gtype								
-Gtype				Agit								

-Agit	Air	Anti	Gtype	Gversion	Med	Name	OD	Orgn	Phase	Strain	Substrain	Supp	Technique	Temp	Vess
-gyratory water bath shaking at 240 rpm	aerobically (25% O2, 70% N2 and 5% CO2)	9E10 Myc tag	fur-8myc	NC_000913.2	M63 minimal glucose	Fur IP ChIP-Seq Anaerobic A	OD600 of ~0.3-0.35	Escherichia coli str. K-12 substr. MG1655	exponential	K-12	MG1655	20 min	RNA-Seq	30 °C (see control sample)	flask
-	anerobically (95% N2, 5% CO2)	Affinity Purified FNR antibody	delta_cra	U00096.2	M63	σ32 30°C rep1	O.D.600nm 0.3	K-12 MG1655	mid-log phase		MG1655star	100ug/L adenine	ChIP-Seq	37 °C	
-	Aerobic	anti-Fur polyclonal antibody	∆fnr	ASM584v2	LB	Fur IP ChIP-Seq Anaerobic C	OD600 of 2.0	Escherichia coli	mid-log			Fe and rifampicin	ChIP-exo	30 degrees C	
-	aerobically	affinity purified anti-Fur antibody	dFNR (PK4854)	NC_000913	M9 minimal complete media	Fur IP ChIP-Seq Anaerobic B	OD600 ≈ 0.5	Escherichia coli K-12	mid-log phase 			Fe		30 °C	
-	anaerobic	SeqA	oxyR-8myc	NC_000913 	glucose (2 g/L) minimal M9 medium	LB 0.4 B2 TEX pos L1 HS2	OD600 of 0.35	MG1655	mid-log pahse			Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)		37°C 	
-	anaerobically (95% N2 and 5% CO2)	anti-RpoS	WT	ChIP-Seq	M9 minimal media	LB 0.4 B2 TEX pos L1 HS1	OD600 of 0.3	Escherichia coli str. K-12 substr. MG1655star	stationary			acetate		43 °C	
-	anaerobically	Pre-cleared IHF polyclonal antibody	wild type		LB media	Wild type control (10 min)	OD600 of about 0.3					150 mg/mL		43 °C (see heat sample)	
-	aerobically (70% N2, 25% O2, and 5% CO2)	anti-myc	Wild-Type		L broth	LB 0.4 B1 TEX pos L1 GA	OD600 of ~0.4					16 µM IPTG and 300 µL Cm20		37°C	
-	Anaerobic	anti-RpoB	Wildtype		M9 medium	σ32 30°C rep2	OD600 of about 0.15					DPD			
-		Pre-cleared FNR antibody	lacking the transcription factor Fur and the small RNA RyhB		MOPS	ChIP-exo GadX pH5.5 2						2g/L glutamine			
-		σ32	gadX-8myc		glucose (2 g/L) minimal W2 medium	ChIP-exo GadX pH5.5 1						absence of 1 g/L arginine			
-		RNA polymerase subunit β	lacking the transcription factor Fur		M9 minimal medium	NsrR_Flagtag_rep3						2 g/L glucose			
-		none	crp Knock-out strain		MOPS minimal glucose media	NsrR_Flagtag_rep2						4 µM IPTG			
-		RNA Polymerase ß monoclonal antibody	TrpR-8myc			NsrR_Flagtag_rep1						16 µM IPTG			
-		anti-FLAG mAb	PhtpG::lacZ delta lacX74/ptrc99A (control vector)			RpoB WT 2						8 µM IPTG and 300 µL Cm20			
-		Pre-cleared H-NS polyclonal antibody	cra-8myc-tagged			RpoB WT 1						1g/L arginine			
-		anti-rpoB	dFNR			Ecoli_wild-type_rep2_anaerobic						0.2% fructose			
-			gadW-8myc			HNS - Aerobic A						0.3 M of NaCl			
-			wildtype			HNS - Aerobic B						0.2% acetate			
-			PK4854			∆fnr - Anaeroibc						0.2%			
-			{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12			TrpR_glucose						DPD and rifampicin			
-			gadE-8myc			WT_ChIPSeq_2						1 µM FeSO4			
-			Combined input			ChIP-exo GadE pH5.5 2						20 mg/L tryptophan			
-			delta-gadE			ChIP-exo GadE pH5.5 1						250 uM of paraquat			
-			ompR-8myc			WT_ChIPSeq_1						0.1mM of FeCl2			
-			lacking the small RNA RyhB			WT PQ 2						Adenine			
-			Flag-tag			ChIP-exo GadW pH5.5 1						rifampicin dissolved in methanol			
-			{delta}tonB, {delta}feoA, {delta}zupT K12			OmpR NaCl 2						nitrate			
-			PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)			OmpR NaCl 1						0.2% glucose			
-			delta-gadX			ChIP-exo GadW pH5.5 2						fructose			
-			delta-gadW			Ptac::fnr - A - 8 µM IPTG						10 µM FeSO4			
-			PurR-8myc			SeqA old deltaSeqA						8 µM IPTG			
-			delta-oxyR			ΔgadW pH5.5 1						0.2mM of DPD			
-			soxR-8myc			ΔoxyR PQ 1						2 hours			
-			ΔseqA			ΔoxyR PQ 2						30 min			
-			PK8263			ΔgadW pH5.5 2						4 µM IPTG and 300 µL Cm20			
-			delta-soxS			∆ryhB Aerobic						presence or absence of 1 g/L arginine			
-			delta-soxR			σ32 ChIP DNA, heat						1mM IPTG			
-			∆hns/∆stpA			Δfur with Fe 2 (RNA-seq)						glucose			
-			soxS-8myc			RpoH induced (20 min)						2h			
-			Wild-type			SoxR PQ 1						10 mM leucine			
-			Δfur			SoxR PQ 2									
-			Lrp-8myc			LB 2.0 B2 TEX neg L1 HS1									
-			ArgR-8myc			PurR_glucose_2									
-			NsrR			PurR_glucose_1									
-			cra Knock-out strain			LB 2.0 B2 TEX neg L1 HS2									
-			ompR deletion mutant			SeqA new rep2									
-						WT with Fe 2 (RNA-seq)									
-						RpoH induced (2.5 min)									
-						Δcra acetate 1									
-						Δcra acetate 2									
-						Nac_ChIPSeq									
-						EC18n185 RpoH 10 min Time course 3									
-						σ32 43°C rep2									
-						RpoB with Fe 1 (ChIP-exo)									
-						CsiR_RNASeq									
-						ΔsoxR PQ 1									
-						EC18n169 RpoH 5 min Time course 2									
-						CsiR_ChIPSeq									
-						HNS - Anaerobic A									
-						Fur IP ChIP-Seq Aerobic A									
-						Fur IP ChIP-Seq Aerobic B									
-						HNS - Anaerobic B									
-						σ32 43°C rep1									
-						LB 2.0 B1 TEX pos L2 HS2									
-						OxyR PQ 2									
-						Wild type control (0 min)									
-						WT acetate 1									
-						WT acetate 2									
-						M63 0.4 B2 TEX pos L1 HS1									
-						M63 0.4 B2 TEX pos L1 HS2									
-						SeqA new rep1									
-						SeqA old rep2									
-						IHF - Anaerobic B									
-						IHF - Anaerobic A									
-						RNAP old rep2									
-						RpoH induced (0 min)									
-						EC18n180 RpoH 10 min Time course 1									
-						EC18n122 RpoH 10 min Time course 4									
-						LB 2.0 B2 TEX pos L1 HS1									
-						Crosslink									
-						LB 2.0 B2 TEX pos L1 HS2									
-						Cra glucose 1									
-						Cra glucose 2									
-						Cra fructose 1									
-						Cra fructose 2									
-						Wild-type Aerobic A									
-						Wild-type Aerobic B									
-						RpoB with DPD and rifampicin 1 (ChIP-exo)									
-						SoxS PQ 2									
-						SoxS PQ 1									
-						EC18n178 RpoH 2.5 min Time course 1									
-						Wild type control (20 min)									
-						pT7_ChIPSeq_1									
-						pT7_ChIPSeq_2									
-						EC18n182 RpoH 0 min Time course 3									
-						RNAP old rep1									
-						Lrp_Leu_1									
-						Lrp_Leu_3									
-						Lrp_Leu_2									
-						RpoB with DPD 1 (ChIP-exo)									
-						Cra acetate 1									
-						Cra acetate 2									
-						EC18n171 RpoH 20 min Time course 2									
-						EC18n179 RpoH 5 min Time course 1									
-						Ptac::fnr - A - 16 µM IPTG									
-						∆fur ∆ryhB Aerobic B									
-						Nac_RNASeq									
-						LB 2.0 B1 TEX pos L1 GA									
-						∆fur Anaerobic A									
-						σ32 30°C short RNase									
-						EC18n181 RpoH 20 min Time course 1									
-						M63 0.4 B2 TEX neg L1 HS1									
-						M63 0.4 B2 TEX neg L1 HS2									
-						EC18n168 RpoH 2.5 min Time course 2									
-						Δcra glucose 1									
-						Δcra glucose 2									
-						Lrp_NH4Cl_2									
-						Lrp_NH4Cl_3									
-						Lrp_NH4Cl_1									
-						LB 2.0 B1 TEX neg L2 HS2									
-						ΔsoxS PQ 1									
-						Δcra fructose 1									
-						Δcra fructose 2									
-						WT_RNASeq									
-						WT glucose 1									
-						WT glucose 2									
-						Wild type control (5 min)									
-						EC18n184 RpoH 5 min Time course 3									
-						Fur IP ChIP-Seq Aerobic C									
-						RpoB with Fe and rifampicin 1 (ChIP-exo)									
-						Fur with Fe 2 (ChIP-exo)									
-						FNR - Anaerobic - A									
-						WT with Fe 1 (RNA-seq)									
-						FNR - Anaerobic - C									
-						FNR - Anaerobic - B									
-						ΔompR NaCl 2									
-						ΔompR NaCl 1									
-						Ecoli_dFNR_rep1_anaerobic									
-						Ptac::fnr - A - 4 µM IPTG									
-						LB 2.0 B2 TEX neg L2 HS2									
-						PurR_Adenine_1									
-						Ecoli_wild-type_rep1_anaerobic									
-						EC18n167 RpoH 0 min Time course 2									
-						Wild-type Anaerobic B									
-						Fur with Fe 1 (ChIP-exo)									
-						FNR - ∆hns∆stpA A									
-						RpoB with Fe 2 (ChIP-exo)									
-						FNR - ∆hns∆stpA B									
-						RpoB ∆cra 2									
-						RpoB with DPD and rifampicin 2 (ChIP-exo)									
-						RpoB ∆cra 1									
-						WT NaCl 1									
-						WT NaCl 2									
-						WT with DPD 1 (RNA-seq)									
-						LB 0.4 B1 TEX neg L1 GA									
-						Ptac::fnr - B - 8 µM IPTG									
-						ArgR_Arginine_2									
-						LB 0.4 B2 TEX neg L1 HS2									
-						LB 0.4 B2 TEX neg L1 HS1									
-						ArgR_Arginine_1									
-						ArgR_NH4Cl_1									
-						Escherichia coli str. K-12 substr. MG1655									
-						OxyR PQ 1									
-						ΔgadX pH5.5 2									
-						∆fur ∆ryhB Anaerobic A									
-						ΔgadX pH5.5 1									
-						Fur IP ChIP-Seq Anaerobic, Iron Deficient B									
-						Δfur with Fe 1 (RNA-seq)									
-						Fur IP ChIP-Seq Anaerobic, Iron Deficient A									
-						ß - Anaerobic - A									
-						ß - Anaerobic - B									
-						σ32 ChIP DNA, control									
-						SeqA new deltaSeqA									
-						M63 0.4 B1 TEX neg L1 GA									
-						TrpR_Trp									
-						Ptac::fnr - B - 16 µM IPTG									
-						ß - Aerobic - A									
-						Ptac::fnr - B - 4 µM IPTG									
-						ß - Aerobic - B									
-						EC18n177 RpoH 0 min Time course 1									
-						σ32 43°C short RNase									
-						∆ryhB Anaerobic									
-						Input ChIP-Seq									
-						Δfur with DPD 1 (RNA-seq)									
-						RpoH induced (5 min)									
-						∆fur Anaerobic B									
-						FNR - Anaerobic - Affinity Purified - B									
-						EC18n186 RpoH 20 min Time course 3									
-						FNR - Anaerobic - Affinity Purified - A									
-						ChIP-exo RpoS pH5.5 2									
-						RpoB with DPD 2 (ChIP-exo)									
-						ChIP-exo RpoS pH5.5 1									
-						ΔsoxR PQ 2									
-						PurR_Adenine_2									
-						Ptac::fnr - C - 16 µM IPTG									
-						WT PQ 1									
-						EC18n170 RpoH 10 min Time course 2									
-						∆fur ∆ryhB Anaerobic B									
-						M63 0.4 B1 TEX pos L1 GA									
-						RpoH induced (10 min)									
-						Wild-type Anaerobic A									
-						ArgR_NH4Cl_2									
-						LB 2.0 B1 TEX neg L1 GA									
-						WT with DPD 2 (RNA-seq)									
-						∆fur Anaerobic [IP vs nput]									
-						EC18n183 RpoH 2.5 min Time course 3									
-						∆fur ∆ryhB Aerobic A									
-						RpoB ∆crp 2									
-						NtrC_ChIPSeq									
-						RpoB ∆crp 1									
-						WT fructose 1									
-						ΔgadE pH5.5 2									
-						ΔgadE pH5.5 1									
-						WT fructose 2									
-						OmpR_ChIPSeq									
-						RpoB with Fe and rifampicin 2 (ChIP-exo)									
-						WT pH5.5 1									
-						WT pH5.5 2									
-						Wild type control (2.5 min)									
-						Ecoli_dFNR_rep2_anaerobic									
-						Fur with DPD 1 (ChIP-exo)									
-						∆fur Aerobic A									
-						∆fur Aerobic B									
-						ΔsoxS PQ 2									
-						Δfur with DPD 2 (RNA-seq)									
-						Fur with DPD 2 (ChIP-exo)									
-						SeqA old rep1									
-						LB 2.0 B2 TEX pos L2 HS2