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11 additions
and
11 deletions
| 1 | "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" | 1 | "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" |
| 2 | -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 3 | -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 4 | -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 5 | "GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" | 2 | "GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" |
| 6 | "GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" | 3 | "GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" |
| 7 | "GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" | 4 | "GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" |
| ... | @@ -14,6 +11,9 @@ | ... | @@ -14,6 +11,9 @@ |
| 14 | "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" | 11 | "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" |
| 15 | "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" | 12 | "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" |
| 16 | "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" | 13 | "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" |
| 14 | +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 15 | +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 16 | +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 17 | "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" | 17 | "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" |
| 18 | "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" | 18 | "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" |
| 19 | "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" | 19 | "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" | ... | ... |
| 1 | "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" | 1 | "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" |
| 2 | -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" | ||
| 3 | -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" | ||
| 4 | -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" | ||
| 5 | -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" | ||
| 6 | -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 7 | -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 8 | -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 9 | "GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" | 2 | "GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" |
| 10 | "GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" | 3 | "GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" |
| 11 | "GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" | 4 | "GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" |
| ... | @@ -18,6 +11,9 @@ | ... | @@ -18,6 +11,9 @@ |
| 18 | "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" | 11 | "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" |
| 19 | "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" | 12 | "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" |
| 20 | "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" | 13 | "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" |
| 14 | +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 15 | +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 16 | +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" | ||
| 21 | "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" | 17 | "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" |
| 22 | "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" | 18 | "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" |
| 23 | "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" | 19 | "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" |
| ... | @@ -33,3 +29,7 @@ | ... | @@ -33,3 +29,7 @@ |
| 33 | "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" | 29 | "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" |
| 34 | "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" | 30 | "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" |
| 35 | "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask","" | 31 | "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask","" |
| 32 | +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" | ||
| 33 | +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" | ||
| 34 | +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" | ||
| 35 | +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" | ... | ... |
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| ... | @@ -147,7 +147,7 @@ if __name__ == "__main__": | ... | @@ -147,7 +147,7 @@ if __name__ == "__main__": |
| 147 | # oFile.write("Serie: {}\tSample: {}\tTag: {}\tContent: {}\n".format(serie, sample, tag, content)) | 147 | # oFile.write("Serie: {}\tSample: {}\tTag: {}\tContent: {}\n".format(serie, sample, tag, content)) |
| 148 | saved_files+=1 | 148 | saved_files+=1 |
| 149 | 149 | ||
| 150 | - with open(os.path.join(options.outputPath, f.replace(".xml", ".complete-report.csv")), "w") as oFile: | 150 | + with open(os.path.join(options.outputPath, "GSE_family.complete-report.csv"), "w") as oFile: |
| 151 | for line in complete_report: | 151 | for line in complete_report: |
| 152 | oFile.write(line + "\n") | 152 | oFile.write(line + "\n") |
| 153 | 153 | ... | ... |
-
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