# Sort into order by fold_enrichment and then by -10*log10(pvalue) column
data.sort(lambda line: line['fold_enrichment'],reverse=True)
data.sort(lambda line: line['-10*log10(pvalue)'],reverse=True)
# Restore first line
data.insert(0,tabdata=header_line)
# Insert "order" column
data.appendColumn("order")
# Perhaps confusingly must also insert initial value "#order"
data[0]['order'] = "#order"
for i in range(1,len(data)):
data[i]['order'] = i
# Reorder columns to put it at the start
data = data.reorderColumns(['order','chr','start','end','length','summit','tags',
'-10*log10(pvalue)','fold_enrichment','FDR(%)'])
# Legnds text
legends_text = """order\tSorting order Pvalue and FE
chr\tChromosome location of binding region
start\tStart coordinate of binding region
end\tEnd coordinate of binding region
summit-100\tSummit - 100bp
summit+100\tSummit + 100bp
summit-1\tSummit of binding region - 1
summit\tSummit of binding region
length\tLength of binding region
summit\tPeak of summit region from the start position of the binding region
tags\tNumber of non-degenerate and position corrected reads in the binding region
-10*LOG10(pvalue)\tTransformed Pvalue -10*log10(Pvalue) for the binding region (e.g. if Pvalue=1e-10, then this value should be 100)
fold_enrichment\tFold enrichment for this region against random Poisson distribution with local lambda
# Sort into order by fold_enrichment and then by -log10(pvalue) column
data.sort(lambda line: line['fold_enrichment'], reverse=True)
data.sort(lambda line: line['-log10(pvalue)'], reverse=True)
# Restore first line
data.insert(0, tabdata=header_line)
# Insert "order" column
data.appendColumn("order")
# Perhaps confusingly must also insert initial value "#order"
data[0]['order'] = "#order"
for i in range(1, len(data)):
data[i]['order'] = i
# Reorder columns to put it at the start
data = data.reorderColumns([
'order', 'chr', 'start', 'end', 'length', 'abs_summit', 'pileup',
'-log10(pvalue)', 'fold_enrichment', '-log10(qvalue)'
])
# Legnds text
legends_text = """order\tSorting order Pvalue and FE
chr\tChromosome location of binding region
start\tStart coordinate of binding region
end\tEnd coordinate of binding region
summit-100\tSummit - 100bp
summit+100\tSummit + 100bp
summit-1\tSummit of binding region - 1
summit\tSummit of binding region
length\tLength of binding region
abs_summit\tCoordinate of region summit
pileup\tNumber of non-degenerate and position corrected reads at summit
-LOG10(pvalue)\tTransformed Pvalue -log10(Pvalue) for the binding region (e.g. if Pvalue=1e-10, then this value should be 10)
# Sort into order by fold_enrichment and then by -10*log10(pvalue) column
data.sort(lambda line: line['fold_enrichment'], reverse=True)
data.sort(lambda line: line['-10*log10(pvalue)'], reverse=True)
# Restore first line
data.insert(0, tabdata=header_line)
# Insert "order" column
data.appendColumn("order")
# Perhaps confusingly must also insert initial value "#order"
data[0]['order'] = "#order"
for i in range(1, len(data)):
data[i]['order'] = i
# Reorder columns to put it at the start
data = data.reorderColumns([
'order', 'chr', 'start', 'end', 'length', 'summit', 'tags',
'-10*log10(pvalue)', 'fold_enrichment', 'FDR(%)'
])
# Legnds text
legends_text = """order\tSorting order Pvalue and FE
chr\tChromosome location of binding region
start\tStart coordinate of binding region
end\tEnd coordinate of binding region
summit-100\tSummit - 100bp
summit+100\tSummit + 100bp
summit-1\tSummit of binding region - 1
summit\tSummit of binding region
length\tLength of binding region
summit\tPeak of summit region from the start position of the binding region
tags\tNumber of non-degenerate and position corrected reads in the binding region
-10*LOG10(pvalue)\tTransformed Pvalue -10*log10(Pvalue) for the binding region (e.g. if Pvalue=1e-10, then this value should be 100)
# Sort into order by fold_enrichment and then by -log10(pvalue) column
data.sort(lambda line: line['fold_enrichment'],reverse=True)
data.sort(lambda line: line['-log10(pvalue)'],reverse=True)
# Restore first line
data.insert(0,tabdata=header_line)
# Insert "order" column
data.appendColumn("order")
# Perhaps confusingly must also insert initial value "#order"
data[0]['order'] = "#order"
for i in range(1,len(data)):
data[i]['order'] = i
# Reorder columns to put it at the start
data = data.reorderColumns(['order','chr','start','end','length','abs_summit','pileup',
'-log10(pvalue)','fold_enrichment','-log10(qvalue)'])
# Legnds text
legends_text = """order\tSorting order Pvalue and FE
chr\tChromosome location of binding region
start\tStart coordinate of binding region
end\tEnd coordinate of binding region
summit-100\tSummit - 100bp
summit+100\tSummit + 100bp
summit-1\tSummit of binding region - 1
summit\tSummit of binding region
length\tLength of binding region
abs_summit\tCoordinate of region summit
pileup\tNumber of non-degenerate and position corrected reads at summit
-LOG10(pvalue)\tTransformed Pvalue -log10(Pvalue) for the binding region (e.g. if Pvalue=1e-10, then this value should be 10)
fold_enrichment\tFold enrichment for this region against random Poisson distribution with local lambda
