else :
stats[row[10]] += 1
all_stats[row[10]] += 1
tot_reads = sum(stats.values())/1.-stats.get('QC',0)
unique_reads = sum([v for k,v in stats.items() if k.startswith('chr')])
repeat_reads = stats.get('multiread',0)
nomap_reads = stats.get('NM',0)
data_row = [fn,format_with_commas(int(tot_reads)),
'%.1f'%(unique_reads/tot_reads*100),format_with_commas(unique_reads),
'%.1f'%(repeat_reads/tot_reads*100),format_with_commas(repeat_reads),
'%.1f'%(nomap_reads/tot_reads*100),format_with_commas(nomap_reads)]
data_rows.append(data_row)
out_f = open(opts.output,'w') if opts.output is not None else sys.stdout
if opts.format == 'python' :
out_f.write(dict(all_stats))
elif opts.format == 'rst' :
doc = ReStDocument(out_f)
table = ReStSimpleTable(header=stats_fields,data=data_rows)
doc.add(table)
doc.write()
elif opts.format == 'tab' :
out_w = writer(out_f,delimiter='\t')
out_w.writerow(stats_fields)
out_w.writerows(data_rows)
if opts.output is not None : out_f.close()
import sys
from reStUtil import ReStDocument, ReStSimpleTable, ReStTable
doc = ReStDocument(sys.stdout)
# very simple
header = ["Column A","Column B","Column C"]
data = [['012','345','678']]
doc.add('Simple simple_table, no text wrap')
doc.add(ReStSimpleTable(header,data))
# word wrapped text
header = ["Food", "Deliciousness", "Notes"]
data = [["hot dogs","moderate-high","Depending on the meat used, hot dogs can provide a delicious snack or a mysterious culinary experiment"],
["cabbage","low-moderate","Best results often enjoyed when cooked with corned beef or braughwurst"],
["pickles and ice cream","low/very high","For pregnant women only"],
]
doc.add('Text wrapped simple_table')
doc.add(ReStSimpleTable(header,data,40))
doc.add('Table directive with title and word wrapped data')
doc.add(ReStTable(header,data,title="Food Analysis",max_col_width=40))
doc.write()
import sys
from reStUtil import ReStDocument, ReStSection, ReStTable
doc = ReStDocument(sys.stdout)
# section 1
sec1 = ReStSection("Section 1",level=1)
sec1.add("The text in section 1")
sec1_1 = ReStSection("Subsection 1.1",level=2)
sec1_1.add("The text in subsection 1.1")
sec1 += sec1_1
sec2 = ReStSection("Section 2",level=1)
sec2.add("The text in section 2")
sec2_1 = ReStSection("Subsection 2.1",level=2)
sec2_1.add("The text in subsection 2.1")
sec2_2 = ReStSection("Subsection 2.2",level=2)
sec2_2.add("Text in subsection 2.2")
sec2.add(sec2_1,sec2_2)
sec3 = ReStSection("Section 3",level=1)
sec3.add("This section has many nested subsections")
sec3.add(ReStSection("Subsection 3.1",level=2))
sec3.add(ReStSection("Subsubsection 3.1.1",level=3))
sec3.add(ReStSection("Subsubsubsection 3.1.1.1",level=4))
sec3.add(ReStSection("Subsubsubsubsection 3.1.1.1.1",level=5))
sec3.add(ReStSection("Subsubsubsubsubsection 3.1.1.1.1.1",level=6))