def save_txt(fpath, all_rows, potential_scaffolds_assemblies_info=None):
# determine width of columns for nice spaces
colwidths = [0] * (len(all_rows[0]['values']) + 1)
for row in all_rows:
for i, cell in enumerate([row['metricName']] +
[val_to_str(this) for this in row['values']]):
colwidths[i] = max(colwidths[i], len(cell))
# output it
txt_file = open(fpath, 'w')
if qconfig.min_contig:
txt_file.write('All statistics are based on contigs of size >= %d bp, unless otherwise noted ' % qconfig.min_contig + \
'(e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).\n')
if potential_scaffolds_assemblies_info:
txt_file.write("Suggestion: " + potential_scaffolds_assemblies_info + " continuous fragments of N's of " \
"length >= 10 bp. You may consider rerunning QUAST using --scaffolds (-s) option!\n")
txt_file.write('\n')
for row in all_rows:
txt_file.write(' '.join(
'%-*s' % (colwidth, cell) for colwidth, cell in zip(
colwidths, [row['metricName']] +
[val_to_str(this) for this in row['values']])) + "\n")
txt_file.close()
def print_file(all_rows, fpath, append_to_existing_file=False):
colwidths = repeat(0)
for row in all_rows:
colwidths = [max(len(v), w) for v, w in zip([row['metricName']] + [val_to_str(v) for v in row['values']], colwidths)]
txt_file = open(fpath, 'a' if append_to_existing_file else 'w')
for row in all_rows:
txt_file.write(' '.join('%-*s' % (colwidth, cell) for colwidth, cell
in zip(colwidths, [row['metricName']] + [val_to_str(v) for v in row['values']])) + '\n')
def print_file(all_rows, fpath, append_to_existing_file=False):
colwidths = repeat(0)
for row in all_rows:
colwidths = [max(len(v), w) for v, w in zip([row['metricName']] + [val_to_str(v) for v in row['values']], colwidths)]
txt_file = open(fpath, 'a' if append_to_existing_file else 'w')
for row in all_rows:
txt_file.write(' '.join('%-*s' % (colwidth, cell) for colwidth, cell
in zip(colwidths, [row['metricName']] + [val_to_str(v) for v in row['values']])) + '\n')
def save_tsv(fpath, all_rows):
tsv_file = open(fpath, 'w')
for row in all_rows:
tsv_file.write('\t'.join([row['metricName']] +
[val_to_str(this)
for this in row['values']]) + "\n")
tsv_file.close()
def save_tsv(fpath, all_rows):
tsv_file = open(fpath, 'w')
for row in all_rows:
tsv_file.write('\t'.join([row['metricName']] + [val_to_str(this) for
this in row['values']]) + "\n")
tsv_file.close()
def save_txt(fpath, all_rows):
# determine width of columns for nice spaces
colwidths = [0] * (len(all_rows[0]['values']) + 1)
for row in all_rows:
for i, cell in enumerate([row['metricName']] +
[val_to_str(this) for this in row['values']]):
colwidths[i] = max(colwidths[i], len(cell))
# output it
txt_file = open(fpath, 'w')
if qconfig.min_contig:
txt_file.write('All statistics are based on contigs of size >= %d bp, unless otherwise noted ' % qconfig.min_contig + \
'(e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).\n')
txt_file.write('\n')
for row in all_rows:
txt_file.write(' '.join(
'%-*s' % (colwidth, cell) for colwidth, cell in zip(
colwidths, [row['metricName']] +
[val_to_str(this) for this in row['values']])) + "\n")
txt_file.close()
def save_txt(fpath, all_rows, potential_scaffolds_assemblies_info=None):
# determine width of columns for nice spaces
colwidths = [0] * (len(all_rows[0]['values']) + 1)
for row in all_rows:
for i, cell in enumerate([row['metricName']] + [val_to_str(this) for
this in row['values']]):
colwidths[i] = max(colwidths[i], len(cell))
# output it
txt_file = open(fpath, 'w')
if qconfig.min_contig:
txt_file.write('All statistics are based on contigs of size >= %d bp, unless otherwise noted ' % qconfig.min_contig + \
'(e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).\n')
if potential_scaffolds_assemblies_info:
txt_file.write("Suggestion: " + potential_scaffolds_assemblies_info + " continuous fragments of N's of " \
"length >= 10 bp. You may consider rerunning QUAST using --scaffolds (-s) option!\n")
txt_file.write('\n')
for row in all_rows:
txt_file.write(' '.join('%-*s' % (colwidth, cell) for colwidth, cell
in zip(colwidths, [row['metricName']] + [val_to_str(this) for this in row['values']])) + "\n")
txt_file.close()
def save_tex(fpath, all_rows, is_transposed=False):
tex_file = open(fpath, 'w')
# Header
tex_file.write('\\documentclass[12pt,a4paper]{article}\n')
tex_file.write('\\begin{document}\n')
tex_file.write('\\begin{table}[ht]\n')
tex_file.write('\\begin{center}\n')
tex_file.write('\\caption{All statistics are based on contigs of size $\geq$ %d bp, unless otherwise noted ' % qconfig.min_contig + \
'(e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).}\n')
rows_n = len(all_rows[0]['values'])
tex_file.write('\\begin{tabular}{|l*{' + val_to_str(rows_n) + '}{|r}|}\n')
tex_file.write('\\hline\n')
# Body
for row in all_rows:
values = row['values']
quality = row['quality'] if ('quality'
in row) else Fields.Quality.EQUAL
if is_transposed or quality not in [
Fields.Quality.MORE_IS_BETTER, Fields.Quality.LESS_IS_BETTER
]:
cells = _mapme(val_to_str, values)
else:
# Checking the first value, assuming the others are the same type and format
num = get_num_from_table_value(values[0])
if num is None: # Not a number
cells = _mapme(val_to_str, values)
else:
nums = _mapme(get_num_from_table_value, values)
best = None
if quality == Fields.Quality.MORE_IS_BETTER:
best = max(n for n in nums if n is not None)
if quality == Fields.Quality.LESS_IS_BETTER:
best = min(n for n in nums if n is not None)
if len([num for num in nums if num != best]) == 0:
cells = _mapme(val_to_str, values)
else:
cells = [
'HIGHLIGHTEDSTART' + val_to_str(v) +
'HIGHLIGHTEDEND' if get_num_from_table_value(v) == best
else val_to_str(v) for v in values
]
row = ' & '.join([row['metricName']] + cells)
# escape characters
for esc_char in "\\ % $ # _ { } ~ ^".split():
row = row.replace(esc_char, '\\' + esc_char)
# more pretty '>=' and '<=', '>'
row = row.replace('>=', '$\\geq$')
row = row.replace('<=', '$\\leq$')
row = row.replace('>', '$>$')
# pretty indent
if row.startswith(Fields.TAB):
row = "\hspace{5mm}" + row.lstrip()
if row.startswith(Fields.HALF_TAB):
row = "\hspace{2mm}" + row.lstrip()
# pretty highlight
row = row.replace('HIGHLIGHTEDSTART', '{\\bf ')
row = row.replace('HIGHLIGHTEDEND', '}')
row += ' \\\\ \\hline'
tex_file.write(row + "\n")
# Footer
tex_file.write('\\end{tabular}\n')
tex_file.write('\\end{center}\n')
tex_file.write('\\end{table}\n')
tex_file.write('\\end{document}\n')
tex_file.close()
if os.path.basename(fpath) == 'report.tex':
pass
def save_tex(fpath, all_rows, is_transposed=False):
tex_file = open(fpath, 'w')
# Header
tex_file.write('\\documentclass[12pt,a4paper]{article}\n')
tex_file.write('\\begin{document}\n')
tex_file.write('\\begin{table}[ht]\n')
tex_file.write('\\begin{center}\n')
tex_file.write('\\caption{All statistics are based on contigs of size $\geq$ %d bp, unless otherwise noted ' % qconfig.min_contig + \
'(e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).}\n')
rows_n = len(all_rows[0]['values'])
tex_file.write('\\begin{tabular}{|l*{' + val_to_str(rows_n) + '}{|r}|}\n')
tex_file.write('\\hline\n')
# Body
for row in all_rows:
values = row['values']
quality = row['quality'] if ('quality' in row) else Fields.Quality.EQUAL
if is_transposed or quality not in [Fields.Quality.MORE_IS_BETTER,
Fields.Quality.LESS_IS_BETTER]:
cells = _mapme(val_to_str, values)
else:
# Checking the first value, assuming the others are the same type and format
num = get_num_from_table_value(values[0])
if num is None: # Not a number
cells = _mapme(val_to_str, values)
else:
nums = _mapme(get_num_from_table_value, values)
best = None
if quality == Fields.Quality.MORE_IS_BETTER:
best = max(n for n in nums if n is not None)
if quality == Fields.Quality.LESS_IS_BETTER:
best = min(n for n in nums if n is not None)
if len([num for num in nums if num != best]) == 0:
cells = _mapme(val_to_str, values)
else:
cells = ['HIGHLIGHTEDSTART' + val_to_str(v) + 'HIGHLIGHTEDEND'
if get_num_from_table_value(v) == best
else val_to_str(v)
for v in values]
row = ' & '.join([row['metricName']] + cells)
# escape characters
for esc_char in "\\ % $ # _ { } ~ ^".split():
row = row.replace(esc_char, '\\' + esc_char)
# more pretty '>=' and '<=', '>'
row = row.replace('>=', '$\\geq$')
row = row.replace('<=', '$\\leq$')
row = row.replace('>', '$>$')
# pretty indent
if row.startswith(Fields.TAB):
row = "\hspace{5mm}" + row.lstrip()
# pretty highlight
row = row.replace('HIGHLIGHTEDSTART', '{\\bf ')
row = row.replace('HIGHLIGHTEDEND', '}')
row += ' \\\\ \\hline'
tex_file.write(row +"\n")
# Footer
tex_file.write('\\end{tabular}\n')
tex_file.write('\\end{center}\n')
tex_file.write('\\end{table}\n')
tex_file.write('\\end{document}\n')
tex_file.close()
if os.path.basename(fpath) == 'report.tex':
pass
