def tab_reorder(fname, column_order, delim='\t'):
f = gzip_opener(fname).open()
for line in f:
if line[0] == '#':
sys.stdout.write(line)
continue
cols = line.rstrip('\n').split(delim)
cols_used = set()
outcols = []
for col_idx in column_order:
if col_idx == '*':
for i, val in enumerate(cols):
if not i in cols_used:
outcols.append(val)
break
else:
outcols.append(cols[col_idx])
if col_idx < 0:
cols_used.add(len(cols) + col_idx)
else:
cols_used.add(col_idx)
sys.stdout.write('%s\n' % '\t'.join(outcols))
f.close()
def tab_view(fname,preview_lines=100,delim='\t',max_size=None, min_size=0):
colsizes = []
coltypes = []
preview_buf = []
prev_count = 0
inpreview = True
try:
f = gzip_opener(fname).open()
for line in f:
if inpreview and line[0] == '#':
preview_buf.append(line)
else:
if inpreview:
cols = line.rstrip().split(delim)
for i,col in enumerate(cols):
if len(colsizes) <= i:
colsizes.append(len(col))
coltypes.append('i')
elif len(col) > colsizes[i]:
colsizes[i] = len(col)
try:
v = int(col)
except:
coltypes[i] = 't'
preview_buf.append(line)
prev_count += 1
if prev_count >= preview_lines:
if max_size:
colsizes = [ min(max_size, int(math.ceil(x * 1.2))) for x in colsizes ]
else:
colsizes = [ max(min_size, int(math.ceil(x * 1.2))) for x in colsizes ]
for preview in preview_buf:
_write_cols(preview,colsizes,coltypes)
preview_buf = None
inpreview=False
else:
_write_cols(line,colsizes,coltypes)
if f != sys.stdin:
f.close()
if preview_buf:
colsizes = [ int(math.ceil(x * 1.2)) for x in colsizes ]
for preview in preview_buf:
_write_cols(preview,colsizes,coltypes)
except KeyboardInterrupt:
print ""
pass
except IOError:
print ""
pass
def tab_combine(outfile, fnames ,delim='\t'):
workbook = xlsxwriter.Workbook(outfile, {'strings_to_numbers': True})
for fname in fnames:
sys.stderr.write(fname.rstrip(".gz").rstrip(".txt"))
sys.stderr.write("... ")
worksheet = workbook.add_worksheet(fname.rstrip(".gz").rstrip(".txt")[:31])
f = gzip_opener(fname).open()
row = 0
for line in f:
cols = line.rstrip().split(delim)
for col, val in enumerate(cols):
worksheet.write(row, col, val)
row += 1
sys.stderr.write("done\n")
f.close()
workbook.close()
def filter_file(fname,criteria,header):
f = gzip_opener(fname).open()
line_num = 0
for line in f:
if line[0] == '#':
sys.stdout.write(line)
continue
if line_num == 0 and header:
sys.stdout.write(line)
line_num += 1
continue
cols = line.strip().split('\t')
good = True
if criteria.filter(cols):
sys.stdout.write(line)
if f != sys.stdin:
f.close()
def tab_tag(fname, colname, colvalue, colidx, delim='\t', noheader=False):
f = gzip_opener(fname).open()
header = not noheader
for line in f:
if line[0] == '#':
sys.stdout.write(line)
continue
cols = line.rstrip('\n').split(delim)
if header:
cols.insert(colidx, colname)
header = False
else:
cols.insert(colidx, colvalue)
sys.stdout.write('%s\n' % '\t'.join(cols))
f.close()
