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xlsx2tsv: python command-line script to convert xlsx (Excel "OOXML") into tab-separated values
#!/usr/bin/env python
"""
xlsx2tsv filename.xlsx [sheet number or name]
Parse a .xlsx (Excel OOXML, which is not OpenOffice) into tab-separated values.
If it has multiple sheets, need to give a sheet number or name.
Outputs honest-to-goodness tsv, no quoting or embedded \\n\\r\\t.
One reason I wrote this is because Mac Excel 2008 export to csv or tsv messes
up encodings, converting everything to something that's not utf8 (macroman
perhaps). This script seems to do better.
The spec for this format is 5220 pages. I did not use it. This was helpful:
http://blogs.msdn.com/excel/archive/2008/08/14/reading-excel-files-from-linux.aspx
But mostly I guessed how the format works. So bugs are guaranteed.
brendan o'connor - anyall.org - gist.github.com/22764
"""
#from __future__ import print_function
import xml.etree.ElementTree as ET
import os,sys,zipfile,re,itertools
def myjoin(seq, sep=" "):
" because str.join() is annoying "
return sep.join(str(x) for x in seq)
args = sys.argv[:]
args.pop(0)
if args:
z = zipfile.ZipFile(args.pop(0))
elif not sys.stdin.isatty():
z = zipfile.ZipFile(sys.stdin)
else:
print __doc__.strip()
sys.exit(1)
n=lambda x: "{http://schemas.openxmlformats.org/spreadsheetml/2006/main}%s" % x
sheet_filenames = [f for f in z.namelist() if re.search("^xl/worksheets/sheet.*xml$", f)]
workbook_x = ET.XML(z.read("xl/workbook.xml"))
sheet_xs = workbook_x.find(n("sheets")).findall(n("sheet"))
def sheet_report():
global sheet_xs
print>>sys.stderr, "Sheets in this file:"
for i,x in enumerate(sheet_xs):
print>>sys.stderr, "%3d: %s" % (i+1, x.get('name'))
sys.exit(1)
def sheet_error(msg):
print>>sys.stderr, msg
sheet_report()
if not args and len(sheet_filenames) > 1:
sheet_error("There are multiple sheets -- need to specify a sheet number or name.")
elif not args and len(sheet_filenames) == 1:
sheet_num = 1
elif args:
sheet_num = args.pop(0)
if isinstance(sheet_num,str) and (not re.search('^[0-9]+$',sheet_num) or int(sheet_num) > len(sheet_filenames)):
name = sheet_num
inds = [i for i,x in enumerate(sheet_xs) if x.get('name')==name]
if not inds: sheet_error("Can't find sheet with name '%s'" % name)
if len(inds)>1: sheet_error("Multiple sheets with name '%s'" % name)
sheet_num = inds[0] + 1
def letter2col_index(letter):
""" A -> 0, B -> 1, Z -> 25, AA -> 26, BA -> 52 """
base26digits = [1+ord(x)-ord("A") for x in letter]
return sum([x*26**(len(base26digits) - k - 1) for k,x in enumerate(base26digits)]) - 1
def flatten(iter):
return list(itertools.chain(*iter))
def cell2text(cell):
if cell is None:
return ""
elif 't' in cell.attrib and cell.attrib['t'] == 's':
# shared string
idx = int(cell.find(n("v")).text)
si = ss_list[idx]
t_elt = si.find(n("t"))
if t_elt is not None:
return t_elt.text
t_elts = si.findall(n("r") + "/" + n("t"))
if t_elts:
text = "".join( (t.text) for t in t_elts )
return text
raise Exception("COULDNT DECODE CELL: %s" % ET.tostring(si))
#return si.find(n("t")).text
#return ET.tostring(si)
else:
v_elt = cell.find(n("v"))
if v_elt is None: return ""
return v_elt.text
ss_xml = z.read("xl/sharedStrings.xml")
ss_list = ET.XML(ss_xml).findall(n("si"))
xml = z.read("xl/worksheets/sheet%s.xml" % sheet_num)
s = ET.fromstring(xml)
rows = s.findall(n("sheetData")+"/"+n("row"))
all_cells = flatten( [[c for c in row.findall(n("c"))] for row in rows] )
max_col = max(letter2col_index(re.search("^[A-Z]+",c.attrib['r']).group()) for c in all_cells)
def make_cells():
return [None] * (max_col+1)
warning_count=0
warning_max = 50
def warning(s):
global warning_count
warning_count += 1
if warning_count > warning_max: return
print>>sys.stderr, "WARNING: %s" % s
def cell_text_clean(text):
s = text.encode("utf-8")
if "\t" in s: warning("Clobbering embedded tab")
if "\n" in s: warning("Clobbering embedded newline")
if "\r" in s: warning("Clobbering embedded carriage return")
s = s.replace("\t"," ").replace("\n"," ").replace("\r"," ")
return s
for row in rows:
cells_elts = row.findall(n("c"))
inds = [] # parallel
for c in cells_elts:
letter = re.search("^[A-Z]+", c.attrib['r']).group()
inds.append(letter2col_index(letter) )
cells = make_cells()
for c,j in zip(cells_elts,inds):
cells[j] = c
#print( *(cell2text( c ).encode("utf-8").replace("\t"," ") for c in cells), sep="\t")
print myjoin((cell_text_clean(cell2text( c )) for c in cells), sep="\t")
if warning_count > warning_max:
print>>sys.stderr, "%d total warnings, %d hidden" % (warning_count, warning_count-warning_max)

Works flawlessly so far for me with Excel 2011 for Mac generated multi-sheet XLS file.

Yup, this has been working perfectly for me. Semi regular in my toolkit at this point. Thanks very much.

Great script, thanks a lot!

lpryszcz commented Jan 8, 2016

Super handy script! I have rewritten it a little in order to save all sheets into a directory at once.
https://github.com/lpryszcz/bin/blob/master/xlsx2tsv.py
http://bioinfoexpert.com/?p=887

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