"""
tablelib.py

Parse, format, and manipulate tabular data.


--Example----------------------------------------------------
##types:string int
name num
mike 23
alex 12
matt 7
-------------------------------------------------------------

File is tab delimited.

Directives are on a single line and begin with two hashes '##'
No space after colon is allowed.

Table can also handle custom types.  Custom types must do the following

 1. default value:
   default = mytype()
   returns default value

 2. convert from string
   val = mytype(string)
   converts from string to custom type

 3. convert to string
   string = str(val)
   converts val of type 'mytype' to a string

 4. type inference (optional)
   type(val)
   returns instance of 'mytype'
   TODO: I could not require this (only map() really needs it and __init__())

"""

# python libs
import copy
from itertools import chain, imap, izip
import os
from sqlite3 import dbapi2 as sqlite
from StringIO import StringIO
import sys

# rasmus libs
from rasmus import util


# table directives
DIR_TYPES = 1


# a special unique null type (more 'null' than None)
NULL = object()


class TableException (Exception):
    """Exception class for Table"""
    def __init__(self, errmsg, filename=None, lineno=None):
        msg = ""
        add_space = False
        add_colon = False

        if filename:
            msg += "%s" % filename
            add_space = True
            add_colon = True

        if lineno:
            add_colon = True
            if add_space:
                msg += " "
            msg += "line %d" % lineno

        if add_colon:
            msg += ": "

        msg = msg + errmsg

        Exception.__init__(self, msg)


#===========================================================================
# Types handling

def guess_type(text):
    """Guess the type of a value encoded in a string."""

    try:
        int(text)
        return int
    except:
        pass

    try:
        float(text)
        return float
    except ValueError:
        pass

    try:
        str2bool(text)
        return bool
    except ValueError:
        pass

    return str


def str2bool(text=None):
    """Parse a boolean stored as a string."""

    if text is None:
        # default value
        return False

    text = text.lower()

    if text == "false":
        return False
    elif text == "true":
        return True
    else:
        raise ValueError("unknown string for bool '%s'" % text)


_type_definitions = [
    ["string", str],
    ["unknown", str],  # backwards compatiable name
    ["str",    str],   # backwards compatiable name
    ["string", unicode],
    ["int",    int],
    ["int",    long],
    ["float",  float],
    ["bool",   bool],
]

# NOTE: ordering of name-type pairs is important
#   the first occurrence of a type gives the perferred name for writing


def parse_type(type_name):
    """Parse a type name into a type."""
    for name, type_object in _type_definitions:
        if type_name == name:
            return type_object
    raise Exception("unknown type '%s'" % type_name)


def format_type(type_object):
    """Format a type into a type name."""
    for name, type_object2 in _type_definitions:
        if type_object == type_object2:
            return name
    raise Exception("unknown type '%s'" % type_object)


#===========================================================================
# Table class

class Table (list):
    """A table of data"""

    def __init__(self, rows=None,
                 headers=None,
                 types={},
                 filename=None,
                 nheaders=1):

        # set table info
        self.headers = copy.copy(headers)
        self.types = copy.copy(types)
        self.comments = []
        self.delim = "\t"
        self.nheaders = nheaders
        self.filename = filename

        # set data
        if rows:
            self._set_data(rows)

    def _set_data(self, rows=[]):
        """Set the table data from an iterable."""
        try:
            # use first row to guess data style
            rows = iter(rows)
            first_row = rows.next()
        except StopIteration:
            # No data given
            return

        if isinstance(first_row, dict):
            # data is a list of dicts
            # set default headers based on first row keys
            if self.headers is None:
                self.headers = sorted(first_row.keys())

            # add data
            self.extend(imap(dict, chain([first_row], rows)))

        elif isinstance(first_row, (list, tuple)):
            # data is a list of lists
            # use first row to determine headers
            if self.nheaders == 0:
                if self.headers is None:
                    self.headers = range(len(first_row))
                rows = chain([first_row], rows)
            else:
                if self.headers is None:
                    self.headers = list(first_row)

            # add data
            self.extend(dict(zip(self.headers, row)) for row in chain([first_row], rows))

        # guess any types not specified
        if len(self) > 0:
            for key in self.headers:
                row = self[0]
                if key not in self.types:
                    self.types[key] = type(row[key])

    def clear(self, headers=None, delim="\t", nheaders=1, types=None):
        """Clear the contents of the table."""

        # clear table info
        self.headers = copy.copy(headers)
        if types is None:
            self.types = {}
        else:
            self.types = copy.copy(types)
        self.comments = []
        self.delim = delim
        self.nheaders = nheaders

        # clear data
        self[:] = []

    def new(self, headers=None):
        """
        Return a new table with the same info but no data.

        headers: if specified, only a subset of the headers will be copied.
        """
        if headers is None:
            headers = self.headers

        tab = type(self)(headers=headers)

        tab.types = util.subdict(self.types, headers)
        tab.comments = copy.copy(self.comments)
        tab.delim = self.delim
        tab.nheaders = self.nheaders

        return tab

    #===================================================================
    # Input/Output

    def read(self, filename, delim="\t", nheaders=1,
             headers=None, types=None, guess_types=True):
        self.extend(self.read_iter(
            filename, delim=delim, nheaders=nheaders,
            headers=headers, types=types,
            guess_types=guess_types))
        return self

    def read_iter(self, filename, delim="\t", nheaders=1,
                  headers=None, types=None, guess_types=True):
        """
        Reads a character delimited file and yields a dict for each row.

        Blank lines are skipped.  Lines that start with a single '#'
        are treated as comments.  Lines starting with '##' are treated as
        directives.
        """
        infile = util.open_stream(filename)

        # remember filename for later saving
        if isinstance(filename, str):
            self.filename = filename

        # clear table
        self.clear(headers, delim, nheaders, types)

        # temps for reading only
        self._tmptypes = None
        first_row = True

        # line number for error reporting
        lineno = 0

        try:
            for line in infile:
                line = line.rstrip('\n')
                lineno += 1

                # skip blank lines
                if len(line) == 0:
                    continue

                # handle comments
                if line[0] == "#":
                    if not self._read_directive(line):
                        self.comments.append(line)
                    continue

                # split row into tokens
                tokens = line.split(delim)

                # if no headers read yet, use this line as a header
                if not self.headers:
                    # parse headers
                    if self.nheaders > 0:
                        self._parse_header(tokens)
                        continue
                    else:
                        # default headers are numbers
                        self.headers = range(len(tokens))
                assert len(tokens) == len(self.headers), tokens

                # populate types
                if first_row:
                    first_row = False
                    if self._tmptypes:
                        # use explicit types
                        assert len(self._tmptypes) == len(self.headers)
                        self.types = dict(zip(self.headers, self._tmptypes))
                    else:
                        # default types
                        if guess_types:
                            for token, header in zip(tokens, self.headers):
                                self.types.setdefault(header,
                                                      guess_type(token))
                        else:
                            for header in self.headers:
                                self.types.setdefault(header, str)

                # parse data
                row = {}
                for header, token in izip(self.headers, tokens):
                    type_object = self.types[header]
                    if type_object is bool:
                        type_object = str2bool
                    row[header] = type_object(token)

                # yield completed row
                yield row

        except Exception, e:
            # report error in parsing input file
            raise TableException(str(e), self.filename, lineno)

        # clear temps
        del self._tmptypes

    def _parse_header(self, tokens):
        """Parse the tokens as headers"""
        self.headers = tokens

        # check that headers are unique
        check = set()
        for header in self.headers:
            if header in check:
                raise TableException("Duplicate header '%s'" % header)
            check.add(header)

    def write(self, filename=sys.stdout, delim="\t", comments=False,
              nheaders=None):
        """Write a table to a file or stream.

           If 'filename' is a string it will be opened as a file.
           If 'filename' is a stream it will be written to directly.
        """
        # remember filename for later saving
        if isinstance(filename, str):
            self.filename = filename

        out = util.open_stream(filename, "w")

        self.write_header(out, delim=delim, comments=comments,
                          nheaders=(nheaders if nheaders is not None
                                    else self.nheaders))

        # tmp variable
        types = self.types

        # write data
        for row in self:
            # code is inlined here for speed
            rowstr = []
            for header in self.headers:
                if header in row:
                    rowstr.append(types[header].__str__(row[header]))
                else:
                    rowstr.append('')
            out.write(delim.join(rowstr))
            out.write('\n')

    def write_header(self, out=sys.stdout, delim="\t", comments=False,
                     nheaders=None):
        # ensure all info is complete.
        # introspect types or use str by default.
        for key in self.headers:
            if key not in self.types:
                if len(self) > 0:
                    self.types[key] = type(self[0][key])
                else:
                    self.types[key] = str

        # ensure types are in directives
        if DIR_TYPES not in self.comments:
            self.comments.insert(0, DIR_TYPES)

        # write comments
        if comments:
            for line in self.comments:
                if isinstance(line, str):
                    out.write(line)
                    out.write('\n')
                else:
                    self._write_directive(line, out, delim)

        # write header
        if nheaders > 0:
            out.write(delim.join(self.headers))
            out.write('\n')

    def write_row(self, out, row, delim="\t"):
        rowstr = []
        types = self.types
        for header in self.headers:
            if header in row:
                rowstr.append(types[header].__str__(row[header]))
            else:
                rowstr.append('')
        out.write(delim.join(rowstr))
        out.write("\n")

    def save(self):
        """
        Writes the table to the last used filename.
        """
        if self.filename is not None:
            self.write(self.filename)
        else:
            raise Exception("Table has no filename")

    #===================================================================
    # Input/Output: Directives

    def _determine_directive(self, line):
        if line.startswith("##types:"):
            return DIR_TYPES
        else:
            return None

    def _read_directive(self, line):
        """Attempt to read a line with a directive"""

        directive = self._determine_directive(line)
        if directive is None:
            return False

        rest = line[line.index(":")+1:]
        self.comments.append(directive)

        if directive == DIR_TYPES:
            self._tmptypes = map(
                parse_type, rest.rstrip('\n').split(self.delim))
            return True
        else:
            return False

    def _write_directive(self, line, out, delim):
        """Write a directive"""

        if line == DIR_TYPES:
            out.write("##types:" + delim.join(format_type(self.types[h])
                                              for h in self.headers) + "\n")

        else:
            raise "unknown directive:", line

    #===================================================================
    # Table manipulation

    def add(self, **kargs):
        """Add a row to the table

           tab.add(col1=val1, col2=val2, col3=val3)
        """
        self.append(kargs)

    def add_col(self, header, coltype=None, default=NULL, pos=None, data=None):
        """Add a column to the table.  You must populate column data yourself.

           header  - name of the column
           coltype - type of the values in that column
           default - default value of the column
           pos     - position to insert column (default: right-end)
        """
        # ensure header is unique
        if header in self.headers:
            raise Exception("header '%s' is already in table" % header)

        # default column position is last column
        if pos is None:
            pos = len(self.headers)

        # default coltype is guessed from data
        if coltype is None:
            if data is None:
                raise Exception("must specify data or coltype")
            else:
                coltype = type(data[0])

        # default value is inferred from column type
        if default is NULL:
            default = coltype()

        # update table info
        self.headers.insert(pos, header)
        self.types[header] = coltype

        # add data
        if data is not None:
            for i in xrange(len(self)):
                self[i][header] = data[i]

    def remove_col(self, *cols):
        """Removes a column from the table"""

        for col in cols:
            self.headers.remove(col)
            del self.types[col]

            for row in self:
                del row[col]

    def rename_col(self, oldname, newname):
        """Renames a column"""

        # change header
        col = self.headers.index(oldname)
        if col == -1:
            raise Exception("column '%s' is not in table" % oldname)

        self.headers[col] = newname

        # change info
        self.types[newname] = self.types[oldname]
        del self.types[oldname]

        # change data
        for row in self:
            row[newname] = row[oldname]
            del row[oldname]

    def get_matrix(self, rowheader="rlabels"):
        """Returns mat, rlabels, clabels

           where mat is a copy of the table as a 2D list
                 rlabels are the row labels
                 clabels are the column labels
        """
        # get labels
        if rowheader is not None and rowheader in self.headers:
            rlabels = self.cget(rowheader)
            clabels = copy.copy(self.headers)
            clabels.remove(rowheader)
        else:
            rlabels = range(len(self))
            clabels = copy.copy(self.headers)

        # get data
        mat = []
        for row in self:
            mat.append(util.mget(row, clabels))

        return mat, rlabels, clabels

    def as_lists(self, cols=None):
        """Iterate over rows as lists"""
        if cols is None:
            cols = self.headers
        for row in self:
            yield [row[header] for header in cols]

    def as_tuples(self, cols=None):
        """Iterate over rows as lists"""
        if cols is None:
            cols = self.headers
        for row in self:
            yield tuple(row[header] for header in cols)

    def filter(self, cond):
        """Returns a table with a subset of rows such that cond(row) == True"""
        tab = self.new()

        for row in self:
            if cond(row):
                tab.append(row)

        return tab

    def map(self, func, headers=None):
        """Returns a new table with each row mapped by function 'func'"""

        if len(self) == 0:
            # handle case of zero length table
            return self.new()

        # determine what table will look like from first row
        first_row = func(self[0])

        # determine headers of new table
        if headers is None:
            # try order new headers the same way as old headers
            headers = first_row.keys()
            lookup = util.list2lookup(self.headers)
            top = len(headers)
            headers.sort(key=lambda x: (lookup.get(x, top), x))

        tab = type(self)(
            chain([first_row], (func(x) for x in self[1:])),
            headers=headers)
        tab.delim = self.delim
        tab.nheaders = self.nheaders

        return tab

    def uniq(self, key=None, col=None):
        """
        Returns a copy of this table with consecutive repeated rows removed
        """
        tab = self.new()

        if len(self) == 0:
            return tab

        if col is not None:
            key = lambda x: x[col]

        if key is None:
            last_row = self[0]
            for row in self[1:]:
                if row != last_row:
                    tab.append(row)
                last_row = row
        else:
            last_row = key(self[0])
            for row in self[1:]:
                key_row = key(row)
                if key_row != last_row:
                    tab.append(row)
                last_row = key_row

        return tab

    def groupby(self, key=None):
        """Groups the row of the table into separate tables based on the
           function key(row).  Returns a dict where the keys are the values
           retruned from key(row) and the values are tables.

           Ex:
           tab = Table([{'name': 'matt', 'major': 'CS'},
                        {'name': 'mike', 'major': 'CS'},
                        {'name': 'alex', 'major': 'bio'}])
           lookup = tab.groupby(lambda x: x['major'])

           lookup ==> {'CS': Table([{'name': 'matt', 'major': 'CS'},
                                    {'name': 'mike', 'major': 'CS'}]),
                       'bio': Table([{'name': 'alex', 'major': 'bio'}])}

           Can also use a column name such as:
           tab.groupby('major')

        """
        groups = {}

        if isinstance(key, str):
            keystr = key
            key = lambda x: x[keystr]

        if key is None:
            raise Exception("must specify keyfunc")

        for row in self:
            key2 = key(row)

            # add new table if necessary
            if key2 not in groups:
                groups[key2] = self.new()

            groups[key2].append(row)

        return groups

    def lookup(self, *keys, **options):
        """Returns a lookup dict based on a column 'key'
           or multiple keys

           extra options:
           default=None
           uselast=False    # allow multiple rows, just use last
        """
        options.setdefault("default", None)
        options.setdefault("uselast", False)
        lookup = util.Dict(dim=len(keys), default=options["default"])
        uselast = options["uselast"]

        for row in self:
            keys2 = util.mget(row, keys)
            ptr = lookup
            for i in xrange(len(keys2) - 1):
                ptr = lookup[keys2[i]]
            if not uselast and keys2[-1] in ptr:
                raise Exception("duplicate key '%s'" % str(keys2[-1]))
            ptr[keys2[-1]] = row

        lookup.insert = False
        return lookup

    def get(self, rows=None, cols=None):
        """Returns a table with a subset of the rows and columns"""

        # determine rows and cols
        if rows is None:
            rows = range(len(self))

        if cols is None:
            cols = self.headers

        tab = self.new(cols)

        # copy data
        for i in rows:
            row = self[i]
            row2 = {}
            for j in cols:
                row2[j] = row[j]
            tab.append(row2)

        return tab

    def cget(self, *cols):
        """Returns columns of the table as separate lists"""

        ret = []

        for col in cols:
            newcol = []
            ret.append(newcol)

            for row in self:
                newcol.append(row[col])

        if len(ret) == 1:
            return ret[0]
        else:
            return ret

    def get_row(self, *rows):
        """Returns row(s) as list(s)"""

        if len(rows) == 1:
            # return one row
            row = self[rows[0]]
            return [row[j] for j in self.headers]

        else:
            # return multiple rows (or zero)
            return [[self[i][j] for j in self.headers]
                    for i in rows]

    def sort(self, cmp=None, key=None, reverse=False, col=None):
        """Sorts the table inplace"""

        if col is not None:
            key = lambda row: row[col]
        elif cmp is None and key is None:
            # sort by first column
            key = lambda row: row[self.headers[0]]

        list.sort(self, cmp=cmp, key=key, reverse=reverse)

    def __getitem__(self, key):
        if isinstance(key, slice):
            # return another table if key is a slice
            tab = self.new()
            tab[:] = list.__getitem__(self, key)
            return tab
        else:
            return list.__getitem__(self, key)

    def __getslice__(self, a, b):
        # for python version compatibility
        return self.__getitem__(slice(a, b))

    def __repr__(self):
        s = StringIO()
        self.write_pretty(s)
        return s.getvalue()

    def write_pretty(self, out=sys.stdout, spacing=2):
        mat2, rlabels, clabels = self.get_matrix(rowheader=None)

        mat = []

        # get headers
        mat.append(clabels)

        # get data
        mat.extend(mat2)

        util.printcols(mat, spacing=spacing, out=out)

    def __str__(self):
        s = StringIO()
        self.write(s)
        return s.getvalue()


#===========================================================================
# Convenience functions

def read_table(filename, delim="\t", headers=None,
               nheaders=1, types=None,
               guess_types=True):
    """Read a Table from a file written in PTF"""

    table = Table()
    table.read(filename, delim=delim, headers=headers,
               nheaders=nheaders, types=types,
               guess_types=guess_types)
    return table


def iter_table(filename, delim="\t", nheaders=1, types=None, guess_types=True):
    """Iterate through the rows of a Table from a file."""
    table = Table()
    return table.read_iter(filename, delim=delim, nheaders=nheaders,
                           types=types, guess_types=guess_types)


def histtab(items, headers=None, item="item", count="count", percent="percent",
            cols=None):
    """Make a histogram table."""
    if cols is not None:
        # items is a Table.
        items = items.as_tuples(cols=cols)
        if headers is None:
            headers = cols + [count, percent]

    if headers is None:
        headers = [item, count, percent]

    h = util.hist_dict(items)
    tab = Table(headers=headers)
    tot = float(sum(h.itervalues()))
    hist_items = h.items()

    if cols is not None:
        for key, val in hist_items:
            row = dict(zip(cols, key))
            row[count] = val
            tab.append(row)
    else:
        for key, val in hist_items:
            tab.append({item: key,
                        count: val})

    if percent is not None:
        for i, (key, val) in enumerate(hist_items):
            tab[i][percent] = val / tot

    tab.sort(col=count, reverse=True)

    return tab


def join_tables(*args, **kwargs):
    """Join together tables into one table.
       Each argument is a tuple (table_i, key_i, cols_i)

       key_i is either a column name or a function that maps a
       table row to a unique key
    """

    if len(args) == 0:
        return Table()

    # determine common keys
    tab, key, cols = args[0]
    if isinstance(key, str):
        keys = tab.cget(key)
        lookups = [tab.lookup(key)]
    else:
        keys = map(key, tab)
        lookup = {}
        for row in tab:
            lookup[key(row)] = row
        lookups = [lookup]

    keyset = set(keys)

    for tab, key, cols in args[1:]:
        if isinstance(key, str):
            keyset = keyset & set(tab.cget(key))
            lookups.append(tab.lookup(key))
        else:
            keyset = keyset & set(map(key, tab))
            lookup = {}
            for row in tab:
                lookup[key(row)] = row

            lookups.append(lookup)

    keys = filter(lambda x: x in keyset, keys)

    # build new table
    if "headers" not in kwargs:
        headers = util.concat(*util.cget(args, 2))
    else:
        headers = kwargs["headers"]
    tab = Table(headers=headers)

    for key in keys:
        row = {}
        for (tab2, key2, cols), lookup in zip(args, lookups):
            row.update(util.subdict(lookup[key], cols))
        tab.append(row)

    return tab


def showtab(tab, name='table'):
    """Show a table in a new xterm"""

    name = name.replace("'", "")
    tmp = util.tempfile(".", "tmp", ".tab")
    tab.write_pretty(file(tmp, "w"))
    os.system("(xterm -T '%s' -n '%s' -e less -S %s; rm %s) &" %
              (name, name, tmp, tmp))


def sqlget(dbfile, query, maxrows=None, headers=None, headernum=False):
    """Get a table from a sqlite file"""

    # open database
    if hasattr(dbfile, "cursor"):
        con = dbfile
        cur = con.cursor()
        auto_close = False
    else:
        con = sqlite.connect(dbfile, isolation_level="DEFERRED")
        cur = con.cursor()
        auto_close = True

    cur.execute(query)

    # infer header names
    if headers is None and not headernum:
        headers = [x[0] for x in cur.description]

    if maxrows is not None:
        lst = []
        try:
            for i in xrange(maxrows):
                lst.append(cur.next())
        except StopIteration:
            pass
        tab = Table(lst, headers=headers)
    else:
        tab = Table(list(cur), headers=headers)

    if auto_close:
        con.close()
    return tab


def sqlexe(dbfile, sql):

    # open database
    if hasattr(dbfile, "cursor"):
        con = dbfile
        cur = con.cursor()
        auto_close = False
    else:
        con = sqlite.connect(dbfile, isolation_level="DEFERRED")
        cur = con.cursor()
        auto_close = True

    cur.execute(sql)

    if auto_close:
        con.close()


def sql_create_table(cur, table_name, tab, overwrite=True):
    """Create an SQL based on a tab"""

    def issubclass2(t1, t2):
        if type(t1) != type:
            return False
        return issubclass(t1, t2)

    # drop old table if needed
    if overwrite:
        cur.execute("DROP TABLE IF EXISTS %s;" % table_name)

    # build columns
    cols = []
    for header in tab.headers:
        t = tab.types[header]

        if issubclass2(t, basestring):
            cols.append("%s TEXT" % header)
        elif issubclass2(t, int):
            cols.append("%s INTEGER" % header)
        elif issubclass2(t, float):
            cols.append("%s FLOAT" % header)
        elif issubclass2(t, bool):
            cols.append("%s BOOLEAN" % header)
        else:
            # default is text
            cols.append("%s TEXT" % header)

    cols = ",".join(cols)

    # create table
    cur.execute("""CREATE TABLE %s (%s);""" % (table_name, cols))


def sqlput(dbfile, table_name, tab, overwrite=True, create=True):
    """Insert a table into a sqlite file"""

    # open database
    if hasattr(dbfile, "cursor"):
        con = dbfile
        cur = con.cursor()
        auto_close = False
    else:
        con = sqlite.connect(dbfile, isolation_level="DEFERRED")
        cur = con.cursor()
        auto_close = True

    # read table from file
    if not isinstance(tab, Table):
        filename = tab
        tab = Table()
        it = tab.read_iter(filename)

        try:
            # force a reading of the headers
            row = it.next()
            rows = chain([row], it)
        except StopIteration:
            rows = []
            pass
    else:
        rows = tab

    if create:
        sql_create_table(cur, table_name, tab, overwrite=overwrite)

    # determine text columns
    def issubclass2(t1, t2):
        if type(t1) != type:
            return False
        return issubclass(t1, t2)

    text = set()
    for header in tab.headers:
        t = tab.types[header]

        if issubclass2(t, basestring) or not (
                issubclass2(t, int) or
                issubclass2(t, float) or
                issubclass2(t, bool)):
            text.add(header)

    # insert rows
    for row in rows:
        vals = []
        for header in tab.headers:
            if header in text:
                vals.append('"%s"' % row[header])
            else:
                vals.append(tab.types[header].__str__(row[header]))
        vals = ",".join(vals)
        cur.execute("INSERT INTO %s VALUES (%s);" % (table_name, vals))

    con.commit()
    if auto_close:
        con.close()


#===========================================================================
# Matrix functions

def matrix2table(mat, rlabels=None, clabels=None, rowheader="rlabels"):
    """
    convert a matrix into a table

    use table.get_matrix()  to convert back to a matrix
    """
    if clabels is None:
        clabels = range(len(mat[0]))
        nheaders = 0
    else:
        nheaders = 1

    if rlabels is None:
        tab = Table(headers=clabels)
    else:
        tab = Table(headers=[rowheader] + clabels)
    tab.nheaders = nheaders

    for i, row in enumerate(mat):
        if rlabels is not None:
            row2 = {rowheader: rlabels[i]}
        else:
            row2 = {}

        for j in xrange(len(mat[i])):
            row2[clabels[j]] = mat[i][j]

        tab.append(row2)

    return tab


def write_matrix(filename, mat, rlabels=None, clabels=None,
                 rowheader="rlabels"):
    tab = matrix2table(mat,
                       rlabels=rlabels,
                       clabels=clabels,
                       rowheader=rowheader)
    tab.write(filename)


def read_matrix(filename, rowheader="rlabels"):
    tab = read_table(filename)
    mat, rlabels, clabels = tab.get_matrix(rowheader=rowheader)
    return mat, rlabels, clabels
