class MacsXLS:
"""Class for reading and manipulating XLS output from MACS
Reads the XLS output file from the MACS peak caller and
processes and stores the information for subsequent manipulation
and output.
To read in data from a MACS output file:
>>> macs = MacsXLS("macs.xls")
This reads in the data and prepends an additional 'order'
column (a list of numbers from one to the number of data
lines).
To get the MACS version:
>>> macs.macs_version
2.0.10
To access the 'header' information (as a Python list):
>>> macs.header
To see the column names (as a Python list):
>>> macs.columns
The data is stored as a TabFile object; to access the data
use the 'data' property, e.g.
>>> for line in macs.data:
... print "Chr %s Start %s End" % (line['chr'],line['start'],line['end'])
To sort the data on a particular column use the 'sort_on'
method, e.g.
>>> macs.sort_on('chr')
(Note that the order column is always recalculated after
sorting.)
"""
def __init__(self,filen=None,fp=None,name=None):
"""Create a new MacsXLS instance
Arguments:
filen: name of the file to read the MACS output from.
If None then fp argument must be supplied instead.
fp: file-like object opened for reading. If None then
filen argument must be supplied instead. If both filen
and fp are supplied then fp will be used preferentially.
"""
# Store data
self.__filen = filen
self.__name = name
self.__macs_version = None
self.__command_line = None
self.__header = []
self.__data = None
# Open file, if necessary
if fp is None:
fp = open(filen,'r')
else:
filen = None
# Iterate over header lines
for line in fp:
line = line.strip()
if line.startswith('#') or line == '':
# Header line
self.__header.append(line)
# Detect/extract data from header
if line.startswith("# This file is generated by MACS version "):
# Look for MACS version
self.__macs_version = line.split()[8]
elif self.__name is None and line.startswith("# name = "):
# Look for 'name' if none set
self.__name = line[len("# name = "):]
elif line.startswith("# Command line: "):
# Look for command line
self.__command_line = line[16:]
else:
if self.__data is None:
# First line of actual data should be the column names
columns = line.split('\t')
# Insert an additional column called 'order'
columns.insert(0,"order")
# Set up TabFile to handle actual data
self.__data = TabFile(column_names=columns)
else:
# Assume it's actual data and store it
self.__data.append(tabdata="\t%s" % line)
# Close the file handle, if we opened it
if filen is not None:
fp.close()
# Check that we actually got a version line
if self.macs_version is None:
raise Exception,"Failed to extract MACS version, not a MACS output file?"
# Populate the 'order' column
self.update_order()
@property
def filen(self):
"""Return the source file name
"""
return self.__filen
@property
def name(self):
"""Return the name property
"""
return self.__name
@property
def macs_version(self):
"""Return the MACS version extracted from the file
"""
return self.__macs_version
@property
def command_line(self):
"""Return the command line string extracted from the header
This is the value associated with the "# Command line: ..."
header line.
Will be 'None' if no matching header line is found, else is
the string following the ':'.
"""
return self.__command_line
@property
def columns(self):
"""Return the column names for the MACS data
Returns a list of the column names from the data
extracted from the file.
"""
return self.__data.header()
@property
def columns_as_xls_header(self):
"""Returns the column name list, with hash prepended
"""
return ['#'+self.columns[0]] + self.columns[1:]
@property
def header(self):
"""Return the header data from the file
Returns a list of lines comprising the header
extracted from the file.
"""
return self.__header
@property
def data(self):
"""Return the data from the file
Returns a TabFile object comprising the data
extracted from the file.
"""
return self.__data
@property
def with_broad_option(self):
"""Returns True if MACS was run with --broad option
If --broad wasn't detected then returns False.
"""
if self.macs_version.startswith('1.'):
# Not an option in MACS 1.*
return False
try:
# Was --broad specified in the command line?
return '--broad' in self.command_line.split()
except AttributeError:
# No command line? Check for 'abs_summit' column
return 'abs_summit' not in self.columns
def sort_on(self,column,reverse=True):
"""Sort data on specified column
Sorts the data in-place, by the specified column.
By default data is sorted in descending order; set
'reverse' argument to False to sort values in ascending
order instead
Note that the 'order' column is automatically updated
after each sorting operation.
Arguments:
column: name of the column to sort on
reverse: if True (default) then sort in descending
order (i.e. largest to smallest). Otherwise sort in
ascending order.
"""
# Sort the data
self.__data.sort(lambda line: line[column],reverse=reverse)
# Update the 'order' column
self.update_order()
def update_order(self):
# Set/update values in 'order' column
for i in range(0,len(self.__data)):
self.__data[i]['order'] = i+1
break
if macs_version is None:
logging.error("couldn't detect MACS version")
sys.exit(1)
else:
print "Input file is from MACS %s" % macs_version
# Don't try to convert output from MACS2
if macs_version.startswith("2."):
logging.error(
"input XLS comes from MACS %s, this version only handles 1.4" %
macs_version)
sys.exit(1)
# Sort into order by fold_enrichment and then by -10*log10(pvalue) column
data.sort(lambda line: line['fold_enrichment'], reverse=True)
data.sort(lambda line: line['-10*log10(pvalue)'], reverse=True)
# Restore first line
data.insert(0, tabdata=header_line)
# Insert "order" column
data.appendColumn("order")
# Perhaps confusingly must also insert initial value "#order"
data[0]['order'] = "#order"
for i in range(1, len(data)):
data[i]['order'] = i
# Reorder columns to put it at the start
data = data.reorderColumns([
'order', 'chr', 'start', 'end', 'length', 'summit', 'tags',
'-10*log10(pvalue)', 'fold_enrichment', 'FDR(%)'
macs_version = line.split()[8]
break
if macs_version is None:
logging.error("couldn't detect MACS version")
sys.exit(1)
else:
print "Input file is from MACS %s" % macs_version
# Don't try to convert output from MACS2
if macs_version.startswith("2."):
logging.error("input XLS comes from MACS %s, this version only handles 1.4" %
macs_version)
sys.exit(1)
# Sort into order by fold_enrichment and then by -10*log10(pvalue) column
data.sort(lambda line: line['fold_enrichment'],reverse=True)
data.sort(lambda line: line['-10*log10(pvalue)'],reverse=True)
# Restore first line
data.insert(0,tabdata=header_line)
# Insert "order" column
data.appendColumn("order")
# Perhaps confusingly must also insert initial value "#order"
data[0]['order'] = "#order"
for i in range(1,len(data)):
data[i]['order'] = i
# Reorder columns to put it at the start
data = data.reorderColumns(['order','chr','start','end','length','summit','tags',
'-10*log10(pvalue)','fold_enrichment','FDR(%)'])
class MacsXLS:
"""Class for reading and manipulating XLS output from MACS
Reads the XLS output file from the MACS peak caller and
processes and stores the information for subsequent manipulation
and output.
To read in data from a MACS output file:
>>> macs = MacsXLS("macs.xls")
This reads in the data and prepends an additional 'order'
column (a list of numbers from one to the number of data
lines).
To get the MACS version:
>>> macs.macs_version
2.0.10
To access the 'header' information (as a Python list):
>>> macs.header
To see the column names (as a Python list):
>>> macs.columns
The data is stored as a TabFile object; to access the data
use the 'data' property, e.g.
>>> for line in macs.data:
... print "Chr %s Start %s End" % (line['chr'],line['start'],line['end'])
To sort the data on a particular column use the 'sort_on'
method, e.g.
>>> macs.sort_on('chr')
(Note that the order column is always recalculated after
sorting.)
"""
def __init__(self,filen=None,fp=None,name=None):
"""Create a new MacsXLS instance
Arguments:
filen: name of the file to read the MACS output from.
If None then fp argument must be supplied instead.
fp: file-like object opened for reading. If None then
filen argument must be supplied instead. If both filen
and fp are supplied then fp will be used preferentially.
"""
# Store data
self.__filen = filen
self.__name = name
self.__macs_version = None
self.__command_line = None
self.__header = []
self.__data = None
# Open file, if necessary
if fp is None:
fp = open(filen,'r')
else:
filen = None
# Iterate over header lines
for line in fp:
line = line.strip()
if line.startswith('#') or line == '':
# Header line
self.__header.append(line)
# Detect/extract data from header
if line.startswith("# This file is generated by MACS version "):
# Look for MACS version
self.__macs_version = line.split()[8]
elif self.__name is None and line.startswith("# name = "):
# Look for 'name' if none set
self.__name = line[len("# name = "):]
elif line.startswith("# Command line: "):
# Look for command line
self.__command_line = line[16:]
else:
if self.__data is None:
# First line of actual data should be the column names
columns = line.split('\t')
# Insert an additional column called 'order'
columns.insert(0,"order")
# Set up TabFile to handle actual data
self.__data = TabFile(column_names=columns)
else:
# Assume it's actual data and store it
self.__data.append(tabdata="\t%s" % line)
# Close the file handle, if we opened it
if filen is not None:
fp.close()
# Check that we actually got a version line
if self.macs_version is None:
raise Exception,"Failed to extract MACS version, not a MACS output file?"
# Populate the 'order' column
self.update_order()
@property
def filen(self):
"""Return the source file name
"""
return self.__filen
@property
def name(self):
"""Return the name property
"""
return self.__name
@property
def macs_version(self):
"""Return the MACS version extracted from the file
"""
return self.__macs_version
@property
def command_line(self):
"""Return the command line string extracted from the header
This is the value associated with the "# Command line: ..."
header line.
Will be 'None' if no matching header line is found, else is
the string following the ':'.
"""
return self.__command_line
@property
def columns(self):
"""Return the column names for the MACS data
Returns a list of the column names from the data
extracted from the file.
"""
return self.__data.header()
@property
def columns_as_xls_header(self):
"""Returns the column name list, with hash prepended
"""
return ['#'+self.columns[0]] + self.columns[1:]
@property
def header(self):
"""Return the header data from the file
Returns a list of lines comprising the header
extracted from the file.
"""
return self.__header
@property
def data(self):
"""Return the data from the file
Returns a TabFile object comprising the data
extracted from the file.
"""
return self.__data
@property
def with_broad_option(self):
"""Returns True if MACS was run with --broad option
If --broad wasn't detected then returns False.
"""
if self.macs_version.startswith('1.'):
# Not an option in MACS 1.*
return False
try:
# Was --broad specified in the command line?
return '--broad' in self.command_line.split()
except AttributeError:
# No command line? Check for 'abs_summit' column
return 'abs_summit' not in self.columns
def sort_on(self,column,reverse=True):
"""Sort data on specified column
Sorts the data in-place, by the specified column.
By default data is sorted in descending order; set
'reverse' argument to False to sort values in ascending
order instead
Note that the 'order' column is automatically updated
after each sorting operation.
Arguments:
column: name of the column to sort on
reverse: if True (default) then sort in descending
order (i.e. largest to smallest). Otherwise sort in
ascending order.
"""
# Sort the data
self.__data.sort(lambda line: line[column],reverse=reverse)
# Update the 'order' column
self.update_order()
def update_order(self):
# Set/update values in 'order' column
for i in range(0,len(self.__data)):
self.__data[i]['order'] = i+1
