diff merge_metaphlan_tables.py @ 0:cac6247cb1d3 draft

graphlan_import

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_metaphlan_tables.py	Tue Aug 26 14:51:29 2014 -0400
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+
+# ============================================================================== 
+# Merge script: from MetaPhlAn output on single sample to a joined "clades vs samples" table
+# Authors: Timothy Tickle ([e-mail]) and Curtis Huttenhower ([e-mail])
+# ==============================================================================
+
+import argparse
+import csv
+import os
+import sys
+
+
+def merge( aaastrIn, astrLabels, iCol, ostm ):
+	"""
+	Outputs the table join of the given pre-split string collection.
+	
+	:param	aaastrIn:	One or more split lines from which data are read.
+	:type	aaastrIn:	collection of collections of string collections
+	:param	astrLabels:	File names of input data.
+	:type	astrLabels:	collection of strings
+	:param	iCol:		Data column in which IDs are matched (zero-indexed).
+	:type	iCol:		int
+	:param	ostm:		Output stream to which matched rows are written.
+	:type	ostm:		output stream
+
+	"""
+	
+	setstrIDs = set()
+	"""The final set of all IDs in any table."""
+	ahashIDs = [{} for i in range( len( aaastrIn ) )]
+	"""One hash of IDs to row numbers for each input datum."""
+	aaastrData = [[] for i in range( len( aaastrIn ) )]
+	"""One data table for each input datum."""
+	aastrHeaders = [[] for i in range( len( aaastrIn ) )]
+	"""The list of non-ID headers for each input datum."""
+	strHeader = "ID"
+	"""The ID column header."""
+
+	# For each input datum in each input stream...
+	pos = 0
+
+	for f in aaastrIn :
+		with open(f) as csvfile :
+			iIn = csv.reader(csvfile, csv.excel_tab)
+
+			# Lines from the current file, empty list to hold data, empty hash to hold ids
+			aastrData, hashIDs = (a[pos] for a in (aaastrData, ahashIDs))
+
+			iLine = -1
+			# For a line in the file
+			for astrLine in iIn:
+				iLine += 1
+
+				# ID is from first column, data are everything else
+				strID, astrData = astrLine[iCol], ( astrLine[:iCol] + astrLine[( iCol + 1 ):] )
+
+				hashIDs[strID] = iLine
+				aastrData.append( astrData )
+
+			# Batch merge every new ID key set
+			setstrIDs.update( hashIDs.keys( ) )
+
+		pos += 1
+
+	# Create writer
+	csvw = csv.writer( ostm, csv.excel_tab, lineterminator='\n' )
+
+	# Make the file names the column names
+	csvw.writerow( [strHeader] + [os.path.splitext(f)[0] for f in astrLabels] )
+
+	# Write out data
+	for strID in sorted( setstrIDs ):
+		astrOut = []
+		for iIn in range( len( aaastrIn ) ):
+			aastrData, hashIDs = (a[iIn] for a in (aaastrData, ahashIDs))
+			# Look up the row number of the current ID in the current dataset, if any
+			iID = hashIDs.get( strID )
+			# If not, start with no data; if yes, pull out stored data row
+			astrData = [0.0] if ( iID == None ) else aastrData[iID]
+			# Pad output data as needed
+			astrData += [None] * ( len( aastrHeaders[iIn] ) - len( astrData ) )
+			astrOut += astrData
+		csvw.writerow( [strID] + astrOut )
+
+
+argp = argparse.ArgumentParser( prog = "merge_metaphlan_tables.py",
+	description = """Performs a table join on one or more metaphlan output files.""")
+argp.add_argument( "aistms",	metavar = "input.txt", nargs = "+",
+	help = "One or more tab-delimited text tables to join" )
+
+__doc__ = "::\n\n\t" + argp.format_help( ).replace( "\n", "\n\t" )
+
+argp.usage = argp.format_usage()[7:]+"\n\n\tPlease make sure to supply file paths to the files to combine. If combining 3 files (Table1.txt, Table2.txt, and Table3.txt) the call should be:\n\n\t\tpython merge_metaphlan_tables.py Table1.txt Table2.txt Table3.txt > output.txt\n\n\tA wildcard to indicate all .txt files that start with Table can be used as follows:\n\n\t\tpython merge_metaphlan_tables.py Table*.txt > output.txt"
+
+
+def _main( ):
+	args = argp.parse_args( )
+	merge(args.aistms, [os.path.split(os.path.basename(f))[1] for f in args.aistms], 0, sys.stdout)
+
+
+if __name__ == "__main__":
+	_main( )