SAM File Re-organizer

transpose.py

#!/usr/bin/env python

############################################
# SAM File Re-organizer
###########################################
#
# what if you took a SAM file and transposed the data, 
# that is, make it so that the rows become columns and vice versa, even keeping 
# optional tags?  Would the file compress better?
#
# Since a BAM file stores "blocks" of data, and when it retrieves data, even for
# random retrieval, it must decompress a block, it should be able to transpose
# the columns to rows and vice versa.  This could save some disk space I reckon. 
# NB: samtools uses "bgzip" to compress the data.
#
# Results
#$ls -alh *sam *bam *gz *bz2 *txt
#-rw-r--r--  1 user  staff   5.1M Mar 10 00:00 in.bam
#-rw-r--r--  1 user  staff    37M Mar 10 00:00 in.sam
#-rw-r--r--  1 user  staff   4.8M Mar 10 00:07 in.sam.bgzip.gz
#-rw-r--r--  1 user  staff   3.8M Mar 10 00:08 in.sam.bzip2.bz2
#-rw-r--r--  1 user  staff   4.5M Mar 10 00:08 in.sam.gzip.gz
#-rw-r--r--  1 user  staff    34M Mar 10 00:01 out.txt
#-rw-r--r--  1 user  staff   3.8M Mar 10 00:02 out.txt.bgzip.gz
#-rw-r--r--  1 user  staff   3.8M Mar 10 00:03 out.txt.bzip2.bz2
#-rw-r--r--  1 user  staff   3.6M Mar 10 00:03 out.txt.gzip.gz

import sys
from optparse import OptionParser

class Data:
	tag_col = 11
	empty_data = "NA"

	def __init__(self):
		self.data = {}
		self.opt_tags = {}
		self.tags = []
		self.n = 0
		for i in xrange(self.tag_col):
			self.data[i] = list()
			self.tags.append(i)

	def add(self, line):
		tokens = line.split('\t')
		# standard data
		for i in xrange(self.tag_col):
			self.data[i].append(tokens[i])
		# optional tags
		local_data = {}
		for i in xrange(self.tag_col, len(tokens)):
			tok = tokens[i]
			tag = tok[:4] # include type (ex. RG:Z)
			value = tok[5:]
			local_data[tag] = value
			if not tag in self.data:
				self.opt_tags[tag] = True
				self.tags.append(tag)
				self.data[tag] = list()
				for j in xrange(self.n):
					self.data[tag].append(self.empty_data) # TODO: is NA safe?
		for tag in self.opt_tags:
			if tag in local_data:
				self.data[tag].append(local_data[tag])
			else:
				self.data[tag].append(self.empty_data)
		self.n += 1
	
	def print_out(self):
		for i in xrange(len(self.tags)):
			tag = self.tags[i]
			sys.stdout.write(str(tag))
			# NB: this could take a lot of memory
			print "\t".join(self.data[tag])

def main(options):
	fh = open(options.input, 'r')
	data = Data();
	for line in fh:
		line = line.rstrip("\r\n")
		if "@" == line[0]:
			print line
		else:
			data.add(line)
	data.print_out()
	fh.close()

def check_option(parser, value, name):
    if None == value:
        print 'Option ' + name + ' required.\n'
        parser.print_help()
        sys.exit(1)

if __name__ == '__main__':
    parser = OptionParser()
    parser.add_option('-i', '--input', dest='input', default=None, help="Input SAM file")

    (options, args) = parser.parse_args()
    if len(args) != 0:
        parser.print_help()
        sys.exit(1)

    check_option(parser, options.input, '-i')

    main(options)