m2p.py

import numpy as np
from scipy.io import loadmat  # this is the SciPy module that loads mat-files
import pandas as pd

def load(infile, dataset=None, idKey='id'):
	mat = loadmat(infile)  # load mat-file
	#print mat.keys()
	if dataset == None:
		for key in mat.keys():
			if key[0] != '_':
				dataset = key
				break
		print 'Assuming you mean to load',dataset,'from',infile
	mdata = mat[dataset]  # variable in mat file
	mdtype = mdata.dtype  # dtypes of structures are "unsized objects"
	ndata = {n: mdata[n][0, 0] for n in mdtype.names}

	# Reconstruct the columns of the data table from just the time series
	# Use the number of intervals to test if a field is a column or metadata
	columns = [n for n, v in ndata.iteritems()]

	# There were supposed to be useful functions instead of this but those 'complained'
	# going the rude but working way now
	dataDict = dict()
	for c in columns:
		curCol = []

		for thing in mdata:
			value = thing[c][0][0]
			if type(value) == np.unicode_:
				value = str(value)
			if c == 'vp_chr':
				value = value[0]
			curCol.append(value)
		dataDict[c] = curCol

	df = pd.DataFrame(dataDict,
		index=dataDict[idKey],
		columns=columns)

	return df

def listIndexes(args):
	df = load(args.infile)
	for item in df.index:
		print str(item)


def main():
	import sys, os
	infile = sys.argv[1]
	df = load(infile)

	for index in df.index:
		print index

		thisType = df.loc[index]
		thisDict = thisType.to_dict()

		thisDict['prm_start'] = [thisDict['pr1_pos'][0],thisDict['pr2_pos'][0]]
		thisDict['prm_end'] = [thisDict['pr1_pos'][1],thisDict['pr2_pos'][1]]
		thisDict.pop('pr1_pos')
		thisDict.pop('pr2_pos')

		thisDict['vp_start'] = [thisDict['vp_pos'][0]]
		thisDict['vp_end'] = [thisDict['vp_pos'][1]]
		thisDict.pop('vp_pos')

		thisDict['win_start'] = [thisDict['win_bnd'][0]]
		thisDict['win_end'] = [thisDict['win_bnd'][1]]
		thisDict.pop('win_bnd')

		thisDict['pr_seq'] = [thisDict.pop('pr1_seq'),thisDict.pop('pr2_seq')]

		thisDict['re_seq'] = [thisDict.pop('re1_seq'),thisDict.pop('re2_seq')]
		thisDict['re_name'] = [thisDict.pop('re1_name'),thisDict.pop('re2_name')]

		sortedKeys = thisDict.keys()
		sortedKeys.sort()

		with open(sys.argv[2]+index+'.tsv', 'w') as f:
			delim='\t'
			for key in sortedKeys:
				value=str(thisDict[key])
				if type(thisDict[key]) == list:
					value=delim.join([str(x) for x in thisDict[key]])
				f.write(str(key) + delim + value + os.linesep)

if __name__ == '__main__':
	main()