import subprocess, os
import sys

def tableview(txt=None, parse_table=None, make_conf=None, conf_dir=None, circos_conf=None, save_dir=None, parsed_conf=None):
        if parse_table is None:
                parse_table = '/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer/bin/parse-table'
        if make_conf is None:
                make_conf = '/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer/bin/make-conf'
        if conf_dir is None:
                conf_dir = '/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer2/data'
        if circos_conf is None:
                circos_conf = '/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer2/etc/circos.conf'
        if save_dir is None:
                save_dir = os.path.dirname(txt)
        if parsed_conf is None:
                #parsed_conf = '/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer/samples/parse-table-02a.conf'
                parsed_conf = '/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer2/etc/parse-table.conf'
        print "[tableview start] file: %s"%(txt)
        subprocess.call(["cat {txt} | {parse_table} -conf {parsed_conf} -segment_order=ascii,size_desc -placement_order=row,col -interpolate_type count -col_order_row -use_col_order_row -col_color_row -use_col_color_row -ribbon_layer_order=size_asc | {make_conf} -dir {conf_dir}".format(txt=txt, parse_table=parse_table, parsed_conf=parsed_conf, make_conf=make_conf, conf_dir=conf_dir)],shell=True)
        #subprocess.call(["cat {txt} | {parse_table} -conf {parsed_conf} | {make_conf} -dir {conf_dir}".format(txt=txt, parse_table=parse_table, parsed_conf=parsed_conf, make_conf=make_conf, conf_dir=conf_dir)],shell=True)
        file_png = txt.split('/')[-1].replace('txt', 'png')
        subprocess.call(["circos -conf {circos_conf} -outputdir {save_dir} -outputfile {file_png} -param random_string=zgvickusamp| grep created".format(circos_conf=circos_conf, save_dir=save_dir, file_png=file_png)],shell=True)
        print "[tableview end] file: %s"%(txt)

def main():
        #tableview(txt='/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer/samples/RRI_union_deduplicates.split_full.type_dis.txt')
        if len(sys.argv) == 1:
            txt = '/Share/home/zhangqf5/gongjing/software/circos-tools-0.22/tools/tableviewer2/samples/RRI_union_deduplicates.split_full.type_dis.txt'
        else:
            txt = sys.argv[1]
        tableview(txt)

if __name__ == '__main__':
        main()

from nested_dict import nested_dict

def read_txt(txt='/Share/home/zhangqf5/gongjing/DNA-RNA-Protein-interaction-correlation-12-18/data/type_dis/RRI_union_deduplicates.split_full.type_dis.human.txt'):
	dis_dict = nested_dict(2, int)
	dis_revise_dict = nested_dict(2, int)
	with open(txt, 'r') as TXT:
		for n,line in enumerate(TXT):
			line = line.strip()
			print n,line
			if n == 0:
				dis_dict['row_order'] = line
			elif n == 1:
				dis_dict['row_color'] = line
			elif n == 2:
				dis_dict['row_rnas'] = line
				col_rna_ls = line.split()[1:]
			else:
				row_rna = line.split()[0]
				val_ls = map(float, line.split()[1:])
				for col_rna, val in zip(col_rna_ls, val_ls):
					dis_dict[row_rna][col_rna] = val
	print dis_dict

	rna_pair_ls = []
	for row_rna in col_rna_ls:
		for col_rna in col_rna_ls:
			dis_revise_dict[row_rna][col_rna] = 0

	for row_rna in col_rna_ls:
		for col_rna in col_rna_ls:
			rna_pair1 = row_rna + '-' + col_rna
			rna_pair2 = col_rna + '-' + row_rna
			if rna_pair1 in rna_pair_ls: 
				continue
			if rna_pair2 in rna_pair_ls:
				continue
			rna_pair_ls.append(rna_pair1)
			rna_pair_ls.append(rna_pair2)
			dis_revise_dict[row_rna][col_rna] += dis_dict[row_rna][col_rna]
			if row_rna == col_rna:
				continue
			dis_revise_dict[row_rna][col_rna] += dis_dict[col_rna][row_rna]
	print dis_revise_dict

	savefn = txt.replace('txt', 'revise.txt')
	with open(savefn, 'w') as SAVEFN:
		print >>SAVEFN, dis_dict['row_order']
		print >>SAVEFN, dis_dict['row_color']
		print >>SAVEFN, dis_dict['row_rnas']
		for row_rna in col_rna_ls:
			row_rna_ls = [dis_revise_dict[row_rna][col_rna] for col_rna in col_rna_ls]
			print >>SAVEFN,row_rna+' '+' '.join(map(str, row_rna_ls))

	return savefn