`get_operons.py` doesn't respect correct item order

[m-jahn]

Hi!
I noticed that the output from get_operons.py is not what I would expect, at least not in all cases.
Something can go wrong when parsing gene-gene relationship. For example, the output that I get contains wrong order of genes, which messes up operon topology (creates long, overlapping operons). For example:

...
7,ID=gene-ABHI20_RS00215
7,ID=gene-ABHI20_RS00220
7,ID=gene-ABHI20_RS00225
7,ID=gene-ABHI20_RS00230
7,ID=gene-ABHI20_RS00235
8,ID=gene-ABHI20_RS00240
9,ID=gene-ABHI20_RS0025050
10,ID=gene-ABHI20_RS0931020
11,ID=gene-ABHI20_RS0025555
12,ID=gene-ABHI20_RS0026060

Please note operon 10 (single gene) with an ID completely out of range and far from the other surrounding genes.

[m-jahn]

Note: already the output from python test.py contains wrong gene pairings. The IDs are not the direct neighbors of each other.

name_1,name_2,true,prob_0,prob_1,prob_2,prob_3,prob_4,prob_5,prob_6,prob_7,prob_8,prob_9,prob,pred
ID=ABHI20_02090,ID=gene-ABHI20_RS02105,-1,0.00075514265,0.0014725765,0.00051546714,0.00017403897,0.000527577,0.0023352494,0.00080376345,0.00055404514,0.0007512311,0.00026002945,0.000814912088389974,0
ID=gene-ABHI20_RS02105,ID=gene-ABHI20_RS02110,-1,0.120339066,0.07780141,0.10428244,0.18543682,0.113555185,0.18073754,0.027168399,0.06753246,0.08814999,0.1102014,0.1075204698368907,0
ID=gene-ABHI20_RS02110,ID=gene-ABHI20_RS02120,-1,0.009948294,0.055011038,0.027716048,0.14856,0.10106449,0.07389276,0.18722852,0.008154969,0.021251122,0.06592596,0.0698753196746111,0
ID=gene-ABHI20_RS02120,ID=gene-ABHI20_RS02140,-1,0.01226064,0.03299162,0.12459856,0.0022397616,0.012645949,0.026573768,0.03839496,0.020958446,0.0066647856,0.006035464,0.02833639595191926,0
ID=gene-ABHI20_RS02125,ID=gene-ABHI20_RS02080,-1,3.752406e-05,0.00027066257,3.9910818e-05,4.1933967e-05,0.0004600208,0.0014021811,0.0001615492,0.0001241954,0.0004664344,1.0329784e-05,0.00030147420893626985,0
ID=gene-ABHI20_RS02130,ID=gene-ABHI20_RS02125,-1,0.048714302,0.07826629,0.038018923,0.18114737,0.047050163,0.03878913,0.10711036,0.019800559,0.04915835,0.066637315,0.06746927611529827,0
ID=gene-ABHI20_RS02135,ID=gene-ABHI20_RS02130,-1,0.06461022,0.07674101,0.049127396,0.036716737,0.096435405,0.4107618,0.006895866,0.02930066,0.08977922,0.06728752,0.09276558379642666,0
ID=gene-ABHI20_RS02140,ID=gene-ABHI20_RS02145,-1,0.97807103,0.96186906,0.9768059,0.990128,0.9690591,0.97138155,0.9923999,0.96397114,0.97009844,0.97177964,0.9745563745498658,1
ID=gene-ABHI20_RS02145,ID=gene-ABHI20_RS02150,-1,0.98889416,0.9805235,0.9847994,0.9743301,0.96824974,0.97818065,0.96282524,0.98112535,0.97857016,0.97669196,0.9774190306663513,1
ID=gene-ABHI20_RS02150,ID=gene-ABHI20_RS02155,-1,0.5446885,0.48835295,0.45583448,0.43100882,0.7160854,0.67601395,0.55606717,0.5423287,0.5979392,0.6755416,0.5683860749006271,1