IndexError when running minimds_inter.py script

[shenlinyong]

The software you developed is fantastic, I'm perfectly fine building 3D models of the intra of chromosomes. But I had trouble building 3D models inter chromosomes.

    856 Reading ../../data/fat/fat_36_Z_1.0mb.bed
    857 Reading ../../data/fat/fat_37_Z_1.0mb.bed
    858 Reading ../../data/fat/fat_38_Z_1.0mb.bed
    859 Reading ../../data/fat/fat_39_Z_1.0mb.bed
    860 Reading ../../data/fat/fat_Z_100kb.bed
    861 Scanning ../../data/fat/fat_1_100kb.bed
    862 Traceback (most recent call last):
    863   File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 168, in <module>
    864     main()
    865   File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 158, in main
    866     structures = interMDS(chrom_names, args.prefix, args.inter_res, args.intra_res, args.partitioned, params)
    867   File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 111, in interMDS
    868     r, t = la.getTransformation(inferred_low, true_low)
    869   File "/home/SLY68/biosoft/miniMDS/linear_algebra.py", line 13, in getTransformation
    870     a.append(structure1.points[num-structure1.offset].pos)
    871 IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices
    872 Scanning ../../data/lean/lean_1_100kb.bed
    873 Scanning ../../data/lean/lean_2_100kb.bed
    874 Scanning ../../data/lean/lean_3_100kb.bed
    875 Scanning ../../data/lean/lean_4_100kb.bed
    876 Scanning ../../data/lean/lean_5_100kb.bed
  ...... 
  69668 Reading ../../data/lean/lean_39_Z_1.0mb.bed
  69669 Reading ../../data/lean/lean_Z_100kb.bed
  69670 Scanning ../../data/lean/lean_1_100kb.bed
  69671 Traceback (most recent call last):
  69672   File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 168, in <module>
  69673     main()
  69674   File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 158, in main
  69675     structures = interMDS(chrom_names, args.prefix, args.inter_res, args.intra_res, args.partitioned, params)
  69676   File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 111, in interMDS
  69677     r, t = la.getTransformation(inferred_low, true_low)
  69678   File "/home/SLY68/biosoft/miniMDS/linear_algebra.py", line 13, in getTransformation
  69679     a.append(structure1.points[num-structure1.offset].pos)
  69680 IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Other chromosomes are OK, and only chr1 has encountered this problem, and chr1 is many times larger than other chromosomes. _1_100kb.bed file is 1901776 lines.

Here is my running script:

for i in {1..39} Z;do
python ~/biosoft/miniMDS/minimds_inter.py -n 50 ../../data/fat/fat 1000000 100000
python ~/biosoft/miniMDS/minimds_inter.py -n 50 ../../data/lean/lean 1000000 100000
done