IndexError when running minimds_inter.py script

[shenlinyong]

The software you developed is fantastic, but I had trouble building 3D models between 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

Here is my running script:

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

[Alexlsy]

The cause of this error is that "num", "structure1.offset" and "structure2.offset" become float.
replace
a.append(structure1.points[num-structure1.offset].pos)
a.append(structure2.points[num-structure2.offset].pos)
(in linear_algebra.py)
with
a.append(structure1.points[int(num)-int(structure1.offset)].pos)
b.append(structure2.points[int(num)-int(structure2.offset)].pos)

can solve this error

[shenlinyong]

Thank you very much for your help. I have modified :

replace
a.append(structure1.points[num-structure1.offset].pos)
a.append(structure2.points[num-structure2.offset].pos)
(in linear_algebra.py)
with
a.append(structure1.points[int(num)-int(structure1.offset)].pos)
b.append(structure2.points[int(num)-int(structure2.offset)].pos)

I'm still having trouble:

 1762 Reading ../../data/lean/lean_39_Z_1.0mb.bed
 1763 Reading ../../data/lean/lean_Z_100kb.bed
 1764 Scanning ../../data/lean/lean_1_100kb.bed
 1765 /home/SLY68/anaconda3/envs/hicpro/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3441: RuntimeWarning: Mean of empty slice.
 1766 out=out, **kwargs)
 1767 /home/SLY68/anaconda3/envs/hicpro/lib/python3.7/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
 1768 ret = ret.dtype.type(ret / rcount)
 1769 Scanning ../../data/lean/lean_2_100kb.bed
 1770 Scanning ../../data/lean/lean_3_100kb.bed
....
 1796 Scanning ../../data/lean/lean_29_100kb.bed
 1797 Traceback (most recent call last):
 1798 File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 168, in <module>
 1799 main()
 1800 File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 158, in main
 1801 structures = interMDS(chrom_names, args.prefix, args.inter_res, args.intra_res, args.partitioned, params)
 1802 File "/home/SLY68/biosoft/miniMDS/minimds_inter.py", line 106, in interMDS
 1803 rescaling_factor = la.radius_of_gyration(true_low)/la.radius_of_gyration(inferred_low)
 1804 File "/home/SLY68/biosoft/miniMDS/linear_algebra.py", line 46, in radius_of_gyration
 1805 return dist_sum/len(coords)
 1806 ZeroDivisionError: division by zero

[Lila14]

The cause of this error is that "num", "structure1.offset" and "structure2.offset" become float. replace a.append(structure1.points[num-structure1.offset].pos) a.append(structure2.points[num-structure2.offset].pos) (in linear_algebra.py) with a.append(structure1.points[int(num)-int(structure1.offset)].pos) b.append(structure2.points[int(num)-int(structure2.offset)].pos)

can solve this error

Thanks, I fixed this!

[Lila14]

It looks like somehow a structure ended up empty. I noticed that you're using a nonhuman genome, I wonder if one of the chromosomes is shorter than 1Mb and couldn't be reduced to that resolution? If you send me the input files I can test.

[shenlinyong]

看起来不知何故，一个结构最终是空的。我注意到您使用的是非人类基因组，我想知道其中一条染色体是否短于 1Mb 并且无法降低到该分辨率？如果你把我可以测试的输入文件发给我。

You are right, some chromosomes are less than 1M in length. The smallest chromosome is only 0.17Mb and the largest chromosome is 196Mb. Therefore, what is the suitable resolution of hic data to use when constructing the 3D structure:

chr1 196449156
chr2 149539284
chr3 110642502
chr4 90861225
chr5 59506338
chr6 36220557
chr7 36382834
chr8 29578256
chr9 23733309
chr10 20453248
chr11 19638187
chr12 20119077
chr13 17905061
chr14 15331188
chr15 12703657
chr16 2706039
chr17 11092391
chr18 11623896
chr19 10455293
chr20 14265659
chr21 6970754
chr22 4686657
chr23 6253421
chr24 6478339
chr25 3067737
chr26 5349051
chr27 5228753
chr28 5437364
chr29 726478
chr30 755666
chr31 2457334
chr32 125424
chr33 3839931
chr34 3469343
chr35 554126
chr36 358375
chr37 157853
chr38 667312
chr39 177356
chrW 9109940
chrZ 86044486

[Lila14]

I would say try 100kb because that will mean no empty chromosomes

…

On Sat, Aug 6, 2022, 9:53 PM shenlinyong ***@***.***> wrote: 看起来不知何故，一个结构最终是空的。我注意到您使用的是非人类基因组，我想知道其中一条染色体是否短于 1Mb 并且无法降低到该分辨率？如果你把我可以测试的输入文件发给我。 You are right, some chromosomes are less than 1M in length. The smallest chromosome is only 0.17Mb and the largest chromosome is 196Mb. Therefore, what is the suitable resolution of hic data to use when constructing the 3D structure: chr1 196449156 chr2 149539284 chr3 110642502 chr4 90861225 chr5 59506338 chr6 36220557 chr7 36382834 chr8 29578256 chr9 23733309 chr10 20453248 chr11 19638187 chr12 20119077 chr13 17905061 chr14 15331188 chr15 12703657 chr16 2706039 chr17 11092391 chr18 11623896 chr19 10455293 chr20 14265659 chr21 6970754 chr22 4686657 chr23 6253421 chr24 6478339 chr25 3067737 chr26 5349051 chr27 5228753 chr28 5437364 chr29 726478 chr30 755666 chr31 2457334 chr32 125424 chr33 3839931 chr34 3469343 chr35 554126 chr36 358375 chr37 157853 chr38 667312 chr39 177356 chrW 9109940 chrZ 86044486 — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADMHIA6V34SPB7Z2KCBH4BDVX4JLNANCNFSM54MAICEQ> . You are receiving this because you commented.Message ID: ***@***.***>