assemble-complexSVs incompatible with EagleC2 output format #79
Description
When trying to use EagleC2 result (AA86.SV_calls.txt) as input for NeoLoop’s assemble-complexSVs, the program raises a parsing error because the output format of EagleC2 is different from what NeoLoop expects.
The current assemble-complexSVs function requires an input format like:
chr11 chr11 ++ 83565000 84315000 inversion
However, the EagleC2 output is in a different format, for example:
chrom1 pos1 chrom2 pos2 ++ +- -+ -- ++/-- +-/-+ original resolution fine-mapped resolution gap info chr9 21020000 chr18 69680000 1.065e-07 0.9961 8.157e-08 1.594e-07 4.047e-07 2.271e-06 25000 10000 0,0
Error traceback:
Traceback (most recent call last):
File "/cluster2/home/futing/miniforge3/envs/neoloop/bin/assemble-complexSVs", line 127, in run
work = assembleSV(clr, args.break_points, span=args.region_size, col=balance,
File "/cluster2/home/futing/miniforge3/envs/neoloop/lib/python3.10/site-packages/neoloop/assembly.py", line 52, in __init__
sv_list = load_translocation_fil(sv_fil, clr.binsize, minIntra)
File "/cluster2/home/futing/miniforge3/envs/neoloop/lib/python3.10/site-packages/neoloop/util.py", line 70, in load_translocation_fil
c1, c2, strands, i1, i2, note = line.rstrip().split()
ValueError: too many values to unpack (expected 6)
I run with the following command:
predictSV --mcool ${dir}/cool/${cell}.mcool \
-O ${cell} -g hg38 --balance-type ICE -p 15
assemble-complexSVs -O ${cell} \
-B ${cell}.SV_calls.txt \
--balance-type ICE --protocol insitu \
--nproc 15 \
-H ${dir}/cool/${cell}.mcool::/resolutions/50000 \
${dir}/cool/${cell}.mcool::/resolutions/10000 \
${dir}/cool/${cell}.mcool::/resolutions/5000
Environment:
- Neoloop 0.4.3.post2
- python 3.10.19
- predictSV 2.1.1
Could you please help to solve this problem?
Or should I revert to an older version of EagleC to make it compatible with NeoLoop?
Thanks!