Multiple steps

[masterzhen119]

I am impressed by your work. However, I think is it possible to provide single line code version. It only needs input and finally out put the haplotypes like althap. Since I am not professional in coding. When I try to mimic your example, I am lost in Step 3.
python3 /home/project11/Hap10/utilities/LinkFragments_brcd_based.py /home/project11/Hap10/test_data/unlinked_fragment_file_filtered /home/project11/Hap10/test_data/frag.txt
python3 /home/project11/Hap10/utilities/splitter.py /home/project11/Hap10/test_data/frag.txt 50 /home/project11/Hap10/test_data/frag_sp.txt
The result is:
35188 fragments linked to larger molecules
0 unlinked fragments with barcodes
0 unlinked fragments without barcodes
4969 duplicate snp-cover. 496 bad and 4440 matched-allele snps
Traceback (most recent call last):
File "/home/project11/Hap10/utilities/splitter.py", line 238, in
molecule_length = int(argv[3])* 1000 # 50000 # length of 10x DNA molecule
ValueError: invalid literal for int() with base 10: '/home/project11/Hap10/test_data/frag_sp.txt'

[sinamajidian]

Hi @masterzhen119
sorry for the inconvenience. The line should be run as

python3 splitter.py frag.txt var_het.vcf 50

I just updated the readme. Please let me know whether it helps.

Regards,
Sina