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farhangus / Sniffles2_plot

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ValueError: invalid literal for int() with base 10: '6,6' #1

Closed evayfang2019 closed 10 months ago

evayfang2019 commented 1 year ago

Hi, farhangus when i ran: python3 sniffles2_plots.py -i ./tmp_samples/sample_merged.vcf -o ./test then reported: ./tmp_samples/sample_merged Traceback (most recent call last): File "xxx/sniffle2_plot/vcf_visulaizer.py", line 31, in main() File "xxx/sniffle2_plot/vcf_visulaizer.py", line 26, in main multi_visulaizer(input_vcf_file, output_path) File "xxx/sniffle2_plot/src/multi_vcf_visualizer.py", line 19, in multi_visulaizer SV_site.sv_sites_per_genome() File "xxx/sniffle2_plot/src/sv_sites_per_genome.py", line 36, in sv_sites_per_genome obj = VCFLineSVPopulation(line) File "xxx/sniffle2_plot/src/vcf_line_parser.py", line 213, in init self.get_genotype(FORMAT, sample_header_names) File "xxx/sniffle2_plot/src/vcf_line_parser.py", line 267, in get_genotype sample_gt.set_dr(gt_value) File "xxx/sniffle2_plot/src/vcf_line_parser.py", line 148, in set_dr self.dr = int(this_dr) ValueError: invalid literal for int() with base 10: '6,6'

Sniffle2_plot might not be suitable for handling my VCF file at the moment, although it was also generated via sniffles.

farhangus commented 1 year ago

Dear evayfang2019, Thanks for your message, I will check it and get back to you. If possible, may i have the VCF file for checking purposes. Best regards

On Fri, Aug 18, 2023 at 7:56 AM evayfang2019 @.***> wrote:

Hi, farhangus when i ran: python3 sniffles2_plots.py -i ./tmp_samples/sample_merged.vcf -o ./test then reported: ./tmp_samples/sample_merged Traceback (most recent call last): File "xxx/sniffle2_plot/vcf_visulaizer.py", line 31, in main() File "xxx/sniffle2_plot/vcf_visulaizer.py", line 26, in main multi_visulaizer(input_vcf_file, output_path) File "xxx/sniffle2_plot/src/multi_vcf_visualizer.py", line 19, in multi_visulaizer SV_site.sv_sites_per_genome() File "xxx/sniffle2_plot/src/sv_sites_per_genome.py", line 36, in sv_sites_per_genome obj = VCFLineSVPopulation(line) File "xxx/sniffle2_plot/src/vcf_line_parser.py", line 213, in init self.get_genotype(FORMAT, sample_header_names) File "xxx/sniffle2_plot/src/vcf_line_parser.py", line 267, in get_genotype sample_gt.set_dr(gt_value) File "xxx/sniffle2_plot/src/vcf_line_parser.py", line 148, in set_dr self.dr = int(this_dr) ValueError: invalid literal for int() with base 10: '6,6'

Sniffle2_plot might not be suitable for handling my VCF file at the moment, although it was also generated via sniffles.

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evayfang2019 commented 1 year ago

Hi, farhangus Thanks for your reply. Please check the vcf file. Best regards evayfang2019.zip

farhangus commented 1 year ago

Dear Evay, Thanks for sending the file,I ran the program on file and the output is attached. Will you please pull the package and rerun it. Please let me know if there is any issue. Command " python3 sniffles2_plots.py -i tmp1/evayfang2019.vcf -o tmp3" Best regards, Farhang

On Fri, Aug 18, 2023 at 11:07 PM evayfang2019 @.***> wrote:

Hi, farhangus Thanks for your reply. Please check the vcf file. Best regards evayfang2019.zip https://github.com/farhangus/sniffle2_plot/files/12384995/evayfang2019.zip

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evayfang2019 commented 1 year ago

Dear Farhang, I've rerun the program and it's running smoothly. Thank you and your outstanding works. Best regards, Evay

farhangus commented 1 year ago

Dear Evay, You are most welcome, and thanks for your feedback. Best regards, Farhang

On Mon, Aug 21, 2023 at 5:25 AM evayfang2019 @.***> wrote:

Dear Farhang, I've rerun the program and it's running smoothly. Thank you and your outstanding works. Best regards, Evay

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