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SunPengChuan / wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
https://wgdi.readthedocs.io/en/latest/
BSD 2-Clause "Simplified" License
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Getting problem at karyotype mapping step #34

Closed mamtamasand closed 1 year ago

mamtamasand commented 1 year ago

Hello Sir I am using WGDI tool for chromosomal rearrangements, I followed the tutorial given, but I am stucked at karyotype mapping step , I have five eudicot species, I want to get the chromosomal rearrangement for multiple species. I have mapped my plant species with AEK given in example files. Please help me out with this step: Till now i have permormed the dotplot analysis, followed by collinearity detection with -icl and WGDI with the "-bi" parameter, and WGDI with the "-c.

For karyotype mapping I am getting this error: File "/home/user/genome_hic/lib/python3.10/site-packages/pandas/core/groupby/grouper.py", line 888, in get_grouper raise KeyError(gpr)

Please suggest.

SunPengChuan commented 1 year ago

Can you provide more error messages?

mamtamasand commented 1 year ago

Traceback (most recent call last): File "/home/user/genome_hic/bin/wgdi", line 10, in sys.exit(main()) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/run.py", line 163, in main module_to_run(arg, value) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/run.py", line 122, in module_to_run run_subprogram(program, conf, name) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/run.py", line 87, in run_subprogram r.run() File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/karyotype_mapping.py", line 178, in run the_other_ancestor_file = self.karyotype_map(data, lens) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/karyotype_mapping.py", line 80, in karyotype_map for chr, group in ancestor.groupby(0): File "/home/user/genome_hic/lib/python3.10/site-packages/pandas/core/frame.py", line 8402, in groupby return DataFrameGroupBy( File "/home/user/genome_hic/lib/python3.10/site-packages/pandas/core/groupby/groupby.py", line 965, in init grouper, exclusions, obj = get_grouper( File "/home/user/genome_hic/lib/python3.10/site-packages/pandas/core/groupby/grouper.py", line 888, in get_grouper raise KeyError(gpr) KeyError: 0

SunPengChuan commented 1 year ago

It feels like there is a problem with the_other_ancestor_file.

mamtamasand commented 1 year ago

okay Thanks for replying Can you provide the input format for the _other_ancestor_file.

mamtamasand commented 1 year ago

From the tutorial it seems that _other_ancestor_file is the result file which will be generated after this program completion.

SunPengChuan commented 1 year ago

Can you send me your your.conf file?

mamtamasand commented 1 year ago

Okay i will send

[karyotype_mapping] blast = matches.blast blast_reverse = false gff1 = Sr_new.gff gff2 = AEK.gff score = 50 evalue = 1e-5 repeat_number = 2 ancestor_left = SR_ancestor.txt ancestor_top = AEK.ancestor.txt the_other_lens = SR.lens blockinfo = corros2_SR.csv blockinfo_reverse = false limit_length = 2 the_other_ancestor_file = resulta2_SR

SunPengChuan commented 1 year ago

Ancestor_left and ancestor_top should only be required to keep one, therefore, ancestor_left here is not necessary.

mamtamasand commented 1 year ago

I have tried with that also then getting this error

index = [group.sort_values(by=11, ascending=False)[:int( Traceback (most recent call last): File "/home/user/genome_hic/bin/wgdi", line 10, in sys.exit(main()) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/run.py", line 163, in main module_to_run(arg, value) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/run.py", line 122, in module_to_run run_subprogram(program, conf, name) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/run.py", line 87, in run_subprogram r.run() File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/karyotype_mapping.py", line 178, in run the_other_ancestor_file = self.karyotype_map(data, lens) File "/home/user/genome_hic/lib/python3.10/site-packages/wgdi/karyotype_mapping.py", line 80, in karyotype_map for chr, group in ancestor.groupby(0): File "/home/user/genome_hic/lib/python3.10/site-packages/pandas/core/frame.py", line 8402, in groupby return DataFrameGroupBy( File "/home/user/genome_hic/lib/python3.10/site-packages/pandas/core/groupby/groupby.py", line 965, in init grouper, exclusions, obj = get_grouper( File "/home/user/genome_hic/lib/python3.10/site-packages/pandas/core/groupby/grouper.py", line 888, in get_grouper raise KeyError(gpr) KeyError: 0

SunPengChuan commented 1 year ago

Please send me the files involved in the package via email (sunpengchuan@gmail.com) so that I can test them.