Meta-data corresponding to Source and Target for Network construction in Gephi

[vinitamehlawat]

Hi @qianjiaqiang

I have used your repo for construction of evolution network for my sars-cov2 data Gblocks_Cleaned_sequences.fasta . In my final outpt I have following files:

• freq_all.txt
• Gblocks_Cleaned_sequences.ma
• net_all.txt
• nodes_all.txt
• pi_pos_all.fasta
• rm_non-ATCG_genomes.ma
• net.csv
• edgeTable.csv
• nodeTable.csv

Now I wanted to construct the network using Gephi But I am not sure which number you used to construct the source and target, because I want to color the source node with State and target with city

Correct me if I am wrong, I checked manually in header of some seq >hCoV-19/India/MH-C179/2020 and found that 155 is source for target 179 means 155 is GJ state and 179 is MHstate

Please suggest me how to extract the State and City information for net.csv from my raw-data so that I can further plot geo-mapping.

Thanks Vinita

[qianjiaqiang]

155 means the 155th line in the seq file if my memory isn't wrong. You can append your State/city name with the "155"/"179" as a label in Gephi with a csv file as following:

155 "State GJ"
...
179 "City MH"

@genesisprophet

[vinitamehlawat]

Hi @qianjiaqiang

Thank you for your prompt response

Could you please suggest which seq file I should look for State/City

1. pi_pos_all.fasta & Gblocks_Cleaned_sequences.ma which are created after running your script in example_data folder
2. sequence.fasta which I used as input fasta file to run VENAS

Thanks Vinita

[qianjiaqiang]

pi_pos_all.fasta

[vinitamehlawat]

@qianjiaqiang Thanku very much !

It works for me