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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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wgd ksd output can not generate the tsv file #67

Closed ljl000 closed 2 years ago

ljl000 commented 2 years ago

Hi, I performed wgd ksd to calculate Ks value by using transcritome data ,but I can't generate the tsv file. I only get a tmp file folder with sevaral GF_xxx.Ks, GF_xxx.fasta and GF_xxx.msa in it. how can i fix this? the result folder just like this... 屏幕快照 2021-09-08 22 25 47

arzwa commented 2 years ago

Did you get an error message related to generating the tsv output? As a workaround you can just concatenate the GF_*.Ks files, you will only need to remove the first line of each file and have that only once on top of the concatenated file. Something like this in python should also work (not tested!) 

import os
import pandas as pd
pd.concat([pd.read_csv(f, sep="\t", index_col=0) for f in os.listdir(".")]).to_csv("ksd.tsv", sep="\t")
arzwa commented 2 years ago

Closing because no response.