Questions tagged [pandas]
Python module widely used in data science designed around database commands and calculations
8
questions
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1answer
40 views
Help to create a dataframe in Python from a FASTA file
I want to create a dataframe in Python starting from a FASTA format file. Given the toy FASTA file that I am attaching, I built this program in Python that returns four colums corresponding to id, ...
1
vote
1answer
64 views
1
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1answer
52 views
Adding multiple dataframes to compare against genotypes - DATE/LOCATION - geotemporal incidences of SARS2 genotypes
I'm trying to reuse some code I have previously used to add extra parameters.
In the initial code, it was used to give a 1/0 counter if a specific mutation was present (first code below)
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0
votes
1answer
104 views
Converting hmmer --tblout to pandas dataframe [closed]
Is there a way to convert a hmmer output to a pandas dataframe? I am also unsure how to load a hmmer tblout table into python via the Bio module. I believe you can call a hmmer format with SeqIO.parse ...
0
votes
1answer
64 views
how do i change a variable with iterator under a for loop in python
This question comes up in my bioinfo class.
I have a csv file containing gene names and the cluster they belong to. I want to run GESA on each individual cluster. So I would like to extract the list ...
2
votes
1answer
82 views
Possibility to save output blastn table in memory using biopython
Is there a possibility, using biopython to save output table of blastn in memory, not in file on hard drive, for process it using pandas for example and then delete it from memory?
I mean, is there a ...
3
votes
1answer
71 views
How to load output from the kegg API in biopython into a pandas dataframe?
Biopython provides a (bit unintuitive) API to access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). I am trying to make use of it, but the output is quite unhandy as a string. What is the best ...
7
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4answers
1k views
How to do `bedtools intersection` using pandas alone?
I have two pandas Dataframes, using python3.x:
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