Questions tagged [pandas]

Python module widely used in data science designed around database commands and calculations

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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
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1answer
64 views

How can I use pandas agg here to avoid iteration?

can anyone help me improve this pandas code? ...
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) ...
0
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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
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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
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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
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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: ...