Questions tagged [python3]

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Running a list of apis via Python's request module

I am running the following Python code with python requests in my Jupiter notebook to get cancer oncology id's from EBI-EMBL. ...
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2 answers
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Error in seaborn plot " Horizontal orientation requires numeric `x` variable"

I am trying to plot a box plot with seaborn with the following code ...
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  • 129
1 vote
3 answers
614 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, ...
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163 views

BWA-MEM2 alignment-Snakemake

I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, ...
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1 vote
0 answers
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3d model of a protein via nucleotide sequence

I really appreciate @Matteo Ferla's detailed answer to my previous question. I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There ...
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1 answer
26 views

querying gdc metadata issues with resulting fields

I have been trying to access metadata from the Genomic Data Commons; however, not all of the information I want is showing up in the resulting tsv file. How do I get sample type and analyte type to ...
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1 answer
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Querying metadata (GDC) using a filter

I have been trying to access the GDC metadata with python through the filter below. However, this code I have been using always yields a blank tsv file. Any help on fixing the code is appreciated! <...
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1 vote
1 answer
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querying metadata (GDC Data Portal) in python3

I am trying to query metadata from the Genomic Data Commons (GDC) Data Portal and used the sample code from its website: ...
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2 votes
2 answers
250 views

Remove Redundant Sequences from FASTA file with Biopython reducing memory footprint

I need help with my Biopython code, I am kind of new to Python and Biopython so please don't be harsh on me. Everything started from here: Remove duplicated sequences in FASTA with Python I answered ...
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2 votes
1 answer
70 views

How can I use pandas agg here to avoid iteration?

can anyone help me improve this pandas code? ...
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1 vote
1 answer
538 views

What changed wwith Python in WDL change from draft 2 to version 1?

I'm updating my WDL from draft 2 (whichs works fine) to version 1. I'm stuck with a Py snippet ...
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1 vote
1 answer
15 views

What is the best way to drop alignment artifacts in sequence objects in biopython?

I have a bunch of sequences created with Roary which I want to preprocess. When I read the sequences (genomics data) I want to translate them to protein sequences ...
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63 views

How to fix NameError?

I am working on a project and am having issues with the following code that I have written in nano: ...
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2 votes
1 answer
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How do you currently track bugs in python using freely available software/websites?

I am starting a project using Python to track, archive, assign and manage bioinformatics bugs. This software will be able to be integrated into project management software or stand alone. How do you ...
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2 votes
1 answer
71 views

cmapPy exception

I'm trying to read gctx files with cmapPy. This is my code: ...
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1 vote
1 answer
333 views

How to predict with the pre-trained DNABERT model?

I was curious to give DNA BERT a try. This is a BERT (Bidirectional Encoder Representations from Transformers) model that was trained on short (k=3,4,5, or 6) k-...
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1 vote
1 answer
539 views

I want to write python program to cut a DNA sequence at an EcoRI restriction site and print the two fragments after cutting

Seq = AAAAAAAAAAATTTTTTTTTTTGAATTCCCCCCCCCCCGGGGGGGGGGG Restriction site = GAATTC I want to cut the sequence at GA/ATTC I tried split method in python but It does not cut at GA/ATTC. Please help
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1 vote
1 answer
190 views

Find CRISPR PAM-sites with python

I am a college student and just started bioinformatics. I am trying to write a script (not for school) that finds all potential NGG and TTTN protospacer adjacent motif sequences in a genome string. I ...
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1 vote
1 answer
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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1 vote
1 answer
38 views

How to find Genotype, from list of mutations:lineage list?

I'm very new to python and I'm getting along nicely (I'd like to believe); however, I must be missing something here. I'm looking to read each and every file and compare each line against one another. ...
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