Questions tagged [python]

python is a programming language, widely used in bioinformatics

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Extract autodocked protein-ligand connections programatically

I have 2 crystal structures, one for my protein and one for my ligand (I have several protein-ligand pairs). I am using AutoDock Vina to simulate docking, which returns another file of the ligand with ...
9
votes
2answers
1k views

How do you generate read-length vs read-quality plot for long-read sequencing data (e.g., MinION)?

How do you generate read-length vs read-quality plot (heat map with histograms in the margin) for long-read sequencing data from the Oxford Nanopore Technologies (ONT) MinION? The MinKNOW software ...
9
votes
3answers
2k views

Running Snakemake in one single conda env

I have been experimenting a lot lately with Snakemake, I love it. Recently I also switched to using conda (--use-conda) in the way that is advertised. However, I have some issues with it, mostly ...
10
votes
3answers
4k views

Converting a VCF into a FASTA given a reference with Python, R

I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R. Samtools/BCFtools (Heng Li) provides a Perl script ...
8
votes
1answer
375 views

Getting protein FASTA sequence based on keyword with python

I would like to gather proteins FASTA sequence from Entrez with python 2.7. I am looking for any proteins that have the keywords: "terminase" and "large" in their name. So far I got this code: ...
8
votes
1answer
304 views

How to get the count of each kmer past 255 using khmer

I have a Fastq file and I want to get the exact count of each possible kmer from this file. On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based ...
7
votes
1answer
483 views

Filtering bases based on phred qualities with pysam

Is there a way to filter bases in BAM files based on phred quallities through python's pysam ? I have a code here that Takes the nucleobases per position from a BAM file using pysam's pileup ...
4
votes
2answers
555 views

Finding a single open reading frame with ribosomal binding site, using Biopython

I'm given a Fasta file, containing a large DNA(over 115,000 long) sequence, and I am tasked with finding a single large open reading frame contained within the DNA sequence using Biopython. I'm ...
3
votes
1answer
244 views

python does not quit when the input file is too big

I have a script that extracts the set of unique kmer pairs from a kmer dump file (& then using them downstream to guess ploidy). The script seems to work correctly (it's reporting a meaningful ...
3
votes
2answers
213 views

Pepsin digest (cleavage) does not work using RE?

Aim is to code the theoretical peptic cleavage of protein sequences in Python. The cleavage (cutting) rule for pepsin is: 1234^567. This is a position, ...