Questions tagged [python]
python is a programming language, widely used in bioinformatics
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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 ...
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Why does it require 4 vectors to calculate a torsion angle?
The BioPython documentation shows the following:
11.6.3 Measuring torsion angles Use the vector representation of the atomic coordinates, and the calc dihedral function from the Vector module:
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How to make 3d model of a protein that not exist in PDB?
I'm working on nsSNPs(Non-synonymous single nucleotide polymorphisms) of protein AKAP13 whose PDB not available.
I did one mutation in this protein and I want to show the effect by 3d modeling without ...
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How to sort multiple FASTA files based on their content?
I have around 10,000 FASTA files of Influenza A virus.
These files contains sequences of each of the 8 segments of the viral genome and I want to separate each genome segment into a different folder ...
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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 ...
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Improving list speed: glycosylation example
I discussed a question with @gaspanic Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions
. The issue emerged was speeding up lists in Python. ...
M__♦
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Using Entrez.efetch() to retrive .fasta file from any NCBI database?
I tried to use these python codes to retrieve a .fasta file from gene database, but the output were the parameters of the report
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Changing the record id in a FASTA file using BioPython
I have the following FASTA file, original.fasta:
>foo
GCTCACACATAGTTGATGCAGATGTTGAATTCACTATGAGGTGGGAGGATGTAGGGCCA
I need ...
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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 ...
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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 ...
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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 ...
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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:
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Extracting the CIGAR string from a BAM via Python?
Is there a standard method in Python to extract a CIGAR string from the BAM?
There are great libraries which parse the CIGAR, e.g. https://pypi.python.org/pypi/cigar/0.1
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Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file
As the title summarizes, I am trying to:
Read a PDB file (for example, 1enh.pdb).
Extract the backbone dihedral angles (phi, psi).
Modify the dihedral angles (phi, ...
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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 ...
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How to translate amino acid sequences to Nucleotide sequences
I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
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HDF5 and BioSQL solutions
I'm looking at better database/storage solutions for NCBI virus data, with all attributes particularly year and country of isolation, together with structural data, possible antibody data, T-cell data ...
M__♦
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Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles
I have been successfully using BioPython's functionality for extracting protein torsion angles using the IC_Chain module. However, I am currently looking to use the ...
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How to map PDB chains to Uniprot IDs using API services
I have a lot of PDB IDs and I need to get uniprot fasta sequences of these PDB IDs special chains by API services. For example, imagine that I need to get fasta sequence of '1kf6' 'A' chain. The ...
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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 ...
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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, ...
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Downloading SRA Files from AWS
I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
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Greedy Motif Search Using Probability Matrices
In my greedy search with pseudocounts algorithm in my bioinformatics course, I did not follow the pseudocode since I wanted to solve the problem in my own way. Unfortunately, although my answer is ...
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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 ...
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Retrieve ID ligand from PDB file
I have thousands of PDB files and I need to extract the following information from each of them: an ID or the name of the small molecule (ligand) present in the complex.
Is there a way to do that ...
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Remove Redundant Sequences from FASTA file in Python
I'm attempting to remove redundant sequences from a fasta file (from NCBI). When I execute this code, it returns the number of spots, not the number of sequences. (Number of spots: 408,293, Number of ...
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Infer the new (Ban et. al) ribosomal nomenlature (ex. uL53 ) from the ribosomal protein's sequence
I'm trying to programmatically construct a name for each protein subchain in any ribosome from Uniprot in accordance with Ban et. al's 2014 proposal (excerpt given below) using PDB's and Uniprot's ...
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Get a list of PDB ids from a list of sequence protein number?
I am working on a project about phosphorylation, and I am creating a database of some proteins. I have a list of protein accession ids for which I need to get the corresponding PDB file for each one ...
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reverse translation from amino acid string to DNA strings
what is the opposite of .translate() function calls ?
I mean let's say I am given an amino acid string CYCLIC, how do I obtain all the possible combinations of DNA ...
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Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions
I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this?
Input: a list of unaligned ...
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Interpreting GWAS results with different settings
I did a bunch of GWAS analysis (linear model without covariates) with applying different quality controls. How to choose the optimal settings when filtering for minor allele frequency (maf), Hardy-...
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How to allow "half windows" in biopython?
I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
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Trying to download a large number of files from ENA programmatically
I am downloading a large number of files from the ENA in Python using Multithreading. As an example, to be more concrete, I tried downloading 12 files simultaneously using 12 threads. I noticed that ...
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How to convert mzXML to mzML format (mass spectrometry files)?
How to convert mzXML to mzML format (mass spectrometry files) preferably under Linux and/or Python?
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How to obtain desired output?
I am working on a project using the following command within nano:
...
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GWAS phenotype data format and preprocessing
I have a set of different phenotypes which I want to use for a GWAS analysis (general linear model). I have a couple of questions and uncertainty about the phenotype data input.
I have control and ...
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How can I get a list of neighboring Hydrogen atoms of an alpha-carbon?
Suppose, I want to find the neighboring Hydrogen atoms of a specific C-alpha atom.
The following was my effort. However, it produces a bunch of empty lists.
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connect same ids with values in id rows (result of effectiveELD)
I can't cope with reworking the result. If id is the same I want to stick those items.
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