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Questions tagged [biopython]

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Biopython / ETE3 get subtree of a newick tree

I can not find a good example how to extract a subtree from a phylogenetic tree with either library. I can load newick files etc, but not sure how to search for a ...
El Dude's user avatar
  • 195
0 votes
0 answers
34 views

What is a 'structure' and a 'model' in BioPython?

What are a 'Structure' and a 'Model' in BioPython? Why did they incorporate 'structure' and 'model' instead of 'Protein' as objects?
user366312's user avatar
0 votes
2 answers
41 views

How does BioPython generate IDs for atoms, residues, chains, and structures?

When we read a protein databank (PDB) file using BioPython, does BioPython assign unique IDs to each atom, each residue, each chain, and each protein? If so, how does BioPython generate those IDs? How ...
user366312's user avatar
1 vote
1 answer
54 views

All against all sequence alignment

I have a large set of protein sequences and would like to create a "similarity matrix" out of them (for phylo trees later). So I have to run n(n-1) ...
El Dude's user avatar
  • 195
1 vote
0 answers
22 views

Biopython PhyloTree to PyVis Network

We are trying to convert a Phylogenetic tree to networkx previously calculated with ...
El Dude's user avatar
  • 195
1 vote
2 answers
87 views

How to parse hmmsearch output?

I did hmmsearch with --notextw and --domtblout and I see several results for ids, I want to ...
bobr's user avatar
  • 11
4 votes
2 answers
179 views

BioPython bootstrap is not reliable?

Here i will show you a minimal working example of code and as you can see the support values for the tree is always 100. I am using synthetic sequences of 100bp for 6 elements. The sequences have been ...
Mirko's user avatar
  • 267
0 votes
0 answers
12 views

Metabolic Modeling

I am trying to identify the flux of IgG antibody in CHO ovary cells with optimised biomass and glucose input ranging from 0 to 10, but I am not sure when I run the FBA analysis what should I define my ...
July's user avatar
  • 1
1 vote
1 answer
92 views

Blastn through NCBIWWW not giving any results, as opposed to the online BLAST

I am trying to create a simple pipeline that takes a file containing various short sequences, and run them through blast. I have an example sequence; ...
Bas Jansen's user avatar
2 votes
1 answer
66 views

Getting ALL Protein entries from Entrez for a particular taxonomic id

I'm trying to get ALL Proteins for a Taxonomic ID from Entrez using Esearch/Efetch and the following command: ...
The August's user avatar
2 votes
1 answer
44 views

retrieving past BLAST requests in bioPython

is there any way to retrieve a BLAST request made using the Biopython library using the request's query_id? Alternatively is it possible to retrieve a query_id before the blast result is complete, and ...
kama's user avatar
  • 21
2 votes
1 answer
42 views

BioPython SeqIO fails with Invalid Alphabet found

I am trying to store a GenBank file that could be read by Geneious later. I found an example how to create the GenBank file here But now I run into Alphabet issues. ...
El Dude's user avatar
  • 195
2 votes
0 answers
83 views

Get SRR numbers from a GSE number

I'm trying to programmatically download files from SRA (with prefetch in sra-tools) starting from a GSE number, using Python. There is an explanation for using entrez-direct on the CLI, using esearch ...
Freek's user avatar
  • 563
3 votes
1 answer
87 views

KeyError '/n' in Bio SeqUtils Package ProtParam Script

I am trying to run a function from the ProtParam script in the Bio.SeqUtils package. The function is for calculating the instability index of a protein. The code I am using in my script with the pre-...
Z_Gonzalez's user avatar
3 votes
2 answers
124 views

Residue numbering in biopython

Is there an out-of-the-box function in the Bio.SeqIO module (in biopython) that can print a protein sequence (in command line) ...
Leptoceratops's user avatar
0 votes
1 answer
141 views

How to calculate the variant allelic fraction (VAF) from VEP output?

This question was also asked on Biostars How can I calculate the variant allelic fraction from the VEP file for multiple human samples? I used the ensembl-vep and it is human data.
Joman's user avatar
  • 39
2 votes
0 answers
26 views

Calculation of Site Frequency Spectrum (SFS) using STR data

Hi everyone I had a question on if it is possible to calculate (Site Frequency Spectrum)SFS using STR data. Please mention if you know any programm that can be used for that! I have tried Arlequin but ...
George X.'s user avatar
4 votes
1 answer
132 views

How can I make this Biopython program (to correct erroneous barcodes) run faster, and is there any alternative method?

This question has also been asked on Biostars I am looking forward to getting a valuable suggestion for a bioinformatic problem. Background: Currently, I am performing a de novo whole genome assembly. ...
VIJITH KUMAR's user avatar
3 votes
1 answer
177 views

Download all pubmed central article ids that have a keyword appearing in their titles/abstracts and also falling between two dates

I am using the following code to download all pubmed central article ids that have a keyword appearing in their titles/abstracts and also falling between two dates. The code seems to work when I ...
Wasim Aftab's user avatar
2 votes
1 answer
88 views

how to do manual search on NCBI with biopython and add link to publication

I'm trying to reproduce a complex manual search on NCBI using BioPython, but obviously something is not right. My command line is not working, but I'd especially like a way to have an accurate search ...
Marine Bergot's user avatar
0 votes
2 answers
343 views

open and read Fasta file (raw data)

I have a big fasta.dataset file containing half a million proteins (1.0 GB). I have four lines for each protein code: line 1:the protein code line 2: protein ...
Amal's user avatar
  • 81
3 votes
3 answers
2k views

How to write FASTA records using "Bio.SeqIO.write()"

Update: Biopython document says that "Bio.SeqIO.FastaIO.FastaWriter" class is obsolete. Now my question becomes how to I use Bio.SeqIO.write() fucntion to ...
Supertech's user avatar
  • 606
5 votes
4 answers
291 views

File I/O error using nglview.show_biopython(structure)

So I have been trying to get into visualizing proteins in python, so after some research I ended up on a tutorial that was teaching you how to visualize a protein from the COVID-19 virus, so I went ...
Jeremiah Wade's user avatar
7 votes
3 answers
2k views

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, ...
epsilone's user avatar
  • 125
5 votes
2 answers
250 views

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 ...
CubeHead's user avatar
  • 425
3 votes
3 answers
182 views

Can I traverse/enumerate PDB one at a time using a Python script without downloading all of them to my local disk?

What would be the total size of all PDB files in RCSB? Can I traverse/enumerate them one at a time using a Python script without downloading all of them to my local disk? If YES, what would be the ...
user366312's user avatar
0 votes
1 answer
2k views

How to extract the protein sequences of a genbank file using R or biopython

sorry for the question, I'm trying to extract the proteins sequences from a genbank file. ...
abraham's user avatar
  • 115
0 votes
1 answer
216 views

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. ...
user366312's user avatar
2 votes
2 answers
603 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 ...
pippo1980's user avatar
  • 1,088