Tag: Biopython

How do I install biopython in anaconda?

Package maintainers recommend using (in the terminal): conda install -c conda-forge biopython We deliberately recommend using Biopython from the conda-forge channel, as this is usually up to date and covers Windows, Mac OS X and Linux. The default Conda channel does have Biopython, but is often out of date. biopython.org/wiki/Packages…

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BlastX through Biopython

BlastX through Biopython 0 I have an unknown gene segment in the Human_gene.txt file and I want to run blastx (translated nucleotide) using the blast module of Biopython by making the E-value threshold 0.0001 and displaying the match result of 50 residues of query and subject. I am trying this…

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A*STAR – Agency for Science, Technology and Research hiring Bioinformatics Specialis, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

 The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is…

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biopython – Pipeline for paired end RNA sequence data to proteins

This is a much more complicated question than it might seem. First, you need to understand how RNA-Seq works, and what your data really is. Your “paired-end files” contain reads, which will contain fragments of transcripts. Since those are only fragments of transcripts, you don’t know what frame they are…

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NcbiblastpCommandline alignment results are different from blast webpage

What you are trying to do is fairly simple, and you are complicating it by: 1) not providing your sequences so that someone can reproduce your attempt; 2) giving a result in a form that is impossible to read. Be honest, can you make any sense of the result you…

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phylogenetics – Biopython reads my tree eternally long

I have a nexus tree (1332 taxa) with a lot of additional data. When I tried to read it through tree = Phylo.read(treepath, “nexus”), my kernel got eternally loaded. If I abort the process, I get the following message: ————————————————————————— KeyboardInterrupt Traceback (most recent call last) Input In [95], in…

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python – How are paths meant to be denoted on for Biopython on mac?

I am trying to run a basic biopython script to rename sequences within a fasta file. I have only ever ran this on a server; i am trying to do it on my macbook but I can’t work out what the correct path to the file should be. on the…

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Parsing GenBank file: get locus tag vs product

As your sample GenBank file was incomplete, I went online to find a sample file that could be used in an example, and I found this file. Using this code and the Bio::GenBankParser module, it was parsed guessing what parts of the structure you were after. In this case, “features”…

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python – Creating a phylogenetic tree with domain annotations using BioPython

You could use ETE3 to implement this as well – it can load the tree as a newick, and then you can set it up with the motifs – from how I understand the documentation you’ll have to have a list of lists for each organism, like so: motifs =…

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socket.gaierror while downloading genbank files w/ biopython

The NCBI Entrez fetch API distinguishes return types rettype=”gb” and rettype=”gbwithparts”, the first can be shorter by giving you CONTIG lines referencing other records, while the later would expand these to give you the full sequence (look for “GenBank (full)” in the website). You can sometimes get a glimpse of…

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ClustalW on Ubuntu – DevDreamz

The section is copied from the BioPython documentation. >>> from Bio.Align.Applications import ClustalwCommandline>>> cline = ClustalwCommandline(“clustalw2″, infile=”opuntia.fasta”)>>> print(cline) clustalw2 -infile=opuntia.fasta If you run from Bio.Align.Applications import ClustalwCommandline cline = ClustalwCommandline(“clustalw2″, infile=”opuntia.fasta”) print(cline) it will do 3 things Import ClustalwCommandline module from BioPython Create a ClustalwCommandline object Print the object’s string…

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biopython – How can i write only a specific elements of the sequences, that i downloaded using Entrez.efetch, to the file( id and sequence itself)

I’m still a begginer at this. I downloaded 20 sequences from NCBI and my task is to allign them with themselves, but I need to separate the data, that I got using Entrez.efetch, so I could use it for allignment and I couldnt write the only specific elements (id and…

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How to get the scientific name given the GenBank accession code to biopython?

Note that output is a dictionary. You can access any appropriate fields if needed. Also, you would want to use efetch, as opposed to esearch. In [1]: from Bio import Entrez In [3]: Entrez.email = ‘##############’ In [28]: handle = Entrez.efetch(db=”nucleotide”, id=”AY851612″, rettype=”gb”, retmode=”text”) In [29]: x = SeqIO.read(handle, ‘genbank’)…

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Using Biopython to Retrieve Isoform Sequences of a Swissprot Entry?

You could use the Proteins API of EBML-EBI and a few lines of Python code. This will give you only the sequence as a string, not as a fully fledged BioPython object. import requests import xml.etree.ElementTree as ET accession = “Q16620” # a dictionary storing the sequence of your isoforms,…

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bioinformatics – how to replace seqIDs in a fasta file with new seqIDs using biopython

I have a fasta file that reads like so: >00009c1cc42953fb4702f6331325c7cc TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGTTGTTAAGTCAGTGGTGAAATCGTGTGGCTCAACCATACGGAGCCATTGAAACTGGCGACCTTGAGTGTAAACGAGGTAGGCGGAATGTGACGTGTAGCGGTGAAATGCTTAGATATGTCACAGAACCCCGATTGCGAAGGCAGCTTACCAGCATACAACTGAC >000118a5e731455e942c61a82a40367a623088d0 AGAGTTTTATCCTGGCTCAGGATGAACGCTAGCGGCAGGCCTAATACATGCAAGTCGGACGGGATCTAAATTTAAGCTTGCTTAAGTTTAGTGAGAGTGGCGCACGGGTGCGTAACGCGTGAGCAACCTACCCATATCAGGGGGATAGCCCGAAGAAATTCGGATTAACACCGCATAACACAGCAATCTCGCATGAGATCACTGTTAAATATTTATAGGATATGGATGGGCTCGCGTGACATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATGTCTAGGGGCTCTGAGAGGAGAATCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTAAGGATTATTGGTCAATGGAGGGAACTCTGAACCAGCCATGCCGCGTGCAGGATGACTGCCCTATGGGTTGTAAACTGCTTTTGTCTGGGAATAAACCTTGATTCGTGAATCAAGCTGAATGTACCAGAAGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCTTTATAAGTCAGAGGTGAAAGACGGCAGCTTAACTGTCGCAGTGCCTTTGATACTGTATAGCTTGAATATCGTTGAAGATGGCGGAATGAGACAAGTAGCGGTGAAATGCATAGATATGTCTCAGAACTCCGATTGCGAAGGCAGCTGTCTAAGCGGCAATTGACGCTGATGCACGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGATAACTGGATGTTGGCGATACACAGTCAGCGTCTTAGCGAAAGCGTTAAGTTATCCACCTGGGGAGTACGCCCGCAAGGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGCTTGAAAGTTAGTGAATGCGACAGAGACGTCTCAGTCCTTCGGGACACGAAACTAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATGTTTAGTTGCCAGCATGTAATGATGGGGACTCTAAACAGACTGCCTGCGTAAGCAGCGAGGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTACGTCCGGGGCTACACACGTGCTACAATGGATGGTACAGCGGGCAGCTACACAGCAATGTGATGCTAATCTCTAAAAGCCATTCACAGTTCGGATAGGGGTCTGCAACTCGACCCCATGAAGTTGGATTCGCTAGTAATCGCGTATCAGCAATGACGCGGT And I want to basically add microbial taxonomy to the seq IDs like so: d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Bacteroidales_RF16_group; g__Bacteroidales_RF16_group; s__uncultured_bacterium|00009c1cc42953fb4702f6331325c7cc d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Sphingobacteriales; f__Sphingobacteriaceae; g__Sphingobacterium; s__uncultured_bacterium|000118a5e731455e942c61a82a40367a623088d0 Where the original seqID is appended to the taxonomy…

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Optimize a script that extract features from Fasta file using biopython

Hey, I have a script that extract features from a large fasta file (1767 MB) using biopython. I am sending it as a bash job via ssh remote server. The job is running for two days now.. Is there a way to optimize my script? I think maybe the problem…

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“No such file or directory: ‘test.xml”

Biopython NcbiblastpCommandline not working: “No such file or directory: ‘test.xml” 0 from Bio.Blast.Applications import NcbiblastpCommandline blastp=r”C:\NCBI\blast-BLAST_VERSION+\bin\blastp.exe” blastp_cline = NcbiblastpCommandline(blastp, query=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.fasta”, db=r’C:/NCBI/blast-BLAST_VERSION+/bin/bos_protein.fasta’, outfmt=5, evalue=0.00001, out=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.XML”) blastp_cline from Bio.Blast import NCBIXML with open(“test.XML”) as result_handle: E_VALUE_THRESH=0.01 blast_records = NCBIXML.parse(result_handle) blast_record = NCBIXML.read(result_handle) for alignment in blast_record.alignments: for hsp in alignment.hsps: if hsp.expect…

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Extracting exact location of interest from genbank file

Extracting exact location of interest from genbank file 3 Hi everyone, I am trying to find any infromation how to extract the known cordinates from the genbank file but had no luck so far. This is how i have my results where the top line is the chromosome and from…

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[BioPython] ModuleNotFoundError: No module named Bio.PDB.SASA

[BioPython] ModuleNotFoundError: No module named Bio.PDB.SASA 2 Hello, I am trying to calculate the solvent accessible surface of pdb files using Biopython. Specifically I am trying to deduce the interaction surface of complex by substracting the solvent accessible surface of both unbound structure to the solvent accessible surface of the…

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Text string using Biopython – Stack Overflow

I’m using Biopython in my code and i need to extract the abstract out of articles. For searching the article I’m using the function: def search(query): Entrez.email=”your.email@example.com” handle = Entrez.esearch(db=’pubmed’, sort=”relevance”, retmax=’20’, retmode=”xml”, term=query) results = Entrez.read(handle) return results I’m looking for the simpliest way to get the text as…

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Index of /~psgendb/local/biopython-1.55.old/Scripts/xbbtools

Name Last modified Size Description Parent Directory   –   nextorf.py 2010-10-07 10:28 9.1K   test.fas 2010-10-07 10:28 517   testrp.fas 2010-10-07 10:28 50K   xbb_blast.py 2010-10-07 10:28 4.7K   xbb_blastbg.py 2010-10-07 10:28 2.3K   xbb_help.py 2010-10-07 10:28 2.2K   xbb_search.py 2010-10-07 10:28 5.0K   xbb_sequence.py 2010-10-07 10:28 399  …

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biopython – Identify side chain atoms in BioPandas dataframe

As you suggest one way of solving your problem would be by selecting all atoms that don’t have backbone atoms names. In a pdb file I believe backbone atoms would be named ‘CA’, ‘HA’, ‘N’, ‘HN’ or ‘H’, ‘C’ and ‘O’. Beware of the N-terminal (where the hydrogens would be…

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biopython – How to blastp with fasta file that contains ~50 sequences

I’m trying to blastp multiple aminoacids sequences using biopython. I just can’t seem to get it right and i cant figure out the handbook for how to do this. I have come up with the following: open(“proteins_PROT.fasta”,”r”) from Bio.Blast.Applications import NcbiblastpCommandline cline = NcbiblastpCommandline(query=”proteins_PROT.fasta”, db=”nr”, evalue=0.001, remote=True, ungapped=True) NcbiblastpCommandline(cmd=’blastp’, query=”proteins_PROT.fasta”,…

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Analyzing and slicing FASTQ file entries using Python

Analyzing and slicing FASTQ file entries using Python 1 I have the code pasted below for running on FASTQ file entries in order to compare specific parts and remove the redundancy of the same sequences (based on the miRNA + umi_seq combination). I save the entry IDs and then make…

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Fasta File Python

Fasta File Python 2 How do I go about extracting elements from a fasta file. For example, if I want a list of all the IDS and then length of a sequence in another list how do I do that in base python without using any libraries? for line in…

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Bioinformatics script using Python/Biopython/Clustalw using stdout to iterate over a directory of proteins

What exactly is the error you are seeing? You shouldn’t set sys.sterr and sys.stdout to string values (the clustalw_cline() function returns the clustal stderr and stdout as strings), as you won’t be able to write anything to stdout from python. I tried to clean up and correct your code below….

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Replace sequences between files using Biopython

As you have written it, every time you write a new sequence, you’re overwriting the previous one. Try storing your records in a list and then writing out the list when the loop is completed. to_write = [] for seq1 in SeqIO.parse(r”c:UsersSergioDesktopnsp.fasta”, “fasta”): for seq2 in SeqIO.parse(r”c:UsersSergioDesktopwsp.fasta”, “fasta”): if seq2.id…

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How to print the first few records using SeqIO from Biopython

There are numerous ways to do this. The most similar to your current structure would be to add a break when the index hits 19 (that is the 20th number since counting starts at 0): from Bio import SeqIO for index, record in enumerate(SeqIO.parse(“e_coli_k12_dh10b.faa”, “fasta”)): print(record.description, len(record.seq)) if index ==…

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python – Biopython cannot export numpy

I am trying to use Biopython using anaconda and the Jupiter notebook with Python3. However, simply import numpy gives the following error: ————————————————————————— ImportError Traceback (most recent call last) File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/__init__.py:23, in <module> 22 try: —> 23 from . import multiarray 24 except ImportError as exc: File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/multiarray.py:10, in <module>…

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SeqIO object get cleared away after being accessed

I’m using Biopython to parse a fastq file, and I found that the SeqIO object get cleared away once I accessed it. from Bio import SeqIO record_fastqIO = SeqIO.parse(‘SRR835775_1.first1000.fastq’,’fastq’) for record in record_fastqIO: print(record.id) This script works perfectly. But if I add one line to the script: from Bio import…

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have trouble in installing biopython package

I would suggest the root of your problem is this line: /usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler (/usr/bin/../libexec/gcc/darwin/ppc/as or /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not installed XCode 4 doesn’t like trying to compile things with the PPC architecture, so you need to stop it trying: env ARCHFLAGS=”-arch i386 -arch x86_64″ python setup.py install (DISCLAIMER: I…

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import – How to make a python module accessible to multiple editors?

I am learning biopython and would like to use Visual Studio Code (VSC—my favorite editor so far) to do coding exercises on the topic. However, the module does not show up when I try to import using VSC. In fact, for my computer the biopython module only works in Spyder….

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MultiProcessing on SeqIO biopython

MultiProcessing on SeqIO biopython 0 Hello, I would like to parse a wheat genome (13Gb) quickly, in order to cut each Sequence and count the fragment lengths and store it in a pandas dataframe. Is it recommendable to use multiprocessing on the SeqIO.parse command? Does it save time? Any experiences/recommendations…

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Writing Biopython output into csv

In your second block of code, your variable names talk about dictionaries, but your they are actually lists: journal_dict = [] datep_dict = [] place_dict = [] So, let’s fix that (this will also be useful later when writing to CSV): record_list = [] for record in records: record_dict =…

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Correlation Distance Metric and Sum of Squared Errors

The sum of squared error is more easily implemented than the correlation distance metric, so I would advise you to use biopython together with the following helper function. It should compute the sum of squared errors for you from the data (assumed to be a numpy array) and biopython’s clusterid…

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biopython – 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, sequence length, sequence, animal name and rows corresponding to all the data available. However,…

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a Rust-backed Python library for DNA translation that is up to 100x faster than Biopython : bioinformatics

Background: I work at SecureDNA1, where we use Biopython pretty extensively. It’s a great library, but often quite slow, and we’ve run into bottlenecks in our processing pipelines around Biopython’s translation speed. I wrote this library to augment Biopython — you can read your sequences out of FASTA files with…

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Extracting organism and seq from fasta

Extracting organism and seq from fasta 0 Hi, I am trying to extract sequences from a fasta file from a database with a specific organism species keyword from a .txt file containing the relevant headers. Do you know how I can do this in python as the biopython guide I’ve…

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Fasta file reading python

Answer by Aidan Golden I think you can just use Biopython,It is indeed wrong today. I edited the answer since it has been possible to use str(sequence) for a long time now.,Very useful answer from 7 years ago! FYI, in current version of biopython(1.69), fasta.seq.tostring() is obsolete, use str(fasta.seq) instead.,Nicely…

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ImportError: cannot import name _aligners [biopython]

I had a problem with this when biopython (as a dependency) was installed during the installation of another package. Solution: pip uninstall biopython pip install biopython This can occur on Biopython version >= 1.72 and has been discussed on the biopython mailing list here. This error occurs when you try…

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biopython – Github Help

1 1 0 biopython,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

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kegg – Github Help

1 1 0 kegg,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

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Question : Improve genbank feature addition

Question Improve genbank feature addition * 60 visibility 0 arrow_circle_up 0 arrow_circle_down I am trying to add more than 70000 new features to a genbank file using biopython. I have this code: from Bio import SeqIO from Bio.SeqFeature import SeqFeature, FeatureLocation fi = “myoriginal.gbk” fo = “mynewfile.gbk” for result in…

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[biopython/biopython] local pairwise alignment using pairwise2

Setup I am reporting a problem with Biopython version, Python version, and operating system as follows: 3.6.13 | packaged by conda-forge | (default, Feb 19 2021, 05:36:01) [GCC 9.3.0] CPython Linux-5.11.0-41-generic-x86_64-with-debian-bullseye-sid 1.78 # also tested on windows-subsystem 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] CPython Linux-5.10.16.3-microsoft-standard-WSL2-x86_64-with-glibc2.31 1.78 Expected behaviour…

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alphafold2: HHblits failed – githubmemory

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

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Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents,…

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Get data from KEGG Brite

Get data from KEGG Brite 0 Hi, I would like to retrieve all the interactions between ligands and target proteins from the KEGG BRITE database. Ideally, each entry will contain a protein name, a list of interacting ligands, its FASTA sequence and an sdf or mol2 coordinates of the ligand,…

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Biopython: Bio.SeqUtils.molecular_weight for a fasta file

I must write a function, given a file_name that can calculate the molecular weight of only the unambiguous sequences and gives as return sequence id and the corresponding molecular weight. I tried to use the Bio.SeqUtils.molecular_weight to calculate the molecular weight, but I couldn’t do it since SeqUtils.molecular_weight works with…

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increasing word size extremely slows down the search

standalone blastp: increasing word size extremely slows down the search 1 Hello, I need to blastp a genome (15,000 seqs) against genome (12,000 seqs) using Biopython. I decided to use local blast and query genome 1 fasta file against genome 2 database ( made by makeblastdb command with second genome…

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Clustal Omega Output Not Correct

Clustal Omega Output Not Correct 1 Hello, I am having an issue with my biopython program. My project is due soon and I can’t figure out what’s going on. I am running this code based on a tutorial, and I’m new to python. Here is my code: from Bio import…

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find the desired AA sequence location in Protein fasta file

find the desired AA sequence location in Protein fasta file 1 I am working with FASTA files of protein. I want to locate the desired AA sequence in every clone of the protein fasta file using pyhton. records=SeqIO.parse(“protein.fasta”, ”fasta”) #to extract protein sequences from FASTA file for record in records:…

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biopython – Updating the GFF3 + Fasta to GeneBank code

I’m trying to convert gff3 and fasta into a gbk file for usage in Mauve. I’ve found a solution but the code is outdated: “””Convert a GFF and associated FASTA file into GenBank format. Usage: gff_to_genbank.py <GFF annotation file> <FASTA sequence file> “”” import sys import os from Bio import…

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BLAST comparision and parsing output in particular format

BioPython : BLAST comparision and parsing output in particular format 1 I have query sequence, Suppose query: NNNNNNNNNNNNNNNNNN Database 1: Homo sapien Database 2: Mycobacterium tuberculosis I compared query sequence with above two Databases using Standalone BLAST individually and I got result as ex. Result1.txt and Result 2.txt. Now, I…

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prody/ProDy – Giters

SYNOPSIS ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well as application development. ProDy also comes with several analysis…

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Index of /~psgendb/doc/local/biopython-1.64.old/Tests/output

Name Last modified Size Description Parent Directory   –   test_AlignIO 2014-05-29 05:23 31K   test_AlignIO_FastaIO 2014-05-29 05:23 60K   test_ClustalOmega_tool 2014-05-29 05:23 1.2K   test_Clustalw 2014-05-29 05:23 5.8K   test_Clustalw_tool 2014-05-29 05:23 1.3K   test_CodonTable 2014-05-29 05:23 21   test_CodonUsage 2014-05-29 05:23 784   test_DocSQL 2014-05-29 05:23 42  …

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Index of /~psgendb/doc/local/biopython-1.55.old/Bio/Nexus

Name Last modified Size Description Parent Directory   –   Nexus.py 2012-02-03 12:02 73K   Nexus.py.bak 2010-10-07 10:28 73K   Nexus.pyc 2011-12-13 14:38 58K   Nodes.py 2012-02-03 12:02 5.6K   Nodes.py.bak 2010-10-07 10:28 5.6K   Nodes.pyc 2011-12-13 14:38 7.4K   Trees.py 2012-02-03 12:02 36K   Trees.py.bak 2010-10-07 10:28 36K  …

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#1000359 – FTBFS: test failure: External MBEDTLS version mismatch

#1000359 – FTBFS: test failure: External MBEDTLS version mismatch – Debian Bug report logs Reported by: Stefano Rivera <stefanor@debian.org> Date: Mon, 22 Nov 2021 02:15:02 UTC Severity: serious Found in version python-biopython/1.79+dfsg-1 Fix blocked by 1000358: ncbi-blast+: Please remove the mbedtls version check Reply or subscribe to this bug. Toggle…

Continue Reading #1000359 – FTBFS: test failure: External MBEDTLS version mismatch

Please rebuild against MBEDTLS 2.16.11

Package: ncbi-blast+ Version: 2.11.0+ds-1 Severity: normal Affects: python-biopython Running blastn outputs: Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime This causes python-biopython to FTBFS: ====================================================================== FAIL: test_blastn (test_NCBI_BLAST_tools.CheckCompleteArgList) Check all blastn arguments are supported. ———————————————————————- Traceback (most recent call last): File “/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py”, line 420, in test_blastn self.check(“blastn”, Applications.NcbiblastnCommandline)…

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how to run CD-Search with python or biopython

how to run CD-Search with python or biopython 0 I’m now using the Biopython Entrez method to handle a great deal of sequencing. But I’m now facing a new problem,that is predicting the conserved domain in the sequence ( my sequences are DNA sequence.) I know this website: www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ….

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Index of /~psgendb/local/biopython-1.55.old/Tests/Motif

Name Last modified Size Description Parent Directory   –   Arnt.sites 2010-10-07 10:28 607   SRF.pfm 2010-10-07 10:28 144   alignace.out 2010-10-07 10:28 8.0K   mast.dna.oops.txt 2010-10-07 10:28 13K   mast.protein.oops.txt 2010-10-07 10:28 34K   mast.protein.tcm.txt 2010-10-07 10:28 16K   meme.dna.oops.txt 2010-10-07 10:28 15K   meme.out 2010-10-07 10:28 10K  …

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Index of /~psgendb/local/biopython-1.64.old/Bio/Graphics/GenomeDiagram

Name Last modified Size Description Parent Directory   –   _AbstractDrawer.py 2014-05-29 05:23 20K   _CircularDrawer.py 2014-05-29 05:23 66K   _Colors.py 2014-05-29 05:23 8.8K   _CrossLink.py 2014-05-29 05:23 3.1K   _Diagram.py 2014-05-29 05:23 19K   _Feature.py 2014-05-29 05:23 9.5K   _FeatureSet.py 2014-05-29 05:23 10K   _Graph.py 2014-05-29 05:23 8.7K  …

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Index of /~psgendb/local/biopython-1.64.old/Bio

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

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Index of /~psgendb/local/biopython-1.64.old/Bio/PDB

Name Last modified Size Description Parent Directory   –   AbstractPropertyMap.py 2014-05-29 05:23 4.0K   Atom.py 2014-05-29 05:23 10K   Chain.py 2014-05-29 05:23 3.9K   DSSP.py 2014-05-29 05:23 11K   Dice.py 2014-05-29 05:23 1.9K   Entity.py 2014-05-29 05:23 8.5K   FragmentMapper.py 2014-05-29 05:23 9.2K   HSExposure.py 2014-05-29 05:23 11K  …

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How Does One Programmatically (Python) Download Pdb Structures By Keyword

How Does One Programmatically (Python) Download Pdb Structures By Keyword 2 I would like to download all hemagglutinin structures for influenza virus from the Protein Data Bank via a python script. I have looked through the PDB and BioPython PDB package on how to do this with no luck. Does…

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How does this array become this matrix?

Greetings. While studying clustering analysis, I got a question which about Distance matrix. In Biopython example code, import numpy as np import pandas as pd from Bio.Cluster import distancematrix data=np.array([[0, 1, 2, 3],[4, 5, 6, 7],[8, 9, 10, 11],[1, 2, 3, 4]]) matrix = distancematrix(data) distances = distancematrix(data, dist=”e”) print(distances)…

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python – Extract fasta files from ID list with Biopython

I am using Biopython to find sequences in a fasta file that match IDs from a .txt file comprising selected IDs. When searching for the ID names in the fasta file manually I do get hits, but the following script doesn’t find/extract any sequences: #!/usr/bin/env python3 from Bio import SeqIO…

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Two problems in Biopython Bio.PDB

I try parsing mmCIF and MMTF in PDB, but there are problem occurs. I installed Biopython 1.78. First problem is: from Bio.PDB.MMCIFParser import MMCIFParser parser = MMCIFParser() structure = parser.get_structure(“1fat”, “1fat.cif”) print(structure) # FileNotFoundError: [Errno 2] No such file or directory: ‘1fat.cif’ when I tried parse mmCIF and PDB file,…

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python – Error while parsing gene bank file using Biopython

This question was migrated from Unix & Linux Stack Exchange because it can be answered on Bioinformatics Stack Exchange. Migrated 8 hours ago. I am trying to extract the protein sequence of specific genes from gene bank like format file obtained from antismash part of which looks like…

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entrez – Download COX1 (COI) gene via biopython using accessions for entire mitochondrial genomes

I have a list of accessions for the the entire mitochondrial genomes for big cats. I need to download the COX1 genes for each of these accessions. Here is one accession and here is a link to its COX1 gene, which I found manually on that page. I have downloaded…

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How to create motifs using biopython when the sequence object contain gaps (-)?

How to create motifs using biopython when the sequence object contain gaps (-)? 0 I have a gapped candidate promoter sequence for motif predictions. I am expecting to get two motifs, 1) left side motif, 2) right side motif. For the task, I am using biopython. Following is my code….

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Biopython download nucleotide records without sequences (or skip huge sequences)

I am trying to download information from NCBI Entrez databases (nucleotide), using Biopython package. I don’t need molecular data at all. I just want to check the textual information about certain records, to see references, authors, journals, and information about voucher specimens from which the genome sample was extracted. My…

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Biopython separate gap score functions for border/internal gaps

Biopython separate gap score functions for border/internal gaps 0 Hi, I would like to define different gap score functions for left/right/internal gaps in Biopython. After reading the documentation (biopython.org/DIST/docs/tutorial/Tutorial.html#sec101, section 6.6.2.5), I found out I can define a gap scoring function for a Bio.Align.PairwiseAligner object. However, it seems like only…

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Presence absence matrix from blast results

Presence absence matrix from blast results 0 I have a many blast output files of genome names, which looks like this. In the first column of the file, it contains all the identified query UIDs, I want to make a presence-absence matrix in csv format in which a column would…

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Use biopython to align SeqRecords stored in dict

I’d like to perform multiple alignments, where a gene from each sample was read in from fasta files. The fasta file represented one sample and had multiple genes. I have read in each sample fasta file and now have a dictionary of genes and their samples and sequences. Here is…

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Getting premature stop codons from exonerate output?

Getting premature stop codons from exonerate output? 1 Hello, Does anyone know a good way to get premature stop codons from exonerate’s protein2genome model?? Unfortunately the Vulgar output doesn’t record stop codons. You also can’t just get the protein sequence from the genomic DNA input (in my case the target…

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Pathogen protein sequence alignment

Pathogen protein sequence alignment 0 How do I filter by taxonomy (i.e. taxid = 2 for Bacteria) using NcbiblastpCommandline in Biopython? Is there a way to do it without downloading and filtering the nr dataset manually? Are there available and downloadable protein dataset that only involves bacteria and viruses? Thanks!…

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parsing – Best way to improve my python fasta parser without using BioPython or anything else?

I am writing my own parser for fasta format. I can’t use Biopython. For now I have done this : def read_file(fasta_file): “Parse fasta file” count = 0 headers = [] sequences = [] aux = [] with open(“yeast.fna”, ‘r’) as infile: for line in infile: record = line.rstrip() if…

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do I need to install MUSCLE and ClustalW for using biopython tool?

I am studying biopython now, but some problem occurs during practice MSA. When I tried to clustalW and MUSCLE, it didn’t works. from Bio.Align.Applications import ClustalwCommandline cline = ClustalwCommandline(“clustalw2″, infile=”lactobacillus.aln”) print(cline) this is clustalW code, I just modified file path and mane. command line said this and did not occurs:…

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Biopython Seqio.Index() And Seqio.Index_Db() Very Slow For Large Sequence

Before switching to Biopython, I thought there are similar indexing features in biopython as in bioperl. However, the biopython SeqIO.index_db() and SeqIO.index() methods are so inefficient that it’s almost impossible to random access a segment of genomic sequence using biopython. I tested the performance of biopython and bioperl in retrieving…

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python – 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. gene complement(516466..532086) /gene=”rtxA” /locus_tag=”VV1_RS17390″ /old_locus_tag=”VV2_0479″ CDS complement(516466..532086) /gene=”rtxA” /locus_tag=”VV1_RS17390″ /old_locus_tag=”VV2_0479″ /inference=”COORDINATES: similar to AA sequence:RefSeq:WP_011081430.1″ /note=”Derived by automated computational analysis using gene prediction method: Protein Homology.” /codon_start=1 /transl_table=11 /product=”MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin RtxA” /protein_id=”WP_011081430.1″ /translation=”MGKPFWRSVEYFFTGNYSADDGNNSIVAIGFGGEIHAYGGDDHV…

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Relative frequencies of the nucleotides in Fasta files

Relative frequencies of the nucleotides in Fasta files 1 I have 2 fasta files (File A, File B) each one contains sequence, How can I report the relative frequencies of the nucleotides in set A and set B with python? Thanks in advance fasta • 558 views Hi check the…

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How can I programmatically add a Hydrogen ‘Atom’ to a ‘Residue’ object?

How can I programmatically add a Hydrogen ‘Atom’ to a ‘Residue’ object? 0 I know the algorithm for creating a Hydrogen atom and adding to a residue: Point3d create_hydrogen(Point3d C, Point3d N, Point3d CA, Point3d H) { H.set(N); H -= C; H.norm(); Point3d tmp2(N); tmp2 -= CA; tmp2.norm(); H +=…

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Getting premature stop codons from exonerate output

Getting premature stop codons from exonerate output 0 Hello, I made alignments with exonerate’s protein2genome model, and I would like to count the number of stop codons in the alignment. Unfortunately the Vulgar output doesn’t record stop codons. So then I thought I might just extract the aligned protein sequence…

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Change biopython pairwise2 output format alignment ?

Change biopython pairwise2 output format alignment ? 1 You can split the resulting text output into lines, then replace the characters as needed. It is a bit hacky but provides the most flexibility. Login before adding your answer. Traffic: 1912 users visited in the last hour Read more here: Source…

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AttributeError: ‘str’ object has no attribute ‘id’ using BioPython, parsing fasta

Thanks for contributing an answer to Stack Overflow!,Connect and share knowledge within a single location that is structured and easy to search.,This script assumes a proper fasta file. It will remove all “.seq” strings at the end of any line. And in a proper fasta file, only the ID lines…

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How to automat the calculation of alignment scores (BLOSUMxx matrix based) between one short peptide sequence and 10000 other peptide sequences (using biopython)

Hi everyone and thanks in advance for any of your help. I am running into an issue recently when trying to calculate the scores of a high number of short peptide alignments (10000). I have to calculate all the alignement scores (calculation based on the BLOSUM62 matrix, but I could…

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How to download complete genome sequence in biopython entrez.esearch

I have to download only complete genome sequences from NCBI (GenBank(full) format). I am intrested in ‘complete geneome’ not ‘whole genome’.,Here is my code for Complete Genome Sequence Parsing into .FASTA files…,You will see there are only six complete E.Coli reference genomes in NCBI (www.ncbi.nlm.nih.gov/genome/167):,To help you, here are the…

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Removing gaps from fasta sequence file

Removing gaps from fasta sequence file 1 I am using python (3.6)/biopython(1.72) to read sequence files. I have an aligned sequence file in fasta format. >Human —————————-MRLRVRLLKRTWPLEVPETEPTL-RSHLRQSLLCT-IPSSTDSEHSSLQN-NEQPSL >Chimpanzee —————————-MRLRVRLLKRTWPLEVPETEPTL-RSRLRQSLLCT-IPSSTDSEHSSLQN-NEQPSL >Dog —————————-MKLRVRLQKRTWPLDLPDAEPTL-RAHLSQALLPS-LPSSTDSEHSSLQN-NDPPSL >Mouse —————————-MKLRVRLQKRTQPLEVPESEPTL-RAHLSQVLLPT-LPSSTDTEHSSLQD-NDQPSL I need to remove the gaps ‘-‘ from the file and have the result file like this:…

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genebank biopython get /chromosome=”22″ or /map=”22q13.33″

genebank biopython get /chromosome=”22″ or /map=”22q13.33″ 1 it is located in the qualifiers field of the feature from Bio import SeqIO recs = SeqIO.parse(“input.gb”, format=”genbank”) # Go over each record for rec in recs: # Go over each feature for feat in rec.features: chr = feat.qualifiers.get(“chromosome”) if chr: print (chr)…

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How to scan NCBI database using Biopython and save information as a fasta file?

How to scan NCBI database using Biopython and save information as a fasta file? 1 Hello, I am attempting to use Entrez to search the keyword “covid” in the nucleotide database and write the top 5 sequence records to a fasta file. I completed the code for question 1, but…

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Convert pdb file to table format or csv

Convert pdb file to table format or csv 0 Is there a way to convert a pdb file into a csv or table? Is there a way to parse a pdb file so that I would get atom, coordinates, atom type, residue in python dictionaries? I have been looking at…

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ncbi – How to use biopython Entrez efetch to get genbank file from “gene” database

I am trying to programmatically get whole genes ( with intron and exon structure as defined by CDS) using Biopython Entrez esearch and efetch utilities. from Bio import Entrez Entrez.email = “myemail@gmail.com” handle = Entrez.esearch(db=”gene”,retmax = “10”,term=”P53 AND Homo Sapiens [organism]”) record = Entrez.read(handle) handle_first_record = Entrez.efetch(db=”gene”,id=record[“IdList”][0],rettype=”gb”,retmode=”text”) info = handle.read()…

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Multiple Sequence Alignment using Biopython

Multiple Sequence Alignment using Biopython 0 Hello, I have one fasta file with four different sequences in it. The command I am instructed to use is pairwise2 in biopython. How can I set up a code that performs pairwise global sequence alignment between each pair of sequences in the fasta…

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Accepted python-biopython 1.79+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 22 Oct 2021 18:10:48 +0200 Source: python-biopython Architecture: source Version: 1.79+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: python-biopython (1.79+dfsg-1) unstable; urgency=medium . * Migrate from Experimental to Unstable. * Mark spelling.patch…

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How can I calculate the distance between a C-alpha atom and its hydrogen bond in a protein?

How can I calculate the distance between a C-alpha atom and its hydrogen bond in a protein? 0 I need to calculate the distance between a given C-alpha atom and the Hydrogen bonds in a protein in BioPython. And, I need to calculate that from a PDB file. Can anyone…

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Biopython’s Esearch for Pubmed does not give the same results as web search

I can think of two factors that might cause different results between Biopython and the web search: Depending on how specific the query you give Biopython is, it will be translated before retrieving results. Example: <sclerosis> will be translated to <“sclerosis”[MeSH Terms] OR “sclerosis”[All Fields]> As GenoMax pointed out, the…

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Cant make blastn work using biopython and NCBIWWW qblast, any thoughts?

Hello all, I’m a beginner level python user experiencing a problem using biopython. I’m taking an online bioinformatics course and the example that we’re working through right now is to take a fasta file (called myseq.fa in the following example), open it then read. Then using the NCBIWWW module we…

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autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

Source: ncbi-acc-download Version: 0.2.7-1 Severity: important Tags: ftbfs Dear Maintainer, I am trying to assess the side effects of an upgrade of the package python-biopython to 1.79 to its reverse dependencies. Pseudo-excuses look alright, except for ncbi-acc-download [1]. [1]: release.debian.org/britney/pseudo-excuses-experimental.html [2]: ci.debian.net/data/autopkgtest/unstable/amd64/n/ncbi-acc-download/15982166/log.gz The full log [2] shows variations around the…

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Extracting named fasta sequences according to list with Biopython

Extracting named fasta sequences according to list with Biopython 0 Hi all, I’m trying to work out a quick script to extract a set of sequence fasta files from a multifasta and write them all to a new, single fasta file. To elaborate, I’ve got a proteome, and I want…

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Accesing reference genome from Genome database (ncbi) with biopython

Accesing reference genome from Genome database (ncbi) with biopython 1 Hello all, I would like to acces to the reference genome RefSeq UID given a taxonomy id using the Genome database with biopython. I will try to explain with images what I mean. I search in the Genome database using…

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