biopython Questions
4
Solved
QIIME requests this (here) regarding the fasta files it receives as input:
The file is a FASTA file, with sequences in the single line format. That is, sequences are not broken up into multiple li...
Cheryllches asked 11/6, 2014 at 7:1
12
Solved
I have a DNA sequence and would like to get reverse complement of it using Python. It is in one of the columns of a CSV file and I'd like to write the reverse complement to another column in the sa...
Gat asked 7/8, 2014 at 17:50
3
Is there a way to use BioPython to convert FASTA files to a Genbank format? There are many answers on how to convert from Genbank to FASTA, but not the other way around.
11
Solved
I am trying to pass BioPython sequences to Ilya Stepanov's implementation of Ukkonen's suffix tree algorithm in iPython's notebook environment. I am stumbling on the argparse component.
I have ne...
Uroscopy asked 5/6, 2015 at 1:12
14
FYI: this is NOT a duplicate!
Before running my python code I installed biopython in the cmd prompt:
pip install biopython
I then get an error saying 'No module named Bio' when try to import i...
Viscometer asked 16/4, 2018 at 1:33
3
Solved
I am using Python and a regular expression to find an ORF (open reading frame).
Find a sub-string a string that is composed ONLY of the letters ATGC (no spaces or new lines) that:
Starts with ATG...
Impunity asked 28/10, 2012 at 23:49
4
Solved
I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe ...
Mitchiner asked 24/11, 2009 at 10:55
4
Solved
I have a file that has thousands of accession numbers:
and looks like this..
>NC_033829.1 Kallithea virus isolate DrosEU46_Kharkiv_2014, complete genome
AGTCAGCAACGTCGATGTGGCGTACAATTTCTTGATTACAT...
3
Solved
New to coding. New to Pytho/biopython; this is my first question online, ever.
How do I open a compressed fasta.gz file to extract info and perform calcuations in my function. Here is a simplified ...
Jeremyjerez asked 13/3, 2017 at 5:45
1
My Mac came installed with python 2.7 as the default python version. But, this version is no longer supported by many packages and software. I searched several online forums regarding how to change...
Outwards asked 30/11, 2020 at 6:33
6
I have some strings,
['SGALWDV', 'GALWDVP', 'ALWDVPS', 'LWDVPSP', 'WDVPSPV']
These strings partially overlap each other. If you manually overlapped them you would get:
SGALWDVPSPV
I want a ...
3
Solved
I have no idea what could be the problem here:
I have some modules from Biopython which I can import easily when using the interactive prompt or executing python scripts via the command-line.
The...
Symons asked 24/9, 2010 at 2:42
5
I was wondering if there is way to get the sequence of proteins from uniprot protein ids. I did check few online softwares but they allow to get one sequence at a time but I have 5536 vlues. Is the...
Hexagram asked 29/9, 2018 at 15:4
11
I have a fasta file as shown below. I would like to convert the three letter codes to one letter code. How can I do this with python or R?
>2ppo
ARGHISLEULEULYS
>3oot
METHISARGARGMET
desir...
Flaminius asked 6/10, 2012 at 13:39
2
Solved
I have list of pmids
i want to get abstracts for both of them in a single url hit
pmids=[17284678,9997]
abstract_dict={}
url = https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
db=pub...
1
Solved
This question is related to bioinformatics. I did not recieve any suggestions in corresponding forums, so I write it here.
I need to remove non-ACTG nucleotides in fasta file and write output to a...
Lugubrious asked 11/7, 2017 at 16:30
1
Solved
I am trying to use Entrez to import publication data into a database. The search part works fine, but when I try to parse:
from Bio import Entrez
def create_publication(pmid):
handle = Entrez.e...
Claudineclaudio asked 22/12, 2016 at 15:42
2
Solved
import gzip
import io
from Bio import SeqIO
infile = "myinfile.fastq.gz"
fileout = open("myoutfile.fastq", "w+")
with io.TextIOWrapper(gzip.open(infile, "r")) as f:
line = f.read()
fileout.write(...
2
Solved
I am new to python and would like to extract abstracts from pubmed using the entrez system from the bio package.
I got the esearch to give me my UIDs (stored in my_list_ges) and I can also download...
3
I have thousands of DNA sequences ranged between 100 to 5000 bp and I need to align and calculate the identity score for specified pairs.
Biopython pairwise2 does a nice job but only for short sequ...
1
Solved
I have a directory with a large number of files that I want to move into folders based on part of the file name. My list of files looks like this:
ID1_geneabc_species1.fa
ID1_genexy_species1.fa
I...
1
Solved
I want to be able to search a Seq object for a subsequnce Seq object accounting for ambiguity codes. For example, the following should be true:
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC impo...
Shavian asked 24/8, 2015 at 22:46
3
Solved
I am writing a function that is supposed to go through a .fasta file of DNA sequences and create a dictionary of nucleotide (nt) and dinucleotide (dnt) frequencies for each sequence in the file. I ...
Sourdough asked 27/5, 2015 at 16:28
3
I am trying to install biopython to run with Python 3.3 on a Windows7 computer.
I have downloaded the biopython executable biopython-1.61.win32-py3.3-beta.exe. When I attempt to run the executabl...
1
Solved
I am using the Phylo package from Biopython to create phylogenetic trees.
For big trees, I need to decrease the fontsize of the leaf nodes. It has been suggested to change matplotlib.pyplot.rcPara...
1 Next >
© 2022 - 2024 — McMap. All rights reserved.