biopython

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Finding/Replacing substrings with annotations in an ASCII file in Python

I\'m having a little coding issue in a bioinformatics project I\'m working on. Basically, my task is to extract motif sequences from a database and use the information to annotate a sequence alignment[详细]

2023-03-02 03:36 分类：问答
Problem with GFF parser by BCBio

I am trying to parse a GFF file using the BCBio GFF parser and I get the following error. Can anybody help me in resolving this problem?[详细]

2023-02-28 01:07 分类：问答
Is there a function that can calculate a score for aligned sequences given the alignment parameters?

I try to score the already-aligned sequences. Let say seq1 = \'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE\'[详细]

2023-02-25 18:52 分类：问答
Script for parsing a biological sequence from a public database in Python

Greetings to the stackoverflow community, I am currently following a bioinformatics module as part of a biomedical degree (I am basically a python newbie) and the following task is required as part o[详细]

2023-02-23 04:17 分类：问答
'module' object is not callable - Bio.IUPAC

When I try, from Bio.Alphabet impor开发者_Go百科t IUPAC from Bio import Seq my_prot = Seq(\"AGTACACTGGT\", IUPAC.protein)[详细]

2023-02-21 18:30 分类：问答
python multiprocessing each with own subprocess (Kubuntu,Mac)

I\'ve created a script that by default creates one multiprocessing Process; then it works fine. When starting multiple processes, it starts to hang, and not always in the same place. The program\'s ab[详细]

2023-02-03 11:22 分类：问答
Phylo BioPython building trees

I trying to build a tree with BioPython, Phylo module. What I\'ve done so far is this image: each name has a four digit number followed by - and a number: this number refer to the number of times th[详细]

2023-01-22 18:44 分类：问答
Fetching genomic sequence efficiently in Python?

How can I fetch genomic sequence efficiently using Python?For example, from a .fa file or some other easily obtained format?I basically want an interface fe开发者_Python百科tch_seq(chrom, strand, star[详细]

2023-01-06 17:47 分类：问答
Print 50 sequences from each line using Clustal

I have a multiple sequence alignment (Clustal) file and I want to read this file and arrange sequences in such a way that it looks more clear and precise in order.[详细]

2022-12-31 01:12 分类：问答
Subprocess fails to catch the standard output

I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess[详细]

2022-12-30 22:18 分类：问答