Questions tagged [python]
python is a programming language, widely used in bioinformatics
597
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To create a new column with Pandas on the basis of two types of column values
I have a data frame df. The below table only represent top 8 rows of the data frame. There are multiple combination of ...
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1
answer
33
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Running a list of apis via Python's request module
I am running the following Python code with python requests in my Jupiter notebook to get cancer oncology id's from EBI-EMBL.
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1
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How to extract residues from specific chain of interest from multiple pdb files?
I'm new to biopython & I'm trying to extract residues from specific chain of each file from a list of 316 pdb files. Eg: 1d8t has four chains A, B, C & D of which my interest is to extract ...
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1
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Python; Question about the append (modifying lists): why modifying a list with append changes others? [closed]
I have a list named dict_eg1 whose values are lists.
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0
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1
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Pipeline for paired end RNA sequence data to proteins
Forgive the basic question here, but I'm super novice at this ...
I have a series of paired-end RNA fastq files (e.g. SRR10720226_1.fastq.gz and ...
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1
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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 ...
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1
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different results of RMSD for the same trajectory file
I want to analyze the RMSD of my trajectory files using MdTraj.
I used two different codes for this purpose:
the first code:
...
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0
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0
answers
163
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How to do enrichment analysis with scipy.stats.hypergeom.sf function
I want to do pathway enrichment analysis in python using scipy.stats.hypergeom.sf function to select pathways that are significantly enriched in at least one tissue....
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2
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Error in seaborn plot " Horizontal orientation requires numeric `x` variable"
I am trying to plot a box plot with seaborn with the following code
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1
answer
271
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How to create drug synergy plot?
I want to replicate the synergy drug response curve with the Python library given in the following paper.
Could you kindly advice on:
Suitable graphics libraries for Python
Code or pseudo code
...
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3
votes
1
answer
341
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Multiple file Python script
I am currently doing an analysis requiring a multiple-input script. I have a directory filled with 900+ samples.
Each sample is comprised of two-files in a fastq format. This is an example of a sample:...
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5
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2
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209
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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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1
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How to sort legends alphabetically in plotly dash with category_orders function
I am using Plotly dash for creating a scatter plot. The legends I am getting in the final figure are randomly placed. I want to sort labels alphabetically from A to Z with ...
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1
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Suggestion for python graphics library to plot aligned protein sequences
I'm working towards developing some visualization method for multiple protein sequences and subsequences using PYTHON. I want to show the alignment of many fragment sequences to the original ...
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1
answer
102
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Missing ',' in line when Biopython reads a nexus tree
I want to edit a tree that I got from BEAST2 treeannotator in nexus-format.
Usually I use the module Phylo from Biopython for such work but ...
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1
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373
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Constructing Two Triangle Heatmaps in One Square
I'm looking to make a two, two range colour scheme heatmap where each range corresponds to a separate triangle in the heatmap square.
I am looking for a relevant guide for this heatmap. Any ...
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1
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Database to download with information of bacteria?
I am looking for tidy tabular dataset that contains known bacteria and fungi down to the species level. Basically a table that includes genus and species names and other higher-level information. For ...
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BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure
I am using the internal_coords module from BioPython in order to compare dihedral angles of two different conformations of the same protein. The conformations are ...
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1
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Identify side chain atoms in BioPandas dataframe
I am currently implementing some metrics I could use for comparing two conformations of the same protein in Python.
For example, I know I could use the RMSD of all protein ATOMS in BioPandas using ...
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2
votes
2
answers
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Replacing column 1 in file1 with matching ID's in file 2
I have downloaded two files:
File1.csv from:
https://depmap.org/portal/download/data_slicer/download?file_path=20220227%2F3c335b7d-c18e-4788-b2e6-512d71f0a339%2Fexport.csv&name=Metabolomics.csv
...
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1
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223
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Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python
I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command ...
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1
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228
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Python argparse error
Hi I am trying to use this python script (running with bash script) to do my analysis. I am getting the following error:
File "my_python_script.py", line 33
logging.info("Reading input2 ...
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2
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Bio.codonalign.codonseq module (cal_dn_ds) for SARS-COV-2
I have calculated the dN,dS ratio for a SARS-COV-2 data set ('NC_045512.2' (Wuhan strain) and 'LC666924.1'), and results in a zero value (for most of the genes).
Is it possible and what is the ...
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1
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tensorflow nn_model for DNA sequences: Matrix size-incompatible: In[0]: [2,1], In[1]: [784,300]
Hope anyone can help a beginner here. I'm building a proof-of concept tensorflow classifier for DNA sequences. However, the NN model does not let through train and test vectors saying the matrix size ...
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1
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if, else statment gives back else value
I have a list of protein sequence ids (names). I want to sort the lines of a table, checking if the id is equal to the first column of the table. I split the table on lines and search for the id via ...
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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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1
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268
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Polygenic Risk Scores
I have run a GWAS and used PRSice (https://www.prsice.info/) to calculate polygenic risk scores on the data collected from the GWAS. I need to check whether alcohol dependence can predict gambling ...
3
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1
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74
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How to extract and visualize sequence logos from CNN kernels?
I created a basic CNN architecture using Tensorflow to classify transcription factor binding sites. My aim is to somehow extract and visualize sequence logos from the convolutional kernels. The model ...
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1
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296
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How to process multiple VCF files present in a 2 folders and create afd plots
This question has also been asked on Biostars
I have 2 directories that contains multiple VCF files.
I want to write code in python that will process all vcf files and create an AFD (allele frequency ...
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3
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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, ...
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533
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Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?
I have a project to write in Python that requires to write a function that given degenerate DNA sequence (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all ...
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'GCLOUD_SDK_PATH' Error
I have run into the following problem
Error: failed to find 'gcloud' binary; set option or environment variable 'GCLOUD_SDK_PATH'
when executing this line of R ...
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1
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376
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makeblastdb creating multiple files of unexpectedly large sizes
I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version ...
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0
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HGVS python package : How to parse complex insertions?
In HGVS package, how to create more complex variants ?
I just wonder how can I parse more complex insertions such as those :
...
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1
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625
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Pymol python script for selecting a residue's sidechain and calculating its center of mass
I trying to write a pythonic PyMol script that loads a PDB, cmd.iterates through the PDB and stores the residues (three letter code) into an array. I then want to loop through this array and ...
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1
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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:
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136
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How to extract part of protein complex separated with HEADER with two molecules from one PDB file
I have a PDB file which contain two molecules (receptor and ligand).
Each molecule will have its own header. All in ONE PDB file.
The header of receptor section looks like this (line 1-6 of the PDB ...
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160
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How do you replace multiple sequence names with new names using python?
I have into a dictionary some sequences. I would like to replace the sequences name for new names contained into a dataframe.
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0
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68
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Converting miRNA names to miRBase version IDs
I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example:
hsa-miR-106a ---> hsa-miR-106a-5p
hsa-miR-373* --> hsa-miR-373-5p
hsa-miR-33 --> hsa-miR-33a-5p
...
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1
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1
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1
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136
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Error while parsing gene bank file using Biopython
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 this
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0
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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 ...
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2
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385
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SyntaxError after end of Snakefile code?
I am trying to run Fastqc on multiple files using Snakemake but am receiving an ambiguous SyntaxError past the last line of code in the Snakefile.
Snakefile:
...
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1
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345
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Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."
I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error "Multiple run or shell keywords in rule run_fastqc".
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list comprehension and codon translation
I'm trying to create a python program that follows the codon translation and turn mRNA sequence into amino acids (see the dictionary). The system has to return an error of the string is not a ...
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2
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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 ...
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3
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172
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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 ...
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1k
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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.
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2
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249
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Permutations of 4 amino acid sequence oligopeptide
I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon.
I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
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4
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1
answer
101
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Counting hexamers in fasta sequence and identify its structure (and interruptions)
I have a lot of fasta files, each one with thousand of reads containing the hexameric motif "CCCTCT". The hexameric motif is highly continuous in most cases but interruptions may occur. I ...
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