Questions tagged [python]

python is a programming language, widely used in bioinformatics

Filter by
Sorted by
Tagged with
0
votes
1answer
48 views

Processed spliced and unspliced count matrices for existing scRNA-seq atlases

Before I do this myself... Is there any compiled batch-corrected dataset of the major scRNA-seq atlases (Mouse Cell Atlas, Mouse Organogenesis Atlas, Mouse Gastrulation Atlas, Tabula Muris, Tabula ...
1
vote
1answer
107 views

Unable to read all alignments in stockholm format : UnicodeDecodeError: 'utf-8'

I have a file in Stockholm format and I am trying to read it using the Biopython package. The code is as follows : ...
3
votes
1answer
75 views

protein secondary structure matching/comparison scoring

I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well. Example: ...
1
vote
2answers
475 views

How to retrieve dataset names from python statsmodels?

The Python statsmodels library grants access to many R-datasets which can be downloaded e.g. with: ...
3
votes
1answer
224 views

pysam or piping samtools view to a python script

Is it faster to use the PySam package to run a python script on a bam for read in samfile.fetch('chr1', 100, 120): print read compared to using a pipe and ...
2
votes
0answers
57 views

Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python

I am writing a Python script to automate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
1
vote
1answer
235 views

Is there any tool for fuzzy sequence matching?

Note: this question was also asked on biostars are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files? For example, I want to know, which ...
0
votes
1answer
385 views

How to convert mzXML to mzML format (mass spectrometry files)?

How to convert mzXML to mzML format (mass spectrometry files) preferably under Linux and/or Python?
0
votes
2answers
409 views

How to loop multiple function in shell script?

I need to extract sequences one after another consecutively from a large fasta files (multiple fasta files) and each extracted files to be saved in new fasta file (I mean the first sequence extracted ...
1
vote
1answer
72 views

working with cutadapt

I'm working with ion torrent data where I apply the program cutadapt. I'm analyzing ITS seq data, as well as Matk. When I'm using cutadapt, I search the information for this genes, and built new ...
2
votes
1answer
64 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
2
votes
2answers
327 views

Efficiently iterate over bed and subset pyranges objects

I am using pyranges and I have two datasets that I want to compare in several genome-wide intervals based on a bed file. For every interval in the bed file, I want to get all overlapping positions ...
0
votes
1answer
50 views

Summing two columns where they share interval overlap

I have two bed files where each column has a numeric score. I want to sum these numbers where there is overlap between the two bed files. How do I do that? Also, I am only interested in the score in ...
0
votes
1answer
122 views

Is there a way to measure cell line similarity using python?

I have a list of cell lines that should be compared against another list of cell lines as pairs. I am trying to find a way in order for me to compare two cells such as MCF7 and 10964c cell lines. I ...
1
vote
1answer
795 views

Filtering fasta files by ID

I have this code to filter some IDs from a fasta file: ...
0
votes
2answers
77 views

read and matching pattern with python

I have read the content of a text file into pandas and needed some help matching the pattern. Here is the pattern, where a can any number greater than zero and <...
2
votes
1answer
555 views

Confidence Interval with Wilcoxon Test in Python for log-normal Distribution

I have a couple arrays of dN/dS scores, and I would like to calculate the confidence interval for each array of data. dN/dS scores are not normally distributed but are log-normally distrbuted, so I ...
1
vote
1answer
36 views

storing SNPs in the genotype file for each chromosome in a separate file

I have already asked this question in another forum but have not got an appropriate answer, so wondering if anyone here can help me? I have a big file with over 3 million columns (SNPs genotypes) and ...
3
votes
2answers
334 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
1
vote
3answers
158 views

Python module for fetching NCBI id for a list of species

I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
2
votes
3answers
309 views

Modifing a GFF3 file and writting to a new file

I modified the GFF3 file with the below code: ...
3
votes
1answer
70 views

Adding an attribute to GFF3 file

I failed to add Note=Gene description to mRNA attribute with the below code: ...
3
votes
2answers
617 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
2
votes
0answers
53 views

Number of reactions per metabolic pathway

What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database such as Kegg, MetaCyc,Reactome is more helpful/reliable ...
1
vote
2answers
85 views

Biopython Failure to break out of loop

After qblast, I wanted to print only details from the first 3 BLAST output. Yet, the code below printed the details of every BLAST output. Why can't I break out of the loop to achieve my desired ...
3
votes
1answer
213 views

Access workdir defined on command line from within Snakefile

Snakemake provides access to a workflow object within a Snakefile. This allows one to, for example, have dynamic programmatic access to the directory containing the ...
1
vote
2answers
126 views

How to efficiently get human gene names from NCBI based on a large list of SNPs

I found a good answer related to my question here: How to get a list of genes corresponding to the list of SNPs (rs ids)? But it says about small number of SNPs. I want to get gene names based on ...
1
vote
1answer
56 views

semantic similarity measurement for cell line ontologies

I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies. The problem I have is that I have found a Python library called Fastsemsim, but it ...
2
votes
1answer
271 views

Is there a way to use BioLemmatizer from Python?

Lemmatization is one of the most important tasks for text normalization in natural language processing (NLP), i.e. using deep learning to understand text data. One of the good lemmatizers I found for ...
7
votes
4answers
1k views

How to do `bedtools intersection` using pandas alone?

I have two pandas Dataframes, using python3.x: ...
3
votes
1answer
147 views

How to select only RNA with Hetero atoms from pdb file with python?

I'm trying to separate RNA from protein in a complex protein/RNA PDB file and I want all RNA info with the hetero atoms in between the bases BUT without H20 etc. In short I want RNA part of pdb file ...
1
vote
1answer
104 views

Pandas automatically rounds GWAS P-value

I am working with a specific GWAS. If I were to run this on the command line grep <rs_id_of_interest> GWAS.txt I would see the GWAS p-value to be on the ...
0
votes
1answer
246 views

Raw Data frame manipulation in python

Using python 3 I need to process qPCR sequencing raw data outputs by searching for the first occurrence of a user defined string and then making a new data frame using all lines after that string. I ...
0
votes
0answers
49 views

How to compare multiple genetic profiles in Python?

I have hundreds of vcf file where each vcf file contains genome profile for a tissue. A portion of the vcf file is as follows: [ I can read each vcf file into a dataframe. So it would be hundreds of ...
1
vote
3answers
286 views

Deep learning RNA sequences

Currently I'm working on a project, which combines deep learning with RNA sequences. I'll try to predict pseudotorsion angles [1] from raw rna sequence. The ideas is to train a neural network with raw ...
2
votes
3answers
796 views

How to reverse complement the DNA sequences for given inverse/reverse coordinates?

I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt ...
1
vote
0answers
20 views

the positions computed by ms

I am doing simulations using a program 'ms': https://snoweye.github.io/phyclust/document/msdoc.pdf If you look at page 3 of this pdf, it explains the output produced by ms. The line which starts ...
4
votes
1answer
179 views

HDF5 and BioSQL solutions

I'm looking at better database/storage solutions for NCBI virus data, with all attributes particularly year and country of isolation, together with structural data, possible antibody data, T-cell data ...
1
vote
3answers
903 views

Calculate the occurrence of motif in sequences (including overlaps) using Python

I need to calculate the occurrences of a motif (including overlaps) in sequences (motif is passed in the first line of standard input and FASTA sequences in subsequent lines). The sequence name starts ...
1
vote
1answer
84 views

Retrieve ID ligand from PDB file

I have thousands of PDB files and I need to extract the following information from each of them: an ID or the name of the small molecule (ligand) present in the complex. Is there a way to do that ...
1
vote
1answer
148 views

How to get Uniprot and swissprot cross references using Biopython

I am struggling to use biopython to gather cross references such as GO annotation from Uniprot/swissprot text files ("DR" in the .txt files) using biopython. From ...
0
votes
1answer
65 views

cooler out of memory

I ran into the following error when using cooler to load a contact pairs file: ...
0
votes
1answer
413 views

filter secondary alignments using pysam

I am new to python and trying to learn. The below is an attempt to filter out secondary reads in a bam using ...
5
votes
2answers
559 views

What does "fetching by region is not available for SAM files" mean?

I am used to gzip/biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant ...
1
vote
2answers
54 views

Is there a tool to convert a variableStep .wig to fixedStep one?

I have a .wig file in this format: variableStep chrom=chr1 span=20 59965 7 59985 10 60005 10 60025 10 and I would like to format it to something like ...
1
vote
1answer
73 views

Aligned base strand in pysam `pileupcolumn`

Is it possible that on the same pileupcolumn object (i.e a specific aligned base) I find the same base but aligned to different strands? For example, can I find a coverage of 50 'A's that align to ...
0
votes
0answers
30 views

How to retrieve the best-scoring Trinity isoform from blastx results

I'm working on a somewhat unusual transcriptome focused on a killer X chromosome. This chromosome has some new genes, with expression levels quite different from their autosomal paralogs. I've found ...
1
vote
0answers
99 views

extracting gene names from pubmed abstracts

I have been extracted number of abstracts from pubmed. now I am having a bunch of abstracts of pubmed articles now from this abstracts I need to extract gene names which are included in abstracts.
3
votes
2answers
230 views

Getting data from fastq by generator

I have a task in a training that I have to read and filter the 'good' reads of big fastq files. I downsampled, got the code working, saving in a python dictionary. But turns out the original files ...
1
vote
2answers
628 views

Chunk alignment in a name sorted bam for parallel processing

I have a bam file with 1 billion alignment reads of which there are 700 million unique reads. I want to split the alignments into chunks for parallel-processing. Multi-alignments of the same read ...

1 2 3
4
5
7