Questions tagged [python]

python is a programming language, widely used in bioinformatics

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0answers
12 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: ...
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0answers
13 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: ...
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1answer
34 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 ...
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0answers
11 views

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

I am attempting to write a tool to be used by my lab to automatically generate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
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11 views

No module error when I use ATD script. How can I fix it?

I am using AutoDockTools and I need to prepare receptor and ligand to docking. I want to use AutoDockTools files that are located in Utilities24 folder. But when I try run this scripts by windows ...
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1answer
82 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 ...
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2answers
24 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?
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2answers
174 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 ...
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0answers
35 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 ...
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1answer
48 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
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2answers
61 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 ...
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1answer
27 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 ...
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0answers
20 views

Extract secondary structures and sequences from dssp files

I have a very messy problem and I really need your help. I have a lot of dssp files in a folder. Every dssp file contains informations about proteins. Also, I have a separate file containing two ...
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1answer
54 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 ...
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1answer
62 views

Filtering fasta files by ID

I have this code to filter some IDs from a fasta file: ...
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2answers
67 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
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1answer
34 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 ...
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1answer
32 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 ...
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2answers
86 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
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2answers
45 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?
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3answers
108 views

Modifing a GFF3 file and writting to a new file

I modified the GFF3 file with the below code: ...
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1answer
36 views

Adding an attribute to GFF3 file

I failed to add Note=Gene description to mRNA attribute with the below code: ...
3
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2answers
104 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: ...
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0answers
38 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 (kegg, metacyc,reactome..) is more helpful/reliable for ...
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2answers
77 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
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1answer
44 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 ...
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2answers
79 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 ...
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1answer
36 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
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1answer
74 views

Is there a way to use BioLemmatizer from Python?

Lemmatization is one of the most important tasks for text normalization in NLP. One of the good lemmatizers I found for biomedical domain is BioLemmatizer. However, it is developed in Java and is ...
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3answers
224 views

How to do `bedtools intersection` using pandas alone?

I have two pandas Dataframes, using python3.x: ...
3
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1answer
39 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
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1answer
54 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 ...
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1answer
110 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 ...
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0answers
41 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 ...
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3answers
172 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
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3answers
254 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 ...
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0answers
19 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 ...
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1answer
142 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
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3answers
237 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
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1answer
39 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
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1answer
62 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 ...
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1answer
55 views

cooler out of memory

I ran into the following error when using cooler to load a contact pairs file: ...
0
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1answer
124 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
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2answers
335 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
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2answers
34 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
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1answer
40 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 ...
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0answers
20 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 ...
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0answers
56 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
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2answers
111 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
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2answers
254 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 ...