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Results tagged with python
Search options not deleted user 650
python is a programming language, widely used in bioinformatics
0 votes
New to DNABERT confused about kmers input
The next line in the manual speaks of a python function they provide that can get k-mers from your sequence, so you don't need to worry about doing this a different way. …
- 2,525
4 votes
Python: How to write duplicate sequences removed from fasta file to new file
Please do not reinvent the wheel - seqkit rmdup does what you want. From the website: rmdup Usage remove duplicated sequences by id/name/sequence Usage: seqkit rmdup [flags] Flags: -n, --by-nam …
- 2,525
5 votes
Remove sequences from a fasta file with IDs from a text file using Python
You can use something like seqkit: https://bioinf.shenwei.me/seqkit/ seqkit has a grep sub-command that is one of the most flexible I've ever seen. Your use case is quite simple, you can use seqkit gr …
- 2,525
5 votes
Running multiple sequence using spades.py on an HPC
I have some time now, so I'm going to take a shot at this, @M__ You need to run spades per read pair. When you specify *_1.fastq.gz as the -1 param, you're giving it every _1 file at once, not one _1 …
- 2,525
1 vote
How to exclude the repetition of gene-gene correlation calculation in python?
You don't need g2 to go from 0 to din.index, just from 0 to g1 - 1. This way, you'll end up calculating just for the "lower triangle": g1-> 0 1 2 3 g2 0 #(0,0 to 0,1-1 = noth …
- 2,525
3 votes
Accepted
Getting rid of duplicates in a dictionary
Not sure how you'd do this in python but you need a group-by operation here. Group by the read name and pick the min length per group. …
- 2,525
1 vote
Accepted
Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."
From a quick look at the manual, it looks like you are supposed to use just the wrapper, not combine the wrapper with a shell. Can you show me an example of such combined usage? The error seems to sug …
- 2,525
2 votes
Snakemake MissingRuleException
You're not using wildcards the way snakemake is equipped to work with them. See: FAQs such as https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-c …
- 2,525