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Danilo Tatoni danilotat

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danilotat / vcf2maf.py
Last active April 1, 2025 09:14
This script takes a VCF as input and returns a minimal MAF compatible for downstream package like MAFtools. It requires a VCF file already annotate with VEP and a python environment with cyvcf2. **USAGE**: `python3 vcf2maf.py -i input.vcf -o output.maf` .
#!/bin/python3
import pandas as pd
import cyvcf2
import re
import argparse
def parse_args():
parser = argparse.ArgumentParser(description="Convert VCF to MAF format")
@danilotat
danilotat / gist:6d1085c2e9c14fd8b8bd122cf3212e54
Created June 26, 2024 22:19
Master directives
Download human RefSeq proteome
```
wget https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz
```
Last awk
`
awk '/^>/ && /BRCA2/ {print; getline; while(!/^>/) {print; getline}}' UP000005640_9606.fasta
@danilotat
danilotat / netmhcpan_launcher.py
Last active October 25, 2024 09:11
import cyvcf2
import pandas as pd
import subprocess
import os
import time
import glob
import argparse
import re
import numpy as np
import shutil
@danilotat
danilotat / boxplot_three_groups_stat.py
Created December 4, 2023 14:39
Plot a boxplot comparing a quantitative (dependent) variable in three groups (defined by the independent variable) applying most common statistical tests. Pvalues or stars like in PRISM.
from decimal import Decimal
from scipy import stats
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib.font_manager as fm
import itertools
def plotBoxplotWithTest3Groups(df: pd.DataFrame, depVar: str, indVar: str, ax: plt.Axes, test: str, prop=None, explicitP=False) -> plt.Axes:
"""
@danilotat
danilotat / query_ensembl.py
Last active February 26, 2024 15:26
Fully remote, it downloads GTF annotation file from Ensembl FTP repo for the provided organism and version, than return .tsv file with gene_id and hgnc_symbol.
#!/usr/bin/python3
import sys
import os
import tempfile
import gzip
import argparse
from ftplib import FTP
@danilotat
danilotat / GeneCards_query.py
Created July 25, 2021 08:10
Query GeneCards to get Entrez ID, symbol from any Ensembl gene ID.
#!/usr/bin/python3
from bs4 import BeautifulSoup
import requests
import html
import time
import argparse
'''
Made in a boring day by @danilotat. Enjoy