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pgsin / main.py
Last active November 28, 2023 19:32
Phosphoproteome on Astral - Figure 1C and 1D
import json
import random
import math
from random import sample
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import cm
from matplotlib.colors import Normalize
@pgsin
pgsin / proteinGroups.txt
Created March 30, 2022 02:54
This file has been truncated, but you can view the full file.
Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Fasta headers Number of proteins Peptides Razor + unique peptides Unique peptides Peptides pHis3_01 Peptides pHis3_02 Peptides pHis3_03 Peptides SMC1_01 Peptides SMC1_02 Peptides SMC1_03 Razor + unique peptides pHis3_01 Razor + unique peptides pHis3_02 Razor + unique peptides pHis3_03 Razor + unique peptides SMC1_01 Razor + unique peptides SMC1_02 Razor + unique peptides SMC1_03 Unique peptides pHis3_01 Unique peptides pHis3_02 Unique peptides pHis3_03 Unique peptides SMC1_01 Unique peptides SMC1_02 Unique peptides SMC1_03 Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Sequence coverage pHis3_01 [%] Sequence coverage pHis3_02 [%] Sequence coverage pHis3_03 [%] Sequence coverage SMC1_01 [%] Sequence coverage SMC1_02 [%] Sequence coverage SMC1_03 [%] Intensity Intensity pHis3_01 Intensity pHis3_02 Int
@pgsin
pgsin / BinaryTreeNode.cs
Created June 3, 2020 21:15
using System;
using System.Collections.Generic;
namespace ConsoleApp9 {
public class BinaryTreeNode {
public int Data { get; }
public BinaryTreeNode Left { get; }
public BinaryTreeNode Right { get; }
public BinaryTreeNode(int data) {
@pgsin
pgsin / BinaryTreeNode.cpp
Created May 30, 2020 18:56
#include <bits/stdc++.h>
using namespace std;
struct BinaryTreeNode {
int data;
BinaryTreeNode* left;
BinaryTreeNode* right;
};
@pgsin
pgsin / proteinGroups.txt
Created March 11, 2020 17:27
Protein groups from SMC1 interactomics tutorial
This file has been truncated, but you can view the full file.
Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Fasta headers Number of proteins Peptides Razor + unique peptides Unique peptides Peptides pHis3_01 Peptides pHis3_02 Peptides pHis3_03 Peptides SMC1_01 Peptides SMC1_02 Peptides SMC1_03 Razor + unique peptides pHis3_01 Razor + unique peptides pHis3_02 Razor + unique peptides pHis3_03 Razor + unique peptides SMC1_01 Razor + unique peptides SMC1_02 Razor + unique peptides SMC1_03 Unique peptides pHis3_01 Unique peptides pHis3_02 Unique peptides pHis3_03 Unique peptides SMC1_01 Unique peptides SMC1_02 Unique peptides SMC1_03 Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Sequence coverage pHis3_01 [%] Sequence coverage pHis3_02 [%] Sequence coverage pHis3_03 [%] Sequence coverage SMC1_01 [%] Sequence coverage SMC1_02 [%] Sequence coverage SMC1_03 [%] Intensity Intensity pHis3_01 Intensity pHis3_02 Int
@pgsin
pgsin / proteinGroups.txt
Created March 11, 2020 17:27
Protein groups from SMC1 interactomics tutorial
This file has been truncated, but you can view the full file.
Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Fasta headers Number of proteins Peptides Razor + unique peptides Unique peptides Peptides pHis3_01 Peptides pHis3_02 Peptides pHis3_03 Peptides SMC1_01 Peptides SMC1_02 Peptides SMC1_03 Razor + unique peptides pHis3_01 Razor + unique peptides pHis3_02 Razor + unique peptides pHis3_03 Razor + unique peptides SMC1_01 Razor + unique peptides SMC1_02 Razor + unique peptides SMC1_03 Unique peptides pHis3_01 Unique peptides pHis3_02 Unique peptides pHis3_03 Unique peptides SMC1_01 Unique peptides SMC1_02 Unique peptides SMC1_03 Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Sequence coverage pHis3_01 [%] Sequence coverage pHis3_02 [%] Sequence coverage pHis3_03 [%] Sequence coverage SMC1_01 [%] Sequence coverage SMC1_02 [%] Sequence coverage SMC1_03 [%] Intensity Intensity pHis3_01 Intensity pHis3_02 Int
@pgsin
pgsin / input.json
Created October 8, 2019 11:48
{"inputs": [[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
@pgsin
pgsin / getGenBankByTaxonomy.py
Last active September 18, 2019 15:05
Get GenBank record of all strains of specific bacteria species
from Bio import Entrez
import os
import gzip
"""
To avoid problems with an access rate (ex. "HTTP Error 429: Too Many Requests")
Read how to get an api-key
https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
"""
Entrez.api_key = '<your api key here>'
@pgsin
pgsin / Snakefile
Last active August 16, 2019 22:11
import os
import re
GENOME = 'data/22'
rule all:
input: expand('output/reports/{SAMPLE}', SAMPLE=[os.path.splitext(i)[0] for i in os.listdir('input/') if not i.startswith('.') and i.endswith(".bam")])
output: touch('output/done')
rule reference_index:
@pgsin
pgsin / MakeTable.cs
Last active September 13, 2018 22:32
using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Text.RegularExpressions;
namespace ImmunopepModel
{
public class Gene
{