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@pgsin
pgsin / BinaryTreeNode.cs
Created Jun 3, 2020
View BinaryTreeNode.cs
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
View BinaryTreeNode.cpp
#include <bits/stdc++.h>
using namespace std;
struct BinaryTreeNode {
int data;
BinaryTreeNode* left;
BinaryTreeNode* right;
};
@pgsin
pgsin / proteinGroups.txt
Created Mar 11, 2020
Protein groups from SMC1 interactomics tutorial
View proteinGroups.txt
This file has been truncated, but you can view the full file.
@pgsin
pgsin / proteinGroups.txt
Created Mar 11, 2020
Protein groups from SMC1 interactomics tutorial
View proteinGroups.txt
This file has been truncated, but you can view the full file.
@pgsin
pgsin / input.json
Created Oct 8, 2019
View input.json
{"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 Sep 18, 2019
Get GenBank record of all strains of specific bacteria species
View getGenBankByTaxonomy.py
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 Aug 16, 2019
View Snakefile
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 Sep 13, 2018
View MakeTable.cs
using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Text.RegularExpressions;
namespace ImmunopepModel
{
public class Gene
{
@pgsin
pgsin / TensorFlowPbTest.cs
Created Aug 22, 2018
View TensorFlowPbTest.cs
using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using TensorFlow;
namespace MachineLearning
{
@pgsin
pgsin / MappingProgram.cs
Created Jul 17, 2018
Mapping database identifiers https://www.uniprot.org/help/api_idmapping
View MappingProgram.cs
using System;
using System.Collections.Generic;
using System.IO;
using System.Net;
using System.Text;
public class MappingExample
{
private const string UniprotServer = "https://www.uniprot.org/";