pgsin’s gists

pgsin / CombinationBenchmark-report-github.md

Created May 24, 2018 14:32

https://codereview.stackexchange.com/questions/194967/get-all-combinations-of-selecting-k-elements-from-an-n-sized-array/195025#195025

BenchmarkDotNet=v0.10.14, OS=Windows 10.0.16299.371 (1709/FallCreatorsUpdate/Redstone3)
Intel Core i7-7820HQ CPU 2.90GHz (Kaby Lake), 1 CPU, 8 logical and 4 physical cores
Frequency=2835937 Hz, Resolution=352.6171 ns, Timer=TSC
  [Host]     : .NET Framework 4.7.1 (CLR 4.0.30319.42000), 32bit LegacyJIT-v4.7.2633.0
  Job-JWVBYN : .NET Framework 4.7.1 (CLR 4.0.30319.42000), 32bit LegacyJIT-v4.7.2633.0

Runtime=Clr  IsBaseline=True

pgsin / Combinations.cs

Last active June 18, 2018 14:12

	using System;

	namespace CombinatoricsLib
	{
	public class Combinations
	{
	private static ulong Factorial(int x, int until = 0)
	{
	ulong res = 1;
	while (x != until)

pgsin / MappingProgram.cs

Created July 17, 2018 23:43

Mapping database identifiers

	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/";

pgsin / MappingProgram.cs

Created July 17, 2018 23:43

Mapping database identifiers https://www.uniprot.org/help/api_idmapping

	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/";

pgsin / TensorFlowPbTest.cs

Created August 22, 2018 09:30

	using System;
	using System.Collections.Generic;
	using System.IO;
	using System.Linq;
	using System.Text;
	using System.Threading.Tasks;
	using TensorFlow;

	namespace MachineLearning
	{

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
	{

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 / 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 / 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 / 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

Pavel Sinitcyn pgsin