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View GitHub Profile
View input.json
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@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>'
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:
View MakeTable.cs
using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Text.RegularExpressions;
namespace ImmunopepModel
{
public class Gene
{
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
{
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/";
@pgsin
pgsin / MappingProgram.cs
Created Jul 17, 2018
Mapping database identifiers
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/";
View Combinations.cs
using System;
namespace CombinatoricsLib
{
public class Combinations
{
private static ulong Factorial(int x, int until = 0)
{
ulong res = 1;
while (x != until)
View CombinationBenchmark-report-github.md
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  
View polyA-SE.fa
>polyA_1
AAAAAAAAAAAAAAAAAAA
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