https://github.com/k3yavi/project-euler

Frequently Used:- Cheastsheet
https://github.com/k3yavi/project-euler

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Frequently Used:- Cheastsheet

• Host: GitHub
• URL: https://github.com/k3yavi/project-euler
• Owner: k3yavi
• Created: 2014-09-19T23:23:08.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2022-04-25T22:43:49.000Z (over 2 years ago)
• Last Synced: 2023-02-26T04:02:06.967Z (almost 2 years ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 1.99 MB
• Stars: 2
• Watchers: 2
• Forks: 2
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

        
# project-euler  

## Freq_Commands

Frequently used Command and library Syntax

#bash

Bash maintains an internal hash of previously found executables in your path. In this case, it has details that at one time there was an executable at /usr/bin/siege, and reuses that path to avoid having to search again.

You can also clear all hashed locations:  

```

hash -r

```

##gnu parallel

convert multiple sam to bam with sorting in parallel

```

parallel -j 16 "samtools view -bS {} | samtools sort - -o {/.}.bam" ::: `ls *.sam`

```

##awk

subsample every Xth read

```

awk 'NR%(4*X)==0 {for(i=1; i<=4; i++) {getline; print}}' full_bcs.fastq > half_bcs.fastq

```

remove things from one file present in another 

`https://stackoverflow.com/a/18477228/6871844`

```

awk '{if (f==1) { r[$0] } else if (! ($0 in r)) { print $0 } } ' f=1 exclude-these.txt f=2 from-this.txt

```

get 5 line after every pattern line

```

awk '/PATTERN/ {for(i=1; i<=5; i++) {getline; print}}' inputfile

```

Can be used in fastq to print every 2nd read

```

awk ' NR%8 == 1 {for(i=1; i<=4; i++) {print;getline} }'

```

compare two columns from different file and get set difference

```

awk 'NR==FNR{c[$1]++;next};c[$1] == 0' geReads.txt txReads.txt| wc -l

```

## python

dictionary argmax

```

max(stats, key=stats.get)

```

combination of 2

```

itertools.combinations(a,2)

```

## FASTA

```

from pyfasta import Fasta

if __name__ == "__main__":

    f = Fasta('file.fasta')

    for contig in fasta:

```

##ipython Notebook:

```

ssh -N -f -L localhost:7777:localhost:7777 avi@feynman

ps aux | grep ssh

kill -9 

ps aux

ipython notebook --no-browser --port=7777

import pandas as pd

import numpy as np

import matplotlib as mpl

mpl.use('Agg')

import matplotlib.pyplot as plt

%matplotlib inline

```

##flux-simulator

```

./flux-simulator -t simulator -x -l -s -p ../../hg19.par

./rsem-prepare-reference --gtf ../data/bigdata/hg19/knownRef_sorted.gtf ../data/bigdata/hg19/chromFa/ ../data/bigdata/hg19/reference

```

##clear cache

```

sync && sudo purge

free && sync && sudo sh -c 'echo 3 >/proc/sys/vm/drop_caches' && free;

```

##extract txp->gene relation from GTF

```

bioawk -c gff '$feature=="transcript" {print $group}' gencode.v26.primary_assembly.annotation.gtf | awk -F ' ' '{print substr($4,2,length($4)-3) ","  substr($2,2,length($2)-3)}' - > txp2gene.tsv

 ```