BOL: Owner

Count number of lines in each file in Linux !

Neel — Fri, 18 Feb 2022 22:43:57 -0600

for FILE in *.rd; do wc -l $FILE; done > allReads.hits

Bash script to split multifasta file !

Neel — Wed, 02 Feb 2022 03:53:30 -0600

#Using awk, we can easily split a file (multi.fa) into chunks of size N (here, N=500), by using the following one-liner:

awk 'BEGIN {n=0;} /^>/ {if(n%500==0){file=sprintf("chunk%d.fa",n);} print >> file; n++; next;} { print >> file; }' < multi.fa

#OR

awk -v chunksize=$(grep ">" multi.fasta -c) 'BEGIN{n=0; chunksize=int(chunksize/10)+1 } /^>/ {if(n%chunksize==0){file=sprintf("chunk%d.fa",n);} print >> file; n++; next;} { print >> file; }' < multi.fasta

#Another great solution is genome tools (gt), which you can find here: http://genometools.org/, which has the following simple command:

gt splitfasta -numfiles 10 multi.fasta

Inreractive SCP / File transfer !

Neel — Tue, 28 Sep 2021 08:14:04 -0500

#!/bin/bash
#next line prints hearer of script
echo "Interactive Script to Copy File (files) / Directory using scp"
#next line check if entered value is not null, and if null it will reask user to enter Destination Server
while [ x$desthost = "x" ]; do
#next line prints what userd should enter, and stores entered value to variable with name desthost
read -p "Destination Server Name : " desthost
#next line finishes while loop
done
#next line check if entered value is not null, and if null it will reask user to enter Destination Path
while [ x$destpath = "x" ]; do
#next line prints what userd should enter, and stores entered value to variable with name destpath
read -p "Destination Path : " destpath
#next line finishes while loop
done
#next line put null value to variable filename
filename='null'
#next line check if entered value is null, and If not null it will reask user to enter file(s) to copy
while ! [ x"$filename" = "x" ]; do
#next line prints what userd should enter, and stores entered value to variable with name filename
read -p "Path to source directory / file : " filename
#next line checks if entered value is not null, and if not null it will copy file(s)
if ! [ x"$filename" = "x" ];
then
#next line prints header
echo -n "Copying $filename ... "
#next like copy pre-entered file(s) or dir to destination path on destination server
scp -r "$filename" "$desthost":"$destpath"
#end of if
fi
#next line finishes while loop
done

Trim the reads in loop using Trimmomatic !

Neel — Thu, 23 Sep 2021 13:13:38 -0500

for infile in *_1.fastq.gz
do
   base=$(basename ${infile} _1.fastq.gz)
   trimmomatic PE ${infile} ${base}_2.fastq.gz \
                ${base}_1.trim.fastq.gz ${base}_1un.trim.fastq.gz \
                ${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz \
                SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15 
done

Commands to Remove White Space In Text Or String Using Awk And Sed In Linux

Neel — Wed, 22 Sep 2021 08:01:34 -0500

text=" ATGGTV AGTGACCTAGAGTGATGA G   GGRTTT"

echo "$text" | sed 's/ //g'
OR
echo "$text" | awk '{ gsub(/ /,""); print }'

Return: ATGGTVAGTGACCTAGAGTGATGAGGGRTTT

echo "$text" | sed 's/^ //g'

echo "$text" | sed 's/ \$//g'

#Multiple space
cat /tmp/test.txt | sed 's/[ ]\+/ /g'

echo "$text1" | awk '{ gsub(/[ ]+/," "); print }'

cat /tmp/test.txt | awk '{ gsub(/[ ]+/," "); print }'

Print in terminal with python !

Neel — Tue, 31 Aug 2021 03:48:58 -0500

#!/usr/bin/env python

import time
import curses

def pbar(window):
    height, width = window.getmaxyx()
    for i in range(10):
        window.addstr(height -1, 0, "[" + ("=" * i) + ">" + (" " * (10 - i )) + "]")
        window.refresh()
        time.sleep(0.5)

curses.wrapper(pbar)

Install Jellyfish on Linux !

Neel — Sat, 28 Aug 2021 02:32:55 -0500

Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/$ sudo apt install jellyfish  
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  linux-headers-4.15.0-144 linux-headers-4.15.0-144-generic linux-headers-4.15.0-147 linux-headers-4.15.0-147-generic linux-headers-4.15.0-151 linux-headers-4.15.0-151-generic linux-image-4.15.0-144-generic
  linux-image-4.15.0-147-generic linux-image-4.15.0-151-generic linux-modules-4.15.0-144-generic linux-modules-4.15.0-147-generic linux-modules-4.15.0-151-generic linux-modules-extra-4.15.0-144-generic
  linux-modules-extra-4.15.0-147-generic linux-modules-extra-4.15.0-151-generic
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  libjellyfish-2.0-2
The following NEW packages will be installed:
  jellyfish libjellyfish-2.0-2
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 418 kB of archives.
After this operation, 808 kB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjellyfish-2.0-2 amd64 2.2.8-3build1 [60.7 kB]
Get:2 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 jellyfish amd64 2.2.8-3build1 [358 kB]
Fetched 418 kB in 1s (429 kB/s)    
Selecting previously unselected package libjellyfish-2.0-2:amd64.
(Reading database ... 329798 files and directories currently installed.)
Preparing to unpack .../libjellyfish-2.0-2_2.2.8-3build1_amd64.deb ...
Unpacking libjellyfish-2.0-2:amd64 (2.2.8-3build1) ...
Selecting previously unselected package jellyfish.
Preparing to unpack .../jellyfish_2.2.8-3build1_amd64.deb ...
Unpacking jellyfish (2.2.8-3build1) ...
Setting up libjellyfish-2.0-2:amd64 (2.2.8-3build1) ...
Setting up jellyfish (2.2.8-3build1) ...
Processing triggers for libc-bin (2.27-3ubuntu1.4) ...
Processing triggers for doc-base (0.10.8) ...
Processing 1 added doc-base file...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...

Perl onliner to print fasta headers !

Neel — Fri, 13 Aug 2021 07:35:49 -0500

#Save all your fasta in seq.fa and run the following ...

perl -ne 'print if /^>/' seq.fa

#Print header with line number

perl -ne 'print "$. $_" if /^>/ ' seq.fa

Commandline to Extract a list of specific read IDs from a bam file

Neel — Fri, 13 Aug 2021 07:30:15 -0500

#Save all the IDs in IDs.txt file

#Run it on BAM file

samtools view file.bam | fgrep -w -f IDs.txt

Install seqwish using conda !

Neel — Thu, 24 Jun 2021 04:44:39 -0500

conda install -c bioconda seqwish 
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/anaconda3/envs/jitENV

  added / updated specs:
    - seqwish


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    seqwish-0.4.1              |       h2e03b76_1         4.6 MB  bioconda
    ------------------------------------------------------------
                                           Total:         4.6 MB

The following NEW packages will be INSTALLED:

  seqwish            bioconda/linux-64::seqwish-0.4.1-h2e03b76_1


Proceed ([y]/n)? y


Downloading and Extracting Packages
seqwish-0.4.1        | 4.6 MB    | ################################################################################################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done