BOL: Owner

Awk command to keep only short the fasta header !

Rahul Nayak — Fri, 27 May 2022 03:36:41 -0500

awk '/^>/ {$0=$1} 1' file.fasta

Bash script to find difference between two files !

Rahul Nayak — Thu, 24 Mar 2022 20:15:38 -0500

#lines which are exist only in file2:

grep -Fxvf file1 file2 > file3

#lines which are exist only in file1:

grep -Fxvf file2 file1 > file3

#lines which are exist in both files:

grep -Fxf file1 file2 > file3

Update conda !

Rahul Nayak — Sat, 12 Mar 2022 07:33:25 -0600

(base) [me@hn1 ME]$ conda update conda
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/me/anaconda3

  added / updated specs:
    - conda


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    coreutils-8.32             |       h7b6447c_0         2.6 MB
    gawk-5.1.0                 |       h7b6447c_0        1007 KB
    libdeflate-1.8             |       h7f8727e_5          51 KB
    xmltodict-0.12.0           |     pyhd3eb1b0_0          13 KB
    ------------------------------------------------------------
                                           Total:         3.7 MB

The following packages will be REMOVED:

  entrez-direct-15.6-he881be0_1
  perl-archive-tar-2.32-pl526_0
  perl-carp-1.38-pl526_3
  perl-common-sense-3.74-pl526_2
  perl-compress-raw-bzip2-2.087-pl526he1b5a44_0
  perl-compress-raw-zlib-2.087-pl526hc9558a2_0
  perl-exporter-5.72-pl526_1
  perl-exporter-tiny-1.002001-pl526_0
  perl-extutils-makemaker-7.36-pl526_1
  perl-io-compress-2.087-pl526he1b5a44_0
  perl-io-zlib-1.10-pl526_2
  perl-json-4.02-pl526_0
  perl-json-xs-2.34-pl526h6bb024c_3
  perl-list-moreutils-0.428-pl526_1
  perl-list-moreutils-xs-0.428-pl526_0
  perl-pathtools-3.75-pl526h14c3975_1
  perl-scalar-list-utils-1.52-pl526h516909a_0
  perl-types-serialiser-1.0-pl526_2
  perl-xsloader-0.24-pl526_0

The following packages will be UPDATED:

  coreutils                      bioconda::coreutils-8.25-1 --> pkgs/main::coreutils-8.32-h7b6447c_0
  jemalloc                       bioconda::jemalloc-4.5.0-0 --> pkgs/main::jemalloc-5.2.1-h2531618_5
  libdeflate            bioconda::libdeflate-1.2-h516909a_1 --> pkgs/main::libdeflate-1.8-h7f8727e_5

The following packages will be SUPERSEDED by a higher-priority channel:

  gawk                   conda-forge::gawk-5.1.0-h516909a_0 --> pkgs/main::gawk-5.1.0-h7b6447c_0

The following packages will be DOWNGRADED:

  xmltodict                                     0.12.0-py_0 --> 0.12.0-pyhd3eb1b0_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
libdeflate-1.8       | 51 KB     | ########################################################################################################################################################## | 100% 
coreutils-8.32       | 2.6 MB    | ########################################################################################################################################################## | 100% 
gawk-5.1.0           | 1007 KB   | ########################################################################################################################################################## | 100% 
xmltodict-0.12.0     | 13 KB     | ########################################################################################################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Command to run PERF !

Rahul Nayak — Sat, 05 Mar 2022 14:21:54 -0600

#Commands to run PERF
PERF --format fasta -t 30 -i reference.fasta -o PERF_output.tsv --include-atomic -m 2 -M 7 -l 12

Bash command to count reads in fastq file !

Rahul Nayak — Sat, 05 Mar 2022 14:07:27 -0600

#ref fastq file
#ref1_1.fq)

echo $(( $(wc -l



Plot kmer stats in bash !
Rahul Nayak — Thu, 03 Mar 2022 04:30:18 -0600
#!/bin/bash
#Counting k-mers for different k 
echo "k,unique,distinct,total"
for k in {1..15}; do
	kat hist -o phiX_$k.hist -m $k phiX.fasta >/dev/null 2>&1
	egrep -v '^#' phiX_$k.hist|awk '{if ($1==1) u=$2; d+=$2; t+=$2*$1;}\
	END{print "'$k',"u","d","t}'
done


Multiline fasta to single line fasta !
Rahul Nayak — Wed, 02 Mar 2022 01:53:05 -0600
perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' in.fasta > out.fasta


Extract all fasta sequences except ids !
Rahul Nayak — Wed, 26 Jan 2022 20:47:07 -0600
awk 'BEGIN{while((getline<"omi_ids_updated.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' genomic.fna > filtered_without_omi.fasta

#extract subseq
seqtk subseq omi_ids.fa omi_single_id.txt > omi_single_id.fa

#cat omi and all the rest
cat omi_single_id.fa filtered_without_omi.fasta > omi_single_id_plus_all.fa

#Extract unique kmer
./uniquekmer -f omi_single_id_plus_all.fa -k 19

# Extract the kmer of omi
seqtk subseq kmercollection.fasta ../omi_single_id.txt > omi_kmer19.fa

#reformat to 19mer
reformat.sh in=omi_kmer19.fa out=omi_kmer19_formated.fa fastawrap=19

#Extract and number the kmers
perl storeKmer.pl omi_kmer19_formated.fa > omi_kmer19_formated_numbered.fa

# cat all *.rd file
cat *.rd > all_reads_hits

#count the lines in each file -- go in folder
for FILE in *; do wc -l $FILE; done > all_hits_lines.txt


Plugin skeleton for ELGG !
Rahul Nayak — Tue, 18 Jan 2022 12:06:55 -0600
The following files for plugin example would go in /mod/example/

actions/
    example/
        action.php
        other_action.php
classes/
    VendorNamespace/
        PluginNamespace/
            ExampleClass.php
languages/
    en.php
vendors/
    example_3rd_party_lib/
views/
    default/
        example/
          component.css
          component.js
          component.png
        forms/
            example/
                action.php
                other_action.php
        object/
            example.php
            example/
                context1.php
                context2.php
        plugins/
            example/
                settings.php
                usersettings.php
        resources/
            example/
                all.css
                all.js
                all.php
                owner.css
                owner.js
                owner.php
        widgets/
            example_widget/
                content.php
                edit.php
elgg-plugin.php
CHANGES.txt
COPYRIGHT.txt
INSTALL.txt
LICENSE.txt
README.txt
composer.json


Corona variant calling steps !
Rahul Nayak — Fri, 25 Jun 2021 09:57:05 -0500
#!/bin/bash

FILE_PATH="data/trimmed_fastq_small/"

find "$FILE_PATH" -name "*.fasta" | 
while IFS= read -r my_file
do
	filename=$(basename "$my_file")
	basename=$(basename "$my_file" .fasta)
 	echo $basename

	mkdir -p results/sam results/bam results/bcf results/vcf
	bwa mem trimmed_fastq_small/$filename > results/sam/$basename.aligned.sam
	samtools view -S -b results/sam/$basename.aligned.sam > results/bam/$basename.aligned.bam
	samtools sort -o results/bam/$basename.sorted.bam results/bam/$basename.aligned.bam 

	bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref_genome/sequences.fasta results/bam/$basename.sorted.bam 
	bcftools call --ploidy 1 -m -v -o results/bcf/$basename.vcf results/bcf/$basename.bcf
	vcfutils.pl varFilter results/bcf/$basename.vcf  > results/vcf/$basename.vcf
	bgzip -c results/bcf/$basename.vcf > results/bcf/$basename.vcf.gz
	tabix -p vcf results/bcf/$basename.vcf.gz

done

mkdir "Variant_Results"
cp -r results/bcf/*.vcf Variant_Results/

rem mkdir "Variant_Results_of_COVID_gz"
rem cp -r results/bcf/*.vcf.gz Variant_Results_of_COVID_gz/
rem cp -r results/bcf/*.vcf.gz.tbi Variant_Results_of_COVID_gz/


bcftools merge results/bcf/*.vcf.gz -Oz -o Merge_Final_Variants.vcf.gz
gunzip Merge_Final_Variants.vcf.gz