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Bash script to convert multiline fasta to single line fasta !

Neel — Thu, 31 Mar 2022 03:50:05 -0500

#file.fa is multiline fasta

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < file.fa

Bash command to explore assembly summary genbank !

Neel — Tue, 29 Mar 2022 02:35:30 -0500

wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt

pip3 install csvkit

csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \
  | tail -n +2 | tr ";" "\n" \
    | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \
      | sort | uniq -c | sort -nr

Commands to Find and replace in file(s0) !

Jit — Sun, 27 Mar 2022 21:52:23 -0500

#Use SED
sed -i 's/my/your/g' test.txt test2.txt test3.txt

#Use FIND and SED
find . -name *.txt -exec sed -i 's/my/your/g' {} \;

#Use AWK
awk '{sub(/{OLD_TERM}/,{NEW_TERM}); print}' {file}
awk '{sub(/my/,your); print}' test.txt
awk '{gsub(/i/,"a"); print}' test.txt

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


Bash script to transfer files to server !
Neel — Mon, 21 Feb 2022 23:21:36 -0600
# rsync options source destination

rsync -azvh --progress PacBio_clean.fa xxx@xxx.xxx.res.in:/home/

# scp source_file_name username@destination_host:destination_folder

scp –rpv /datafile xxx@192.168.1.100:/home/me