Command line to create blast uniref database !
...0.fasta > uniref90filt formatdb -t uniref90filt -i uniref90filt #When using NCBI BLAST+ the 'formatdb' command should be replaced by the equivalent 'makeblastdb' command: mak...1011 days ago
Inreractive SCP / File transfer !
#!/bin/bash #next line prints hearer of script echo "Interactive Script to Copy File (...st = "x" ]; do #next line prints what userd should enter, and...f null it will reask user to enter Destination Path while [ x...lename #next line checks if entered value is not null, and if...1011 days ago
Command line to download blast database / protein
...ov/blast/db/ # Database detail / description nr.*tar.gz | Non-redundant protein sequences from GenPep...oad wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' #cat them into one cat nr.*.tar.gz | tar -...1004 days ago
Download desire version of Blast software !
...ng blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #Slurm template #!/bin/bash #SBATCH --partition=longjobs #SBATCH --nodes=1 #SBATCH --ntasks-per-node=32 #SBATCH --ti...1003 days ago
1003 days ago
Downloading mmseqs databases !
...ProtKB/Swiss-Prot Aminoacid yes https://uniprot.org - NR Aminoacid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - NT Nucleotide...1003 days ago
989 days ago
Onliner to convert multi line fasta to single line fasta !
#Oneliner to convert awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > fileres.fa #Then delete the first empty line tail -n +2 fileres.fa > fileout.fa989 days ago
Perl onliner to check the ids in two files !
perl -lane 'BEGIN{open(A,"ids2.txt"); while(){chomp; $k{$_}++}} if (defined($k{$F[0]})) {print "$_\t$F[0]\t1"} else {print "$_\tNA\t0"}; ' ids1.txt > aaa.xls988 days ago
Installing Covid19 Environment !
...################## | 100% fonts-conda-forge-1 | 4 KB |...################## | 100% fontconfig-2.13.1 | 357 KB |...################## | 100% font-ttf-ubuntu-0.83 | 1.9 MB |...################## | 100% font-ttf-inconsolata | 94 KB |...984 days ago