Results for "sed"
Bio-Scripts
Download the genome from NCBI using bash script/command
...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...2524 days ago
Unzip all the genome file and remove all fasta header except first one
...f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print $0} ' $f | sed '/^>/{s/ /_/g}' > $f.fa #then sed '1!{/^\>/d;}' $f > $f.fa...2523 days ago
Download the gff files from NCBI using bash script/command
...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...2515 days ago
Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2254 days ago
- # bash cat INFILE.fastq | paste - - - - |cut -f 1, 2| sed 's/@/>/'g | tr -s "/t" "/n" > OUTFILE.fasta...ioawk -c fastx '{print ">"$name"\n"$seq}' input.fastq > output.fasta #Sed sed -n '1~4s/^@/>/p;2~4p' IN...
842 days ago
Installing Platypus on Ubuntu !
...ote: Total 1394 (delta 0), reused 0 (delta 0), pack-reused 1394 Receiving objects: 100%...9 /usr/local/lib/libhts.so.2 sed -e '/^static_libs=/s/@static_...ILE_OFFSET_BITS=64 -g -Wno-unused-function creating build/lib....s-discards-qualifiers -Wno-unused-function -Wno-unneeded-intern...2011 days ago
- ...o "num bp: "$NUM_BP NUM_SNP=`cat $1 |grep -v "#" | awk -F "\t" '{if (!match($NF, "0/1")) print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$8}' | tr ';' ' ' | sed s/AB=//g | awk -v WEIGHT=0 '{...
1596 days ago
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.chrom.sizes...1357 days ago
Tadpole is 250x faster than SPADes assembler !
...nk, set mode=discard): tossjunk=f Remove reads that cannot be used for assembly....(msd) Shave or rinse kmers at most this deep. exploredist=300 (sed) Quit after exploring this fa...968 days ago
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
...GTGACCTAGAGTGATGA G GGRTTT" echo "$text" | sed 's/ //g' OR echo "$text" |...GGTVAGTGACCTAGAGTGATGAGGGRTTT echo "$text" | sed 's/^ //g' echo "$text" | s...\$//g' #Multiple space cat /tmp/test.txt | sed 's/[ ]\+/ /g' echo "$text1...948 days ago
