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How to remove a break line \n in awk when print the result

Dear all,

I have an inputfile.txt which contains the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/248/415/GCF_000248415.2_ASM24841v2
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/011/135/GCF_001011135.1_ASM101113v1
..
..
..

I used the command which purpose is to download genome assemblies from NCBI website

awk 'BEGIN{FS=OFS="/";filesuffix="genomic.fna.gz"}{ftpdir=$0;asm=$10;file=asm"_"filesuffix;print "wget "ftpdir,file}' inputfile.txt > outputfile.sh

The problem is that it generates a string with break lines like this:

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/248/415/GCF_000248415.2_ASM24841v2

/GCF_000248415.2_ASM24841v2

_genomic.fna.gz

And I want it to be one line like this:

wget_ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/248/415/GCF_000248415.2_ASM24841v2/GCF_000248415.2_ASM24841v2_genomic.fna.gz

How can I achieve it?

Thanks!

bash linux awk
• 1,071 views • link
updated by Ram Ram • written by xatabadich • xatabadich

2 answers 

awk -F '/' '{printf("%s/%s_genomic.fna.gz\n",$0,$NF);}'  input.txt > urls.txt

and then

wget --input-file=urls.txt

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum 
$ perl -pe 's/\n/, /' inputfile.txt
$ tr '\n' ',' < inputfile.txt
• 0 views • link
written by cpad0112 cpad0112

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