paste columns into one line in command line

Question

[newbiebio]

I have a txt files(very huge one) about genes, the txt file contains gene names, gene entrez_id, chrom,start, end and sequence columns. I want to put gene names, gene entrez_id, chr, start and end columns into one, and sequence will be in a new line. Basically, I want to convert txt file to fasta format with Linux command. ex: > SAMD11_148398_chr1_879534_879961 GGTTGC

I tried to use online converter, but my file is so huge, so it will be good to use command line to convert.

[venu]

Did you try anything? If yes, please show us, people here try to correct your code. If not, try awk.

[newbiebio]

I tried some online tools, but it failed. I was thinking use awk. And Pierre's just gave me exactly what I wanted.

[iraun]

I would suggest you to write an example of input and output lines. Just to let the people figure out more easily what are you expecting :)

[newbiebio]

Thanks to both of you.very efficient

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

Remember to accept one (or more) answers as correct (use the check-mark symbol against the answer).

Answer 1

[Pierre Lindenbaum]

awk '{printf(">%s_%s_%s_%s_%s\n%s\n",$1,$2,$3,$4,$5,$6);' input.txt > out.txt

[newbiebio]

Thank you, Pierre. I used the code. It works.

[venu]

Pierre, isn't it required to close } ?

Wondering how it worked for OP without closing the {.

Answer 2

[Tao]

If your input format is like ">SAMD11_148398_chr1_879534_879961 GGTTGC", then use the following command:

awk '{print $1"\n"$2}' input_file > output_file

But if your input is like "SAMD11 148398 chr1 879534 879961 GGTTGC" and you want to convert it to two lines:

>SAMD11_148398_chr1_879534_879961
GGTTGC

Use Pierre's answer!

[newbiebio]

I used Pierre's answer. It works. Thank you also.