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.
2 answers
awk '{printf(">%s_%s_%s_%s_%s\n%s\n",$1,$2,$3,$4,$5,$6);' input.txt > out.txt
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!
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Did you try anything? If yes, please show us, people here try to correct your code. If not, try
awk.I tried some online tools, but it failed. I was thinking use awk. And Pierre's just gave me exactly what I wanted.
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 :)
Thanks to both of you.very efficient
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