tab to fasta file conversion

Question

[blooming.daisy333]

can someone kindly help me out how to convert tab delimited protein file (ID in one column and sequence in second column) into fasta file ?? any simple solution plz

thanks

[st.ph.n]

Try something-there are multiple solutions. If you get stuck, post your efforts and errors.

[cpad0112]

some example data?

[GenoMax]

Something like

protein1      AGCHCGCGAC
protein2      GAGCSFATHCK

[Eric Lim]

Biopython version: A: Biopython: SeqIO.write () function to write dictionary object to fasta file

[nora]

it is easy to make, using for example the interface galaxy, this function is present here

Answer 1

[drkennetz]

I think you could do this with awk, give this a try:

awk '{print ">"$1"\n"$2}' tab.tsv > seqs.fa

Let me know if that works for you!

Dennis

edit: $1 is your name column and $2 is your sequence column, so switch those if the order is sequence, name.

Answer 2

[cpad0112]

if first column doesn't have >:

awk -v OFS="\n" '{print ">"$1,$2}' test.txt
sed -e 's/^/>/;s/\t/\n/g' test.txt 
parallel  --colsep '\t'  echo -e '\>{1}\\n{2}'  :::: test.txt