Convert a Tab-separated (ID and sequence) sequence file to FASTA.
Turning a two-column ID and sequence table into FASTA
Yes, this page converts Tab-separated (ID and sequence) to FASTA. Each line's first column becomes the name on a header line, and its second column becomes the sequence beneath that header. The input holds nothing but those two columns, and no sequence-type question is asked for this pair.
What carries over from each row
In the sample on this page, three rows named seq1 to seq3, each 39 letters, become three records with the same names and letters, and the first header line reads >seq1. The input has no quality scores, descriptions, or features to carry over.
Going the other way
The reverse route, FASTA to Tab-separated (ID and sequence), is available. It keeps only each record's ID, so any description text after the ID on a FASTA header line is not kept. If you move a FASTA file through the two-column format and back, those descriptions are gone for good.
Other outputs from a two-column table
Tab-separated (ID and sequence) to FASTQ (Sanger PHRED+33) is blocked, because the input has no per-base quality scores to write; the converter suggests starting from a file that has scores, or choosing a sequence-only output. Tab-separated (ID and sequence) to GenBank is available: it asks once whether the file holds DNA, RNA, or protein, requires every record ID to contain no spaces or other whitespace, and writes every letter in the same case. With DNA chosen, the sample on this page converts there with its three IDs and sequence letters unchanged.
If the table is refused
If the upload cannot be read, the page says only that it could not be read as Tab-separated (ID and sequence) and asks you to check that it is a valid file. The message does not name a cause, so check that each line holds an ID, a tab, and then the sequence. Uploads are limited to 50 MB.
Run it with Biopython
For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.
from Bio import SeqIO
count = SeqIO.convert("input.tab", "tab",
"output.fasta", "fasta")
print("Converted %i records" % count)Sample input file: Tab-separated (ID and sequence)
Copy this example into a file, or download it, to try a Tab-separated (ID and sequence) conversion.
Download sample (sample.tsv, 135 bytes)
Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.