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Exporting sequences from Excel

I'm starting a bioinformatics project and I've been given an excel sheet with two columns: one containing a number assigned to the sequence and one containing the sequence. I have to build a bootstrap tree using all the sequences and there's over 7000 of them. Manually exporting all the sequences and assigning them to a file of the corresponding number would be incredibly tedious and time consuming, is there any other way of doing it that would be faster?

I'm planning on using Mega to build the tree as it's the fastest option that I'm aware of and I'll be working in either Windows or BioLinux depending on what options I can come up with for separating out the sequences.

Thanks in advance

excel export tree building
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written by avocado_toast • avocado_toast

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written by WouterDeCoster WouterDeCoster

3 answers

Export it to a csv, or tsv, transliterate the delimiter to a newline, and you'll have something approximately resembling a fasta file.

Then tell your collaborator/boss off for ever giving you sequence data in any form of MS Office format.

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written by Joe Joe

Assuming 1st column contains the number and the 2nd column contains the sequence:

  1. Export the file as tab-separated values
  2. awk 'BEGIN{FS="\t";OFS="\n"}{print ">"$1,$2}' exportedFile.tsv > seqs.fna
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written by 5heikki 5heikki
  1. make sure that first column has sequence ID/Identifier and second column has entire sequence. Now export the file as tsv.
  2. Download seqkit and execute seqkit tab2fx exported_seq.tsv -o exported_seq.fa
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written by cpad0112 cpad0112

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