index of change_id_to_name_fasta.py out of range

[Cactusolo]

Hi I think the line 14 in change_id_to_name_fasta.py
has to be:
idn[spls[0]] = spls[1]
rather than:
idn[spls[3]] = spls[4]

Since the tutorial said:

change_id_to_name_fasta.py This will allow you to change names in a user input fasta file with a list of given names. The input is a tab delimited file containing the current names in the first column and the names to be replaced with in the second.
python change_id_to_name_fasta.py Table.tsv InputFasta.fa OutputFile

That means the table should only has two columns: old name spls[0] and new name to replace spls[1]

Pardon me if I misinterpret it :0

Miao

[blackrim]

Hm, that may be the case but do you have an example that I can check?.

[josephwb]

I think this is fine. The (tsv) table in question is that produced by setup_clade.py (with a name like TAXON_NCBIID.table), and has 7 columns. The columns spls[3] and spls[4] represent the sequence ID and species common name, respectively.

The related file, change_ncbi_to_name_fasta.py, uses different columns from the same table; it converts from the NCBI species ID (spls[1]) to the common name.