clearcut: any way to reassign names of tree tips?

Commands in mothur
1

Hi,
After I ran the clearcut command, I noticed the tree it generated labels the tree tips with the fasta sequence names (e.g. M01098_115_000000000-B5M22_1_1101_14755_2524… I blame the sequence facility for generating these names) instead of OTU (e.g. Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxellaceae_unclassified;). Is there a way to reassign the tree tip names to OTU in mothur or would I have to find some other software to help me do this?
Thanks!

2

Those names are generated by the sequencer. make.contigs has a rename option that you can use, but it uses sequential numbers. For what you’re hoping to accomplish, I think you’d need to write your own script or find a different program.

Pat

3

Ok. I found help creating a Python script to reassign tree tip names for anyone interested.

4

I would be interested in that script! I would like to create a tree with OTU names, to match the output of the shared and taxonomy files

5

Hi,
Here’s the script (generated by my colleague and includes notes since I’m not familiar with Python). Sorry that it didn’t paste very well, but hopefully it’ll work for you!

What I first did:

  1. Run get.oturep in mothur to request a fasta of representative sequences.

  2. Rename the sequences in rep.fasta to exactly match the desired final OTU names (Python script below):


from Bio import SeqIO           # imports the Biopython library "SeqIO"
import re                              # imports python regular expressions

<br>
fasta = SeqIO.parse(handle='File.fasta', format='fasta')             # reads in your fasta

new_names = []                    # create an empty container which we will put the renamed sequences in

# loops through the fasta, prints the sequence id and the sequence description
# then it looks in the sequence description for something that looks like 'Otu#####|###' and keeps only the Otu#### part
# creates a temporary variable 'otu', then assigns this variable to the sequence id
# then it adds the renamed sequences to the 'new_names' container
for seq in fasta:
print(seq.id)                                        # I use print statements like this when I'm building my for loops
print(seq.description)                          # they arent necessary for the actual loop but they really help
otu = re.search('(Otu[0-9]+)\|[0-9]+', seq.description)
print(otu.group(1))                              # this one lets me know my regular expression works
seq.id = otu.group(1)
new_names.append(seq)

SeqIO.write(sequences=new_names, format='fasta', handle='File_renamed.fasta')             # writes the sequences to a new fasta

<br>
# this little block verifies that the renamed fasta does indeed have the correct ID
test = SeqIO.parse(handle='File_renamed.fasta', format='fasta')
for seq in test:
print(seq.id)

<br>
# I highly recommend Biopython.  I use the PyCharm community edition IDE.  It's free.
# I ran this script by putting your fasta in the same directory as the script, then pressing ctrl+shift+F10 in Pycharm

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`

3. Generate a new phylogenetic tree from this fasta containing the renamed sequences.

Good luck!