Hello Lu and everyone,
This is an old thread, but it would help me a lot if we could core
extract an alignment in fasta format from the stripSubsets
core_alignment.xmfa file.
Using 6 aligned genomes, and following Lu's instructions exactly, I am
getting 6 error messages:
MAUVE>perl xmfa2fasta.pl 6.diffeliz.core_alignment.xmfa
Use of uninitialized value $seqs[6] in substr at xmfa2fasta.pl line 78.
Use of uninitialized value $seqs[7] in substr at xmfa2fasta.pl line 78.
Use of uninitialized value $seqs[8] in substr at xmfa2fasta.pl line 78.
Use of uninitialized value $seqs[9] in substr at xmfa2fasta.pl line 78.
Use of uninitialized value $seqs[10] in substr at xmfa2fasta.pl line 78.
Use of uninitialized value $seqs[11] in substr at xmfa2fasta.pl line 78..
A fasta output file is generated, but it is obviously not correct. Has
this script been updated lately?
I can provide more details if needed.
Thanks!
Peter
On 07/26/2013 7:28 AM, Lu Cheng wrote:
Dear All,
I would like to share a script which extracts core alignment in fasta
format from Mauve output.
Let us use the example in the following link
https://code.google.com/p/clonalorigin/wiki/FromGenomeAssemblyToRecombination
Our goal is to extract the core alignment for the input 4 genomes.
Step 1: get the alignment using progressiveMauve, run
progressiveMauve --output=full_alignment.xmfa genome1.gbk genome2.gbk
genome3.gbk genome4.gbk
Step 2: extract LCBs shared by all genomes
stripSubsetLCBs full_alignment.xmfa full_alignment.xmfa.bbcols
core_alignment.xmfa 500 4
the first number "500" is the minimum length of the LCB; the second
number "4" indicates the minimum number of genomes that share a LCB
Step 3: concatenate all the LCBs
perl xmfa2fasta.pl core_alignment.xmfa
You will get "core_alignment.fasta" in the current directory.
Cheers,
Lu Cheng
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