Closed rbeinart closed 7 years ago
Hi Roxanne,
Thanks for this. Now anvi-summarize
for pan genomes does report aligned sequences in PCs (unless the flag --skip-alignments
with anvi-pan-genome
, in which case it will simply report unaligned sequences). This will be in the next stable release after some more testing.
Now we have the functionality in the super class I will also implement an anvi-export-pc-alignments
program so aligned sequences for individual PCs can be acquired rapidly without summary.
Best,
This is done. We now have a new program to do it outside of summaries:
$ anvi-export-pc-alignments -h
usage: anvi-export-pc-alignments [-h] [-p PAN_DB] [-g GENOMES_STORAGE]
[-o FILE_PATH] [--pc-id PROTEIN_CLUSTER_ID]
[--pc-ids-file FILE_PATH]
[-C COLLECTION_NAME] [-b BIN_NAME]
[--list-collections] [--list-bins]
Export aligned sequences from anvi'o pan genomes
optional arguments:
-h, --help show this help message and exit
INPUT FILES:
Input files from the pangenome analysis.
-p PAN_DB, --pan-db PAN_DB
Anvi'o pan database
-g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
Anvi'o genomes storage file
OUTPUT FILE:
You get to chose an output file name to report things. The default will be
an ugly name. So, be explicit.
-o FILE_PATH, --output-file FILE_PATH
File path to store results.
SELECTION:
Which protein clusters should be exported. You can ask for a single PC, or
multiple ones listed in a file, or you can use a collection and bin name
to list PCs of interest. If you give nothing, this program will export
alignments for every single PC found in the profile database (and this is
called 'customer service').
--pc-id PROTEIN_CLUSTER_ID
Protein cluster ID you are interested in.
--pc-ids-file FILE_PATH
Text file for protein clusters (each line should
contain be a unique protein cluster id).
-C COLLECTION_NAME, --collection-name COLLECTION_NAME
Collection name.
-b BIN_NAME, --bin-id BIN_NAME
Bin name you are interested in.
OTHER STUFF:
Yes. Stuff that are not like the ones above.
--list-collections Show available collections and exit.
--list-bins List available bins in a collection and exit.
Hello, As suggested on the Google Group, I am posting here to request that a function be added to export PC alignments from the pangenomics analysis pipeline.
Thanks! -Roxanne-