Create fasta file for unbinned contigs

[Camila Lin]

Hi there,

I'm wondering if there's a way to write contigs that are not binned in any bins in a single fasta file? 

I tried `anvi-export-collection`, but only get a list of splits.

Thanks,

Camila

[A. Murat Eren]

Hi Camila,

Sorry there is no straightforward way to get those sequences out. But it is possible. Try this:

anvi-export-collection -p PROFILE.db \

                       -C COLLECTION_NAME \

                       -O COLLECTION \

                        --include-unbinned

grep UNBINNED_ITEMS_BIN COLLECTION.txt | awk 'BEGIN{FS="_split_"}{print $1}' | sort | uniq > UNBINNED_CONTIG_NAMES.txt

anvi-export-contigs -c CONTIGS.db \

                    --contigs-of-interest UNBINNED_CONTIG_NAMES.txt \

                    -o UNBINNED_CONTIGS.fa

The FASTA File UNBINNED_CONTIGS.fa will contain all the contig sequences that were not binned in your collection COLLECTION_NAME.

Best,

--

A. Murat Eren (Meren) | he/him
http://merenlab.org :: twitter

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Camila Lin]

Hi Meren,

Thank you for your reply.

I was able to generate the UNBINNED_CONTIG_NAMES.txt, however, anvi'o failed to write the fasta file. The error message I got was:

usage: anvi-export-contigs [-h] -c CONTIGS_DB [--splits-mode] -o FILE_PATH

                           [--version] [--debug] [--force]

anvi-export-contigs: error: unrecognized arguments: --contigs-of-interest

I was using Anvi'o 6.0 and 6.2, and I got the same error message. Seems like the command anvi-export-contigs doesn't have --contigs-of-interest flag. 

Thanks,

Camila

[A. Murat Eren]

Sorry, Camila, I realized only after your e-mail that this is a feature that will be in the v7 (which will be released within the next month or two (fingers crossed)).

Until then you will need to consult your local bioinformatics guru :) Apologies for the inconvenience.

Best wishes,

--

A. Murat Eren (Meren) | he/him
http://merenlab.org :: twitter

To view this discussion on the web visit https://groups.google.com/d/msgid/anvio/a8b84030-fe08-46f7-ab4c-fd927fcbf0fan%40googlegroups.com.