[FEATURE REQUEST] Preserve prodigal metadata for anvi-export-gene-calls

[Ge0rges]

The need

Identifying things like RBS motif, start codon, etc. can come in handy with gene-aware analyses. Such analyses may become more frequent in the future especially given the current effort

to soon implement a general framework for storing the coordinates of any type of genomic feature

#2152

The solution

From @ivagljiva on discord:

to modify what we store in the [contigs] DB, and then add a flag to anvi-export-gene-calls (ie, in the genes_in_contigs table) to include that information in the output.

Perhaps this should be relegated to the effort mentioned by @semiller10 in #2152, but I thought it pertinent to bring it up.

Beneficiaries

Anyone doing gene aware analyses.

[meren]

Just a quick note as I'm passing through this: When we do this we need to think of a way that doesn't require a specific design that locks us in with Prodigal for gene calling. A generic design that can keep track of additional features for genes (or genomic regions, or nucleotides, or codons) that can also be populated from Prodigal output.

[Ge0rges]

Because I understand this exists in the context of broader changes that need be done (that are beyond my current mastery of the Anvi'o codebase), here is a temporary pseudo-solution for anyone who ends up here.

I wrote this script which essentially piggy backs on Anvi'o prodigal caller and response parser:

import sys
sys.path.insert(1, '/path/to/anvio/anvio/drivers')
from prodigal import Prodigal

class ExtendedProdigal(Prodigal):
    def __init__(self):
        super().__init__()

        self.available_parsers = {'v2.6.3': self.extended_parser,
                                  'v2.6.2': self.extended_parser,
                                  'v2.6.0': self.extended_parser}
        
        super().check_version()

    def extended_parser(self, defline):
        """parses this, but keep more information than the default anvio parser:

            204_10M_MERGED.PERFECT.gz.keep_contig_1720_7 # 7086 # 7262 # 1 # ID=3_7;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.294

        """
    
        hit = self._Prodigal__parser_1(defline)
        
        fields = defline.split()

        additional_attributes = fields[8].split(';')

        hit['start_codon'] = additional_attributes[2].split('=')[1]
        hit['rbs_motif'] = additional_attributes[3].split('=')[1]
        hit['rbs_spacer'] = additional_attributes[4].split('=')[1]
        hit['gc_cont'] = additional_attributes[5].split('=')[1]

        return hit

prodigal = ExtendedProdigal()
prodigal.num_threads = int(sys.argv[3])
gene_calls, amino_acids = prodigal.process(sys.argv[1], sys.argv[2])

This won't update your contigs database or otherwise modify any Anvi'o functionality, however if you call it with a FASTA as input, it will return the same dict anvi'o generates in addition to keeping the other prodigal outputs chosen here (e.g. 'gc_cont'). Example run command python prodigal_caller.py mags/Pelagibacter_r-contigs.fna output_folder 40 where the format is python script_name.py input_fasta_path output_folder_for_anvio thread_number.

[Ge0rges]

@meren sidenote: while working on this I noticed an important typo here. I believe that line should read v2.6.0. I didn't want to make a pull request just for that one typo though (but I can if you'd like!).

[meren]

Thanks for letting me know about the typo, @Ge0rges. I'm not sure how did it survive this long. I guess because no one is using Prodigal v2.6.0 anymore.

Your temporary workaround is masterful and beautiful. Regarding the original feature request: this has been a difficult one to address because it requires a change in the way we keep gene calls in our relevant table with the addition of a few new columns, which will likely add millions of additional data points to that table, increasing the contigs-db size by a lot while only being relevant to a fraction of the users.

A better solution would be to extend that table if anvi-gen-contigs-db receives a specific flag (i.e., --store-extended-gene-call-data) to store larger amount of information regarding gene calls, rather than doing it every time anvi-gen-contigs-db. But since this table will already go through a change soon with the eukaryotic gene calls, I've been sitting on my hands :)

[Ge0rges]

That makes sense. I was wondering if the revamped mentioned in #2152 is thought of to affect the contigs-db or to involve the creation of new type of artifact centered around genomes/MAGs? If the latter was the case, this feature could be relegated to that artifact rather than expanding on contigs-db.

[meren]

I think it will have to be new, optional tables in contigs-db. We already have the code to mark nucleotide, codon/amino acid positions in contig sequences in contigs-db files, but they are not used outside of anvi'o structure currently. We will have to make them more accessible to mainstream programs :)

The best way to get these things done is to have a project in the lab that needs this solution to be in place. That's why there is a delay currently :(

[Ge0rges]

Hi @meren I've run into an issue with my workaround and wanted to see if you had any ideas. My goal is to get list of gene calls, and a list of functions, (for an anvio curated MAG, i.e. bin in my contigs DB/ a fasta file) that I can use separately and then downstream match the gene_callers_id to execute other analyses.

The issue with my workaround is that it produces an export of gene calls with gene_callers_id different to those that are already in the contigs db. But simultaneously, I need that extra metadata from the more extensive prodigal output parsing.

What would be the good way to go about this? I thought of modifying the function annotation commands to take in a fasta file as well but that seems pretty daunting and perhaps inefficient?

[meren]

Dear @Ge0rges, I just sent a PR for anvio-dev (#2306), which replaces prodigal with pyrodigal. The PR also includes a new parameter for anvi-gen-contigs-database, --full-gene-calling-report, that I hope offers a partial solution to this issue. When an output file path is provided to --full-gene-calling-report, anvi-gen-contigs-database generates an additional TAB-delimited file that includes all data from the gene caller and looks like this:

gene_callers_id	contig	start	stop	direction	partial	partial_begin	partial_end	confidence	gc_cont	rbs_motif	rbs_spacer	score	cscore	rscore	sscore	start_type	translation_table	tscore	uscore	sequence	translated_sequence
0	NC_009091	169	1327	f	False	False	False	99.99	0.3013			153.96808116167358	151.14841116167358	-0.9874499999999999	2.8196700000000003	ATG	11	2.8971	0.9100200000000003	ATGGAAATTATTTGTAATCAAAATGAATTA(...)	MEIICNQNELNNAIQLVSKAVASRPTHPIL(...)
1	NC_009091	1388	2036	f	False	False	False	99.99	0.2885	GGA/GAG/AGG	5-10bp	81.87259573141999	71.58136573142	2.71875	10.291229999999999	ATG	11	2.8971	4.67538	ATGGTCCTTAATTATGGAAATGGTGAAAAT(...)	MVLNYGNGENVWMHPPVHRILGWYSRPSNL(...)
2	NC_009091	2039	4379	f	False	False	False	99.99	0.3260	GGA/GAG/AGG	5-10bp	352.2303246874159	347.0894946874159	2.71875	5.14083	ATG	11	2.8971	-0.47502	ATGATAAATCAAGAAAATAATGATCTATAT(...)	MINQENNDLYDLNEALQVENLTLNDYEEIC(...)
3	NC_009091	4426	5887	f	False	False	False	99.99	0.3347			194.19481790304437	188.61028790304437	-0.9874499999999999	5.584530000000002	ATG	11	2.8971	3.6748800000000017	ATGTGCGGAATAGTTGGAATCGTTTCTTCA(...)	MCGIVGIVSSDDVNQQIYDSLLLLQHRGQD(...)
4	NC_009091	5883	8325	r	False	False	False	99.99	0.2731			318.93104438253084	315.33533438253085	-0.9874499999999999	3.5957100000000004	ATG	11	2.8971	1.6860600000000003	ATGGATAAGAAAAACTTCACTTCTATCTCA(...)	MDKKNFTSISLQEEMQRSYLEYAMSVIVGR(...)
5	NC_009091	8402	9266	r	False	False	False	99.99	0.2719			99.52927145207937	93.12346145207937	-0.9874499999999999	6.405809999999998	ATG	11	2.8971	4.496159999999998	ATGAAAAAGTTTTTACAAAGAATACTCTGG(...)	MKKFLQRILWISLISFYFLQIKKVQAIVPY(...)
6	NC_009091	9262	10219	r	False	False	False	99.99	0.3239			107.44082411540528	104.45237411540528	-0.9874499999999999	2.9884500000000003	ATG	11	2.8971	1.0788000000000002	ATGATTAATAGGATTCAAGACAAAAAAGAA(...)	MINRIQDKKEISKKLKERAIFEGFTIAGIA(...)
7	NC_009091	10365	11100	f	False	False	False	99.99	0.3319			71.66956065705634	79.71184065705633	-0.9874499999999999	-8.042279999999998	TTG	11	-9.60915	2.55432	TTGGTTGAATCTAATCAAAATCAAGATTCC(...)	MVESNQNQDSNLGSRLQQDLKNDLIAGLLV(...)
8	NC_009091	11103	11721	f	False	False	False	99.99	0.2993			69.10757680331382	69.03014680331381	-0.9874499999999999	0.07743000000000055	ATG	11	2.8971	-1.8322199999999995	ATGCATAATAGATCTCTTTCTAGAGAATTA(...)	MHNRSLSRELSLISLGLIKDKGDLKLNKFQ(...)
(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)	(...)

The gene_callers_id column here will obviously match to the gene calls stored in the contigs-db file.

What do you think about this as a solution?

[Ge0rges]

Hi @meren sorry this slipped by me for too long (I was on vacation last month). Your solution is great. I had worked around my work around so I lost focus of this, but this is an elegant feature to add to Anvio. Thanks for working on it! Feel free to close this issue.

[meren]

Perfect :) Thank you for the feedback, @Ge0rges. I'm closing the issue.