fix: issue #59

[ali-yz]

fix the same species genes in og bug by checking for both gene.xref and species.

the is the diff for the outputs of the following command before and after the fix is applied.

command:

fastoma-collect-subhogs --pickle-folder pickle_folders/    --roothogs-folder omamer_rhogs/    --gene-id-pickle-file gene_id_dic_xml.pickle    --out FastOMA_HOGs.orthoxml    --marker-groups-fasta OrthologousGroups.tsv    --roothog-tsv RootHOGs.tsv    --species-tree species_tree_checked.nwk    --id-transform noop    -vv

Diff:

(FastOMA_Runs) ➜  case_input_copy diff FastOMA_HOGs.orthoxml ../case_input/FastOMA_HOGs.orthoxml                
2c2
< <orthoXML xmlns="http://orthoXML.org/2011/" origin="FastOMA 0.3.5+dev" originVersion="2025-02-15 22:09:37" version="0.5">
---
> <orthoXML xmlns="http://orthoXML.org/2011/" origin="FastOMA 0.3.5+dev" originVersion="2025-02-15 21:23:59" version="0.5">
(FastOMA_Runs) ➜  case_input_copy diff OrthologousGroupsFasta/OG_0000001.fa ../case_input/OrthologousGroupsFasta/OG_0000001.fa           
29a30,39
> >mRNA:Solyc09g090150.4.1 mRNA:Solyc09g090150.4.1||LA128||1002026622 mRNA:Solyc09g090150.4.1 [LA128]
> LFILQSSQLKIMEIIKFSLCFFLLFSCCFSQIEQQQSFLWQKLQYQQQHRRGRAKTDCRI
> SSLSAREPTYKFNSEAGTTEFWDRNLEEFECAGVAAVRNEIQPNGLLLPHYNNAPQLLYI
> VQGSGILGTVIPGCAETFESPQRERSMRGEEGRSEGGSQYRTGGDRHQKVRRFRQGDVLA
> LPAGITLWLYNNRQEQLVTVALLDVSNPANQLDLQFRHFFLAGNPNPKGLSGSRYEEEIQ
> SRKQHEQGGQPQQQQPGNLFDGFDLDILAEVFNVDQNLAKNLQGREDQRGQIIRAENLDV
> LSPEFEEEQPHRPGRGSRPNGLEETICAMRLRENLGRTSRADVYNPRGGRISTLNSHKLP
> ILNWLQLSAEKGNLYQNAVMAPYWNLNAHSIIYIIRGTGRIQVVGDTGNSVFDDEVREGQ
> MIVVPQNFAIMKKAGDQGLEYIAFKTNDQAITSALAGRLSAILAMPEEVLMNSYQISRQE
> ARSLKYNREETCVFAGRKSTGYSTRAMEYALTAVEAFLKV
564a575,584
> >mRNA:Solyc03g005580.2.1 mRNA:Solyc03g005580.2.1||SWEET||1058015128 mRNA:Solyc03g005580.2.1 [SWEET]
> MASKSSFLCFFFCFLVVCQISFAQIFERQQIWQRLQHQQQHRALRSKTECQIERLNAQEP
> NRRFESEAGVVEFWDATQEQFECAGVQAVRHEIRRNGLLLPYYSNTPQLFYIVQGSGVHS
> TIFPGCAETFETESPLDRRAQSGDRGQRSLDRHQKVRRFQAGDILALPAGVTHWTYNDGE
> EPIISVSLIDTSNVANQLDLTFRKFFLAGNPQRGVQQQVLGRQQETTSQYGRRGSEQEKG
> GNMLSGFDPQVLSEAFNVDVEVIRKIQEEAPERGIIVLAENLRFLLPEEKEEEEEEREWH
> SRRGFPLNGLEETFCTMKLRENIGHPTRSDVYNPRGGRISTVNSNSLPVLNWLQLSAERG
> TLYNNAIVAPHWNLNAHSIIYIIRGSGRFQVVGNAGKSVFDDQVRQGQLIVVPQNFAIVK
> KAGEQGLDYIAFKTNDNAMISPLAGRLSAIRAMPEEVLMNSYQISRQEAKSLKFNRDELS
> VFGPGARSSRQYA

[sinamajidian]

Great! thanks
we might want to report the species name here (since there are same gene names in different species)

            for gene_xref, _ in group_members:
                tsv.write(f"{group_name}\t{gene_xref}\t{omamer_roothog}\n")

but to keep it with minimal changes and stay with current format, I prefer the current version.