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How to add the corresponding taxonomic level prefix based on the taxonomy name? #82

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YeGuoZJU opened this issue Jul 10, 2023 · 6 comments
Closed

How to add the corresponding taxonomic level prefix based on the taxonomy name? #82

YeGuoZJU opened this issue Jul 10, 2023 · 6 comments

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@YeGuoZJU
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YeGuoZJU commented Jul 10, 2023 •
edited

Dear Dr. Shen,Thank you for such a handy tool！

I have a question. I use metawrap classify_bins to assign taxonomy to genomic bins, and the result show as follow:

bin.10.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae
bin.6.fa Bacteria;Bacillota;Clostridia;Eubacteriales
bin.17.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae;Anaerostipes;Anaerostipes hadrus
bin.21.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
bin.4.fa Bacteria;Bacillota;Clostridia;uncultured Clostridia bacterium
bin.8.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae
bin.15.fa Bacteria;Bacillota
bin.19.fa Bacteria;Verrucomicrobiota;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila
bin.23.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
bin.3.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Tannerellaceae;Parabacteroides
bin.12.fa Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae;Methanobrevibacter;Methanobrevibacter smithii
bin.7.fa Bacteria;Bacillota;Negativicutes;Acidaminococcales;Acidaminococcaceae;Phascolarctobacterium;Phascolarctobacterium faecium
bin.16.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae;Anaerobutyricum;Anaerobutyricum hallii
bin.11.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides uniformis
bin.2.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae
bin.13.fa Bacteria;Bacillota;Clostridia;Eubacteriales
bin.5.fa Bacteria
bin.9.fa Bacteria;Bacillota;Clostridia;Eubacteriales
bin.18.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae
bin.22.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Phocaeicola

I want to add the corresponding taxonomic level prefix according to their taxonomy name, like this:

bin.1.fa d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium bifidum

I have tried many times without success, can you give me some advice? Thank you very much!
@shenwei356
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https://bioinf.shenwei.me/taxonkit/usage/#reformat

 taxonkit reformat --verbose -i 2 -P -F -T test.tsv \
    | cut -f 1,3

bin.5.fa        k__Bacteria;p__;c__;o__;f__;g__;s__
bin.9.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__;g__;s__
bin.18.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;g__;s__
bin.22.fa       k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__

Well, I think ;p__;c__;o__;f__;g__;s__ should be optional removed for Bacteria.

shenwei356 added a commit that referenced this issue Jul 11, 2023
@shenwei356
reformat: The flag -T/--trim also does not add prefix for missing ran…
434330e 
…k lower than current rank. #82
@shenwei356
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Try the new binary:

taxonkit_linux_amd64.tar.gz

taxonkit reformat --verbose -i 2 -P -T test.tsv \
    | cut -f 1,3
bin.5.fa        k__Bacteria;;;;;;
bin.9.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;;;
bin.18.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;;
bin.22.fa       k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;

You can also remove the tailing semicolon with sed.

taxonkit reformat --verbose -i 2 -P -T test.tsv \
    | cut -f 1,3 \
    | sed -E  's/;+$//'
bin.5.fa        k__Bacteria
bin.9.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales
bin.18.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae
bin.22.fa       k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola

@YeGuoZJU
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Try the new binary:

taxonkit_linux_amd64.tar.gz

taxonkit reformat --verbose -i 2 -P -T test.tsv \
    | cut -f 1,3
bin.5.fa        k__Bacteria;;;;;;
bin.9.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;;;
bin.18.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;;
bin.22.fa       k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;

You can also remove the tailing semicolon with sed.

taxonkit reformat --verbose -i 2 -P -T test.tsv \
    | cut -f 1,3 \
    | sed -E  's/;+$//'
bin.5.fa        k__Bacteria
bin.9.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales
bin.18.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae
bin.22.fa       k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola

Thank you very much for your reply. According to your suggestion, I have fulfilled my request.
Unfortunately, I have a puzzle about the result,

bin.10.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae
bin.6.fa Bacteria;Bacillota;Clostridia;Eubacteriales
bin.17.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae;Anaerostipes;Anaerostipes hadrus
bin.21.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
bin.4.fa Bacteria;Bacillota;Clostridia;uncultured Clostridia bacterium
bin.8.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae
bin.15.fa Bacteria;Bacillota
bin.19.fa Bacteria;Verrucomicrobiota;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila
bin.23.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
bin.3.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Tannerellaceae;Parabacteroides
bin.12.fa Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae;Methanobrevibacter;Methanobrevibacter smithii
bin.7.fa Bacteria;Bacillota;Negativicutes;Acidaminococcales;Acidaminococcaceae;Phascolarctobacterium;Phascolarctobacterium faecium
bin.16.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae;Anaerobutyricum;Anaerobutyricum hallii
bin.11.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides uniformis
bin.2.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae
bin.13.fa Bacteria;Bacillota;Clostridia;Eubacteriales
bin.5.fa Bacteria
bin.9.fa Bacteria;Bacillota;Clostridia;Eubacteriales
bin.18.fa Bacteria;Bacillota;Clostridia;Eubacteriales;Lachnospiraceae
bin.22.fa Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Phocaeicola

image

the result:

image

the item bin.15.fa don't show any message, but what should not be displayed is a k__Bacteria;p__Bacillota similar to such as the first two levels of bin.13.fa or bin.2.fa ？

Sorry to bother you again, thank you for your reply

shenwei356 added a commit that referenced this issue Jul 11, 2023
@shenwei356
reformat: For lineages with more than one node, if it fails to query …
8f9e148 
…TaxId with the parent-child pair, use the last child only. #82
@shenwei356
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Since some taxon names are ambiguous/duplicated, taxonkit reformat uses the parent-child pair to query the TaxIds, for lineages with more than one node.

For example, in bin.13.fa Bacteria;Bacillota;Clostridia;Eubacteriales, Clostridia;Eubacteriales is used. It works because in the NCBI taxonomy, Clostridia is the parent node of Eubacteriales.

$ echo Eubacteriales | taxonkit name2taxid | taxonkit lineage -i 2
Eubacteriales   186802  cellular organisms;Bacteria;Terrabacteria group;Bacillota;Clostridia;Eubacteriales

However, in bin.15.fa Bacteria;Bacillota which is a simplified lineage provided by the binner, Bacteria is not the parent of Bacillota. So it failed to check the TaxId.

$ echo Bacillota | taxonkit name2taxid | taxonkit lineage -i 2
Bacillota       1239    cellular organisms;Bacteria;Terrabacteria group;Bacillota

I just fixed this. Now, for lineages with more than one node, if it fails to query TaxId with the parent-child pair, try with the last child only.

$ taxonkit reformat --verbose -i 2 -P -T test.tsv \
    | cut -f 1,3 \
    | sed -E  's/;+$//'
12:33:54.455 [INFO] parsing complete lineages from field 2
12:33:54.455 [INFO] parsing merged file: /home/shenwei/.taxonkit/names.dmp
12:33:54.455 [INFO] parsing names file: /home/shenwei/.taxonkit/names.dmp
12:33:54.455 [INFO] parsing delnodes file: /home/shenwei/.taxonkit/names.dmp
12:33:54.455 [INFO] parsing nodes file: /home/shenwei/.taxonkit/nodes.dmp
12:33:54.483 [INFO] 71301 merged nodes parsed
12:33:54.565 [INFO] 468129 delnodes parsed
12:33:55.820 [INFO] 2499662 names parsed
12:33:56.062 [INFO] 2499662 nodes parsed
12:33:56.062 [INFO] creating links: child name -> parent name -> taxid
12:34:00.677 [INFO] created links: child name -> parent name -> taxid
bin.10.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae
bin.6.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales
bin.17.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus
bin.21.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Oscillospiraceae
bin.4.fa        k__Bacteria;p__Bacillota;c__Clostridia;;;;s__uncultured Clostridia bacterium
bin.8.fa        k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae
bin.15.fa       k__Bacteria;p__Bacillota
bin.19.fa       k__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansia muciniphila
bin.23.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Oscillospiraceae
bin.3.fa        k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides
bin.12.fa       k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter smithii
bin.7.fa        k__Bacteria;p__Bacillota;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium;s__Phascolarctobacterium faecium
bin.16.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;g__Anaerobutyricum;s__Anaerobutyricum hallii
bin.11.fa       k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides uniformis
bin.2.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae
bin.13.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales
bin.5.fa        k__Bacteria
bin.9.fa        k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales
bin.18.fa       k__Bacteria;p__Bacillota;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae
bin.22.fa       k__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola

taxonkit_linux_amd64.tar.gz

@shenwei356
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It would be much easier if TaxIds of the bins are available. So you can specify the taxid column with -I.

@YeGuoZJU
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It would be much easier if TaxIds of the bins are available. So you can specify the taxid column with -I.

Thank you Dr. Shen for your patient answer. Surely, If the result of metawrap classify_bins could provide the TaxIds of the bins , it could be an easy task.

All in all, thank you very much ! wish you all the best.

@shenwei356 shenwei356 mentioned this issue Aug 18, 2023
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