Support Metaphlan4 format

[TheOafidian]

The amount of rows before the profile differs between metaphlan3 and 4. Therefore taxpasta was not working on metaphlan4 output under the current circumstances. Since the header is formatted the same between both versions, a quick scan for the first field of the header could ensure the table is read from the right line in both formats.

I did not find any issues raised for this, so I just added the code I've used on my local example of to get it to work on the new format.

• [x] fix #111
• [x] description of feature/fix
• [x] tests added/passed
• [ ] add an entry to the changelog

[jfy133]

Thanks @TheOafidian !

I'll leave this up to @Midnighter to decide if he's OK with this system, however I can predict already he will ask for example test data to be added from MetaPhlAn4. Would you be able to upload some too? (Can be the one you found the issue from, but you can manually remove any sample-identification info)

[codecov-commenter]

Codecov Report

Patch coverage: 84.33% and project coverage change: +0.17 :tada:

Comparison is base (f60efe6) 81.99% compared to head (06c1191) 82.17%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #107 +/- ## ========================================== + Coverage 81.99% 82.17% +0.17% ========================================== Files 106 110 +4 Lines 1594 1677 +83 Branches 281 299 +18 ========================================== + Hits 1307 1378 +71 - Misses 247 255 +8 - Partials 40 44 +4 ``` | [Impacted Files](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [.../application/metaphlan/metaphlan\_profile\_reader.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL21ldGFwaGxhbi9tZXRhcGhsYW5fcHJvZmlsZV9yZWFkZXIucHk=) | `67.56% <50.00%> (-32.44%)` | :arrow_down: | | [...ucture/application/application\_service\_registry.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2FwcGxpY2F0aW9uX3NlcnZpY2VfcmVnaXN0cnkucHk=) | `93.16% <83.33%> (+0.26%)` | :arrow_up: | | [...rc/taxpasta/infrastructure/application/\_\_init\_\_.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [...pasta/infrastructure/application/ganon/\_\_init\_\_.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [.../infrastructure/application/ganon/ganon\_profile.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL2dhbm9uX3Byb2ZpbGUucHk=) | `100.00% <100.00%> (ø)` | | | [...tructure/application/ganon/ganon\_profile\_reader.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL2dhbm9uX3Byb2ZpbGVfcmVhZGVyLnB5) | `100.00% <100.00%> (ø)` | | | [...ion/ganon/ganon\_profile\_standardisation\_service.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL2dhbm9uX3Byb2ZpbGVfc3RhbmRhcmRpc2F0aW9uX3NlcnZpY2UucHk=) | `100.00% <100.00%> (ø)` | | | [...a/infrastructure/application/supported\_profiler.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/107?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL3N1cHBvcnRlZF9wcm9maWxlci5weQ==) | `100.00% <100.00%> (ø)` | |

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[Midnighter]

Just to be sure, the extra line is a default feature of MetaPhlAn4 and not due to some option that you have set?

[TheOafidian]

Hey @Midnighter, don't have time to go look for an example on my work laptop right now, but indeed I've used default args. I've found in the Metaphlan4 tutorial an example of output where this new line is also present like it was in my data.

[jfy133]

Some test data thanks to @apcamargo

https://github.com/taxprofiler/taxpasta/issues/111#issuecomment-1606547819