added collapsing stratified table #126
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| @@ -126,10 +126,10 @@ Option | Description | |||
| `--input`, `-i` (required) | Path to input profile. | |||
| `--map`, `-m` (required) | Path to mapping of source features to target features. | |||
| `--output`, `-o` (required) | Path to output profile. | |||
| `--frac`, `-f` | Count each target feature as 1 / _k_ (_k_ is the number of targets mapped to a source). Otherwise, count as one. | |||
| `--divide`, `-d` | Count each target feature as 1 / _k_ (_k_ is the number of targets mapped to a source). Otherwise, count as one. | |||
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Check --frac parameter. Previously was --normalize, and is now inconsistent within the codebase.
--frac actually does sound more intuitive than --divide.
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It was modified during a previous effort in replacing Travis CI with GitHub Actions (I changed some trivial code in order to fire a PR...). Now it should be consistently --divide.
| @@ -126,10 +126,10 @@ Option | Description | |||
| `--input`, `-i` (required) | Path to input profile. | |||
| `--map`, `-m` (required) | Path to mapping of source features to target features. | |||
| `--output`, `-o` (required) | Path to output profile. | |||
| `--frac`, `-f` | Count each target feature as 1 / _k_ (_k_ is the number of targets mapped to a source). Otherwise, count as one. | |||
| `--divide`, `-d` | Count each target feature as 1 / _k_ (_k_ is the number of targets mapped to a source). Otherwise, count as one. | |||
| `--field`, `-f` | Index of field to be collapsed in a stratified profile. For example, use `-f 2` to collapse "gene" in "microbe\|gene". | |||
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Perhaps a future feature update where the field can be a name like 'gene' instead of an index.
Index is fine for now, but this is something to consider for ease of use for end users.
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Good point! One reason this hasn't been implemented is that QIIME 2 has mandatory index headers (like #FeatureID). We need to think about where else we can store these field definitions.
| @@ -223,9 +224,13 @@ def collapse_wf(input_fp: str, | |||
| if not mapping: | |||
| exit(f'No source-target relationship is found in {basename(map_fp)}.') | |||
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| # convert field index | |||
| if field: | |||
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This is change a user-entered field number (starting from 1) into a Python list index (starting from 0).
This PR adds support for collapsing a stratified table.
For example, the input profile
phylum_ko.tsvis like:One wants to collapse KOs into modules using a mapping file
ko-to-module.tsv, while leaving phyla the same:One can do (2 means the second field in each feature ID):
The output will be like:
@droush