Comments (3)
Sounds like a good plan, but maybe the verbs could be rethought. The verbs and descriptions are quite different and some of the proposed verbs might have other conflicting meanings.
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It's more that the descriptions in my original issue were written as reminders for me and are kind of bad:
- The 'read' program (currently read_files) reads the alignment files in and writes some extra information that isn't directly available in the alignments.
- The 'assign' program (currently assign_reads) assigns the reads in the original sample to the reference lineages and writes the assignments for groups that are requested.
- The 'filter' (currently build_sample) program filters the set of the original reads based on the output from the 'assign' program and writes the assigned reads to corresponding files.
Feel free to suggest better names; however I imagine most users want the filtered reads and thus there shouldn't really be a need for them to run any of the subprograms. They are there mostly for us to use in development.
from mgems.
Solved in #5 . The commands are mGEMS bin (bin reads) and mGEMS extract (extract bins from mixed sample).
from mgems.
Related Issues (15)
- Support reading Themisto files in directly HOT 1
- Create better error messages HOT 1
- Incorporate the steps performed with shell commands HOT 1
- Add kallisto support HOT 1
- Filter mSWEEP input HOT 2
- `Error: basic_string` when using mSWEEP abundances with bootstrap iterations in them as input HOT 1
- Add option to write the raw read assignments to reference groups table HOT 1
- Add option to write unassigned reads HOT 1
- Create a conda recipe for easy installation HOT 1
- Add option to exclude multi-group reads HOT 1
- Improve usage documentation
- `Error: stold exiting` if input file(s) are compressed with unsupported compression type HOT 1
- `Error: stoul exiting` if input pseudoalignments from paired reads have unequal numbers of reads HOT 1
- Improve `mGEMS extract`
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