alienzj

A question about the NetID output

2

Hi, @LiChenPU How to get HMDB ID in NetID_output file ? I try to match it using formula, but failed. First of all, the column of HMDB formula is redundant....

Updated the code to support parsing kreport file when it contain S1 or T label of taxonomy classification.

Dear Jen @jenniferlu717 , does kreport2map.py support to generate strain level profile from Kraken2 report?

gzip support

1

Support gzip read and write.

RecursionError: maximum recursion depth exceeded while getting the str of an object

3

``` Command error: Traceback (most recent call last): File "/home/jiezhu/.conda/envs/bactopia/share/bactopia-2.1.x/conda/envs/assemble_genome-2.1.x/bin/unicycler", line 10, in sys.exit(main()) File "/home/jiezhu/.conda/envs/bactopia/share/bactopia-2.1.x/conda/envs/assemble_genome-2.1.x/lib/python3.8/site-packages/unicycler/unicycler.py", line 82, in main determine_copy_depth(graph) File "/home/jiezhu/.conda/envs/bactopia/share/bactopia-2.1.x/conda/envs/assemble_genome-2.1.x/lib/python3.8/site-packages/unicycler/assembly_graph_copy_depth.py", line 74, in determine_copy_depth determine_copy_depth_part_2(graph, settings.COPY_PROPAGATION_TOLERANCE, copy_depth_table)...

Support list all files

1

Can dirscan list all files of each directory ?

Report: Large memory usage when run `mp_cal_abundance`

1

Before run `mp_cal_abundance`:  Then run `mp_cal_abundance`:  What I got: 

Error of mp_import_metaphlan

7

When I run mp_import_metaphlan to import metaphlan4 profile, it occur error like below: ``` mpse

Biomarker discovery explanation and new package's feature discussion

36

Dear MPSE developer, Recently I try to use MicrobiotaProcess to do microbiome data analysis. This is a very nice R package as far as I know. So, I installed it...

Questions about `mp_import_dada2` and `mp_cal_rarecurve` function

6

[seqtab_no_chimeras_filtlen.rds.txt](https://github.com/YuLab-SMU/MicrobiotaProcess/files/8629999/seqtab_no_chimeras_filtlen.rds.txt) [taxa_gtdb.rds.txt](https://github.com/YuLab-SMU/MicrobiotaProcess/files/8630000/taxa_gtdb.rds.txt) [metadata_full_dada2_simple.txt](https://github.com/YuLab-SMU/MicrobiotaProcess/files/8630003/metadata_full_dada2_simple.txt) ``` seqtabfile