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More robustly parse metaphlan profile #41

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@alienzj alienzj commented May 25, 2022

We welcome feedback and issue reporting for all bioBakery tools through our Discourse site. For users that would like to directly contribute to the tools we are happy to field PRs to address bug fixes. Please note the turn around time on our end might be a bit long to field these but that does not mean we don't value the contribution! We currently don't accept PRs to add new functionality to tools but we would be happy to receive your feedback on Discourse.

Also, we will make sure to attribute your contribution in our User’s manual(README.md) and in any associated paper Acknowledgements.

Description

If meet #, humann should just parse next line.

Related Issue

If metaphlan profile contain the line like below:

#mpa_v30_CHOCOPhlAn_201901
#metaphlan 47-H.rmhost.1.fq.gz,47-H.rmhost.2.fq.gz --input_type fastq --ignore_markers s__Ruminococcus_obeum_CAG_39.markers.txt -t rel_ab_w_read_stats --unknown_estimation --add_viruses --output_file profile.tsv --sample_id 47-H
#SampleID       47-H

It will report error:

Traceback (most recent call last):                                                                                                                                   
  File "/home/zhujie/.conda/envs/bioenv3.9/bin/humann", line 10, in <module>                                                                                         
    sys.exit(main())                                                                                                                                                 
  File "/home/zhujie/.conda/envs/bioenv3.9/lib/python3.9/site-packages/humann/humann.py", line 975, in main                                                          
    custom_database = prescreen.create_custom_database(config.nucleotide_database, bug_file)                                                                         
  File "/home/zhujie/.conda/envs/bioenv3.9/lib/python3.9/site-packages/humann/search/prescreen.py", line 102, in create_custom_database
    read_percent=float(data[-2])
IndexError: list index out of range

Screenshots (if appropriate):

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