metabolisHMM

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Original single-marker-phylogeny workflow outputs sequences of hits for a given single marker and a phylogeny of that marker. Oftentimes want to view the presence/absence of a marker on a complete...

elizabethmcd

dev branch

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- [ ] - Separate workflow scripts - [ ] - Conda installation & packaging of DB markers - [ ] - Multithreading? - [ ] - Main reformatting, utils,...

elizabethmcd

#57 check first that user genomes do not contain hyphens/dashes because downstream parsing of each genome : HMM pair needs to split on "-" and therefore have to convert to...

elizabethmcd

markers and phylogeny

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In `create-genome-phylogeny` no list for "all". RAXML also errors with options ``` # different ribosomal markers for archaea/bacteria/all bacteria_list = ['rpL14_bact','rpL15_bact','rpL16_bact','rpL18_bact','rpL22_bact','rpL24_bact','rpL2_bact','rpL3_bact','rpL4_bact','rpL5_bact','rpL6_bact','rpS10_bact','rpS17_bact','rpS19_bact','rpS3_bact','rpS8_bact'] archaea_list = ['rpL14_arch','rpL15_arch','rpL16_arch','rpL18_arch','rpL22_arch','rpL24_arch','rpL2_arch','rpL3_arch','rpL4_arch','rpL5_arch','rpL6_arch', 'rpS10_arch','rpS17_arch','rpS19_arch','rpS3_arch','rpS8_arch'] if DOMAIN == 'archaea': prot_list=archaea_list...

elizabethmcd

Errors with matplotlib, seaborn, numpy in more updated versions. Update and retest. Also put version requirements in requirements.txt and conda package installation recommendations

elizabethmcd

The directory of curated metabolic markers could not be found.

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Hi, I am running the 'summarize-markers' as ``` summarize-metabolism --input aquifer-genomes/ --output summary --metadata groups.csv ``` but I am getting the following error: ``` ############################################# metabolisHMM v1.4.0 The directory of...

sarah872

Retrieving protein-coding sequence from a giving function

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Hey @elizabethmcd good afternoon! I have a very newbie issue related to my results: I run the summarize metabolism option on my isolated genomes, and now I´m interested on checking...

Streptomyces1

Create a conda release

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Hi @elizabethmcd , thank you for providing this package. I'm excited to use it. I believe providing a conda release for it would greatly improve it and attract users. I'm...

vinisalazar

Include missing files in sdist for #46 Tested with ``` ++ mktemp -d + D=/tmp/tmp.SuiScHd1E5 + trap 'rm -rf /tmp/tmp.SuiScHd1E5' EXIT + python -m venv /tmp/tmp.SuiScHd1E5 + python setup.py sdist...

thatch