add recipe for pbptyper

[rpetit3]

This PR adds pbptyper, a tool for in silico PBP typing of S. pneumoniae assemblies

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[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	pbptyper-1.0.0-hdfd78af_0.tar.bz2	LinuxArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

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Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
pbptyper	1.0.0--hdfd78af_0	show gzip -dc LinuxArtifacts/images/pbptyper:1.0.0--hdfd78af_0.tar.gz | docker load

[rpetit3]

Testing

Conda

conda install LinuxArtifacts/packages/noarch/pbptyper-1.0.0-hdfd78af_0.tar.bz2

which pbptyper
/home/robert_petit/miniconda3/envs/test-pbptyper/bin/pbptyper

pbptyper --version
pbptyper, version 1.0.0

pbptyper --help

 Usage: pbptyper [OPTIONS]

 In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies

╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│    --version                  Show the version and exit.                                                                                                      │
│ *  --assembly        TEXT     Input assembly in FASTA format (gzip is OK) [required]                                                                          │
│    --db              TEXT     Path to the input database [default: /home/robert_petit/miniconda3/envs/test-pbptyper/share/pbptyper-1.0.0]                        │
│    --prefix          TEXT     Prefix to use for output files [default: basename of input]                                                                     │
│    --outdir          TEXT     Directory to save output files [default: ./]                                                                                    │
│    --min_pident      INTEGER  Minimum percent identity to count a hit [default: 95]                                                                           │
│    --min_coverage    INTEGER  Minimum percent coverage to count a hit [default: 95]                                                                           │
│    --help                     Show this message and exit.                                                                                                     │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯


# Testing 
pbptyper --assembly test/SRR2912551.fna.gz
Running TBLASTN for 1A...
TBLASTN results written to ./SRR2912551.fna-1A.tblastn.tsv

Running TBLASTN for 2B...
TBLASTN results written to ./SRR2912551.fna-2B.tblastn.tsv

Running TBLASTN for 2X...
TBLASTN results written to ./SRR2912551.fna-2X.tblastn.tsv

                                            Predicted PBP Type
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┓
┃ sample         ┃ pbptype ┃ 1A_coverage ┃ 1A_pident ┃ 2B_coverage ┃ 2B_pident ┃ 2X_coverage ┃ 2X_pident ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━┩
│ SRR2912551.fna │ 23:0:2  │ 100         │ 100.000   │ 100         │ 100.000   │ 100         │ 100.000   │
└────────────────┴─────────┴─────────────┴───────────┴─────────────┴───────────┴─────────────┴───────────┘
Predicted pbp type result written to ./SRR2912551.fna.tsv

ls -lh *.tsv
-rw-r--r-- 1 robert_petit robert_petit 160K Aug  3 18:47 SRR2912551.fna-1A.tblastn.tsv
-rw-r--r-- 1 robert_petit robert_petit 210K Aug  3 18:47 SRR2912551.fna-2B.tblastn.tsv
-rw-r--r-- 1 robert_petit robert_petit 420K Aug  3 18:47 SRR2912551.fna-2X.tblastn.tsv
-rw-r--r-- 1 robert_petit robert_petit  139 Aug  3 18:47 SRR2912551.fna.tsv

Docker

gzip -dc LinuxArtifacts/images/pbptyper:1.0.0--hdfd78af_0.tar.gz | docker load
docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/pbptyper:1.0.0--hdfd78af_0 pbptyper --assembly /data/test/SRR8654742.fna --outdir /data/
Running TBLASTN for 1A...
TBLASTN results written to /data/SRR8654742-1A.tblastn.tsv

Running TBLASTN for 2B...
TBLASTN results written to /data/SRR8654742-2B.tblastn.tsv

Running TBLASTN for 2X...
TBLASTN results written to /data/SRR8654742-2X.tblastn.tsv

                               Predicted PBP Type
┏━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┓
┃ sample  ┃ pbptype ┃ 1A_cov… ┃ 1A_pid… ┃ 2B_cov… ┃ 2B_pid… ┃ 2X_cov… ┃ 2X_pi… ┃
┡━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━┩
│ SRR865… │ NEW:53… │ 100     │ 99.275  │ 100     │ 100.000 │ 100     │ 100.0… │
└─────────┴─────────┴─────────┴─────────┴─────────┴─────────┴─────────┴────────┘
Predicted pbp type result written to /data/SRR8654742.tsv


ls -lh *.tsv
-rw-r--r-- 1 robert_petit robert_petit 161K Aug  3 18:49 SRR8654742-1A.tblastn.tsv
-rw-r--r-- 1 robert_petit robert_petit 237K Aug  3 18:49 SRR8654742-2B.tblastn.tsv
-rw-r--r-- 1 robert_petit robert_petit 430K Aug  3 18:49 SRR8654742-2X.tblastn.tsv
-rw-r--r-- 1 robert_petit robert_petit  137 Aug  3 18:49 SRR8654742.tsv

Everything looks good

[rpetit3]

@BiocondaBot please add label

[dpryan79]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

[rpetit3]

Thank you!