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Original Project site: [PPR Code Prediction Server - From PPR to RNA](http://yinlab.hzau.edu.cn/pprcode/)

## NOTE
This original website is somehow out-of-date.
This original website is Down.

Please switch to Colab release or docker release.

<div><a href="https://colab.research.google.com/github/YaoYinYing/PPRCODE_Guideline/blob/master/PPRCODE.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a></div>
Please switch to Colab release or docker release or Biolib release.

## Three ways to run PPRCODE
1. [WebServer](http://yinlab.hzau.edu.cn/pprcode/): **No longer maintained**
1. [WebServer from BioLib](https://biolib.com/YaoYinYing/pprcode/);
**the [original webserver](http://yinlab.hzau.edu.cn/pprcode/) provided by [Yin Lab](http://yinlab.hzau.edu.cn/) is down and will be no longer maintained.**
2. [Colab Reimplementation](https://colab.research.google.com/github/YaoYinYing/PPRCODE_Guideline/blob/master/PPRCODE.ipynb)
3. Docker image

## Run PPRCODE locally in docker
1. Install docker daemon following the [officical getting-started page](https://www.docker.com/get-started/)
1. Install docker daemon following the [official getting-started page](https://www.docker.com/get-started/)
2. Clone this repo
```shell
git clone https://github.com/YaoYinYing/PPRCODE_Guideline
Expand All @@ -43,7 +42,7 @@ Please switch to Colab release or docker release.
cd <repo>/PPRCODE_Guideline
pip install -r docker/requirements.txt
```
5. Run `run_docker.py` to your data
5. Run `run_docker.py` to an example data
```shell
conda activate pprcode
mkdir test
Expand All @@ -52,48 +51,100 @@ Please switch to Colab release or docker release.
wget -qnc http://yinlab.hzau.edu.cn/pprcode/ppr_example.fasta -P test
# use PS_Scan as default program
python /repo/PPRCODE_Guideline/docker/run_docker.py --job_dir test/ --save_dir ./save-1 --plot_item=bar,score,edge,ppr,rna
python /repo/PPRCODE_Guideline/docker/run_docker.py --fasta test/PPR_example.fasta --save_dir ./save-1 --plot_item=bar,score,edge,ppr,rna
# or use pprfinder provided by Small's Lab
python /repo/PPRCODE_Guideline/docker/run_docker.py --job_dir test/ --save_dir ./save-2 --plot_item=bar,score,edge,ppr,rna --program=pprfinder
python /repo/PPRCODE_Guideline/docker/run_docker.py --fasta test/PPR_example.fasta --save_dir ./save-2 --plot_item=bar,score,edge,ppr,rna --program=pprfinder
```
6. Advance options
```shell
python /repo/PPRCODE_Guideline/docker/run_docker.py --helpfull
python /repo/PPRCODE_Guideline/docker/run_docker.py --helpfull
Docker launch script for PPRCODE docker image.
flags:
/repo/PPRCODE_Guideline/docker/run_docker.py:
--bin_dir: Where additional required binaries locate.
(default: '/app/bin/')
--[no]debug: debug messages
(default: 'false')
--docker_image_name: Name of the PPRCODE Docker image.
(default: 'pprcode')
--docker_user: UID:GID with which to run the Docker container. The output directories will be owned by this user:group. By default, this is the current user. Valid options are: uid or uid:gid, non-numeric values
are not recognised by Docker unless that user has been created within the container.
(default: '1005:50')
--fasta: input FASTA file(s) for scan.
--[no]fix_gap: Fix gap in sequence scanning results. Turn it off so that the results will not be weird.
(default: 'false')
--plot_color_scheme: <Accent|Accent_r|Blues|Blues_r|BrBG|BrBG_r|BuGn|BuGn_r|BuPu|BuPu_r|CMRmap|CMRmap_r|Dark2|Dark2_r|GnBu|GnBu_r|Greens|Greens_r|Greys|Greys_r|OrRd|OrRd_r|Oranges|Oranges_r|PRGn|PRGn_r|Paired|Pai
red_r|Pastel1|Pastel1_r|Pastel2|Pastel2_r|PiYG|PiYG_r|PuBu|PuBuGn|PuBuGn_r|PuBu_r|PuOr|PuOr_r|PuRd|PuRd_r|Purples|Purples_r|RdBu|RdBu_r|RdGy|RdGy_r|RdPu|RdPu_r|RdYlBu|RdYlBu_r|RdYlGn|RdYlGn_r|Reds|Reds_r|Set1|S
et1_r|Set2|Set2_r|Set3|Set3_r|Spectral|Spectral_r|Wistia|Wistia_r|YlGn|YlGnBu|YlGnBu_r|YlGn_r|YlOrBr|YlOrBr_r|YlOrRd|YlOrRd_r|afmhot|afmhot_r|autumn|autumn_r|binary|binary_r|bone|bone_r|brg|brg_r|bwr|bwr_r|civi
dis|cividis_r|cool|cool_r|coolwarm|coolwarm_r|copper|copper_r|cubehelix|cubehelix_r|flag|flag_r|gist_earth|gist_earth_r|gist_gray|gist_gray_r|gist_heat|gist_heat_r|gist_ncar|gist_ncar_r|gist_rainbow|gist_rainbo
w_r|gist_stern|gist_stern_r|gist_yarg|gist_yarg_r|gnuplot|gnuplot2|gnuplot2_r|gnuplot_r|gray|gray_r|hot|hot_r|hsv|hsv_r|inferno|inferno_r|jet|jet_r|magma|magma_r|nipy_spectral|nipy_spectral_r|ocean>: Color
scheme for plot
(default: 'RdBu')
--plot_item: plot PPRCODE results in what ways.
(default: 'bar,ppr,rna,type,edge')
(a comma separated list)
--profile_dir: Where additional required profiles locate.
(default: '/app/profiles/')
--program: <ps_scan|pprfinder>: Choose a proper algorithm to process your sequence. PPRCODE use PS_Scan(ps_scan) by default. However, you may use PPRfinder(pprfinder) from Small's Lab
(default: 'ps_scan')
--[no]report: Generate a human-friendly report file in xlsx format
(default: 'true')
--[no]run_benchmark: Fetch a benchmark dataset. **This could make your job running messy.**
(default: 'false')
--save_dir: Path to save run results.
(default: './results')
absl.app:
-?,--[no]help: show this help
(default: 'false')
--[no]helpfull: show full help
(default: 'false')
--[no]helpshort: show this help
(default: 'false')
--[no]helpxml: like --helpfull, but generates XML output
(default: 'false')
--[no]only_check_args: Set to true to validate args and exit.
(default: 'false')
--[no]pdb: Alias for --pdb_post_mortem.
(default: 'false')
--[no]pdb_post_mortem: Set to true to handle uncaught exceptions with PDB post mortem.
(default: 'false')
--profile_file: Dump profile information to a file (for python -m pstats). Implies --run_with_profiling.
--[no]run_with_pdb: Set to true for PDB debug mode
(default: 'false')
--[no]run_with_profiling: Set to true for profiling the script. Execution will be slower, and the output format might change over time.
(default: 'false')
--[no]use_cprofile_for_profiling: Use cProfile instead of the profile module for profiling. This has no effect unless --run_with_profiling is set.
(default: 'true')
absl.logging:
--[no]alsologtostderr: also log to stderr?
(default: 'false')
--log_dir: directory to write logfiles into
(default: '')
--logger_levels: Specify log level of loggers. The format is a CSV list of `name:level`. Where `name` is the logger name used with `logging.getLogger()`, and `level` is a level name (INFO, DEBUG, etc). e.g.
`myapp.foo:INFO,other.logger:DEBUG`
(default: '')
--[no]logtostderr: Should only log to stderr?
(default: 'false')
--[no]showprefixforinfo: If False, do not prepend prefix to info messages when it's logged to stderr, --verbosity is set to INFO level, and python logging is used.
(default: 'true')
--stderrthreshold: log messages at this level, or more severe, to stderr in addition to the logfile. Possible values are 'debug', 'info', 'warning', 'error', and 'fatal'. Obsoletes --alsologtostderr. Using
--alsologtostderr cancels the effect of this flag. Please also note that this flag is subject to --verbosity and requires logfile not be stderr.
(default: 'fatal')
-v,--verbosity: Logging verbosity level. Messages logged at this level or lower will be included. Set to 1 for debug logging. If the flag was not set or supplied, the value will be changed from the default of -1
(warning) to 0 (info) after flags are parsed.
(default: '-1')
(an integer)
/repo/PPRCODE_Guideline/docker/run_docker.py:
--bin_dir: Where additional required binaries locate.
(default: '/app/bin/')
--[no]debug: debug messages
(default: 'false')
--docker_image_name: Name of the PPRCODE Docker image.
(default: 'pprcode')
--docker_user: UID:GID with which to run the Docker container. The output directories will be owned by this user:group. By default, this is the current user. Valid options are: uid or uid:gid, non-numeric values
are not recognised by Docker unless that user has been created within the container.
(default: '1005:50')
--[no]fix_gap: Fix gap in sequence scanning results. Turn it off so that the results will not be weird.
(default: 'false')
--job_dir: input directory of FASTA file(s) for scan.
--plot_color_scheme: <Accent|Accent_r|Blues|Blues_r|BrBG|BrBG_r|BuGn|BuGn_r|BuPu|BuPu_r|CMRmap|CMRmap_r|Dark2|Dark2_r|GnBu|GnBu_r|Greens|Greens_r|Greys|Greys_r|OrRd|OrRd_r|Oranges|Oranges_r|PRGn|PRGn_r|Paired|Pai
red_r|Pastel1|Pastel1_r|Pastel2|Pastel2_r|PiYG|PiYG_r|PuBu|PuBuGn|PuBuGn_r|PuBu_r|PuOr|PuOr_r|PuRd|PuRd_r|Purples|Purples_r|RdBu|RdBu_r|RdGy|RdGy_r|RdPu|RdPu_r|RdYlBu|RdYlBu_r|RdYlGn|RdYlGn_r|Reds|Reds_r|Set1|S
et1_r|Set2|Set2_r|Set3|Set3_r|Spectral|Spectral_r|Wistia|Wistia_r|YlGn|YlGnBu|YlGnBu_r|YlGn_r|YlOrBr|YlOrBr_r|YlOrRd|YlOrRd_r|afmhot|afmhot_r|autumn|autumn_r|binary|binary_r|bone|bone_r|brg|brg_r|bwr|bwr_r|civi
dis|cividis_r|cool|cool_r|coolwarm|coolwarm_r|copper|copper_r|cubehelix|cubehelix_r|flag|flag_r|gist_earth|gist_earth_r|gist_gray|gist_gray_r|gist_heat|gist_heat_r|gist_ncar|gist_ncar_r|gist_rainbow|gist_rainbo
w_r|gist_stern|gist_stern_r|gist_yarg|gist_yarg_r|gnuplot|gnuplot2|gnuplot2_r|gnuplot_r|gray|gray_r|hot|hot_r|hsv|hsv_r|inferno|inferno_r|jet|jet_r|magma|magma_r|nipy_spectral|nipy_spectral_r|ocean>: Color
scheme for plot
(default: 'RdBu')
--plot_item: plot PPRCODE results in what ways.
(default: 'bar,ppr,rna,type,edge')
(a comma separated list)
--profile_dir: Where additional required profiles locate.
(default: '/app/profiles/')
--program: <ps_scan|pprfinder>: Choose a proper algorithm to process your sequence. PPRCODE use PS_Scan(ps_scan) by default. However, you may use PPRfinder(pprfinder) from Small's Lab
(default: 'ps_scan')
--[no]report: Generate a human-friendly report file in xlsx format
(default: 'true')
--[no]run_benchmark: Fetch a benchmark dataset. **This could make your job running messy.**
(default: 'false')
--save_dir: Path to save run results.
(default: './results')
absl.flags:
--flagfile: Insert flag definitions from the given file into the command line.
(default: '')
--undefok: comma-separated list of flag names that it is okay to specify on the command line even if the program does not define a flag with that name. IMPORTANT: flags in this list that have arguments MUST use
the --flag=value format.
(default: '')
```
Expand All @@ -113,22 +164,18 @@ PPR proteins are typically characterized by tandem degenerate repeats of a 35-am
### _Q_: How do I submit a sequence to the PPRCODE prediction server?
Go to the [PPRCODE prediction server](http://yinlab.hzau.edu.cn/pprcode/) submission form directly and do the following:
Go to the [PPRCODE prediction server in BioLib](https://biolib.com/YaoYinYing/pprcode/) submission form directly and do the following:
1. Paste your FASTA sequence in the upper text area.
2. Enter your email address.
3. Click the Submit button.
After the submission, the webpage will be automatically refreshed several times until the job is finished.
2. Modify the options if needed.
3. Click the Run button.
After the submission, the webpage will be automatically run for several second until the job is finished.
You may also click the link marked _**"Click here for a sample input sequence"**_ above the sequence area to input a demo, in which we have prepared a ZmPPR10 and an non-PPR for program testing.
### _Q_: How long does it take to finish a task?
Less than three minutes for each sequence.
Less than three second for each sequence.
### _Q_: How many sequences can I submit in one submission?
We can now process 30 sequences in parallel. However, submission of more than 100 is not recommended due to the instability of network environment.
As many as you want.
### _Q_: How much time do I have before my job is removed in server?
Jobs may be removed **one week after they complete** to conserve disk space, and their result pages will also be unavailable.
### _Q_: What does the prediction result mean?
The result page contains a table like the following:
Expand Down Expand Up @@ -165,15 +212,6 @@ and finally you will also get a predicted sequence like this:
### _Q_: Why does the prediction result of my sequence look like a mess?
ProSite identifies the sequence and motifs of a PPR protein by its similarity to the general P-type PPR. Sequences with low identity will hardly be predicted. In this circumstance, manual correction is strongly recommended.
### _Q_: What do the error codes mean?
#### error code: 404
The result is not found in database, which may be deleted, or the submission id contained in address is not complete.
You need to resubmit your sequence, or check the right job id.
#### error code: 500
An internal error occurs in our program. This is often caused by the input sequence or email address.
**The server only accept sequences in FASTA format.**
## Troubleshoot
If there is any problem and advice with the website, you are welcome to contact us via [email](mailto:[email protected]).
Expand Down

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