Intro...
Functional Gene Pipeline Scripts contains a set of python scripts that allows to run one or more individual tools offered by RDP FunGene Pipeline (http://fungene.cme.msu.edu). These tools are offered a modular fashion allowing researchers to choose the appropriate subset based on their needs.
The path to the programs and resources are specfied in file config.ini. Modify the example config_skel.ini and rename it as config.ini.
The directory examplefiles contains the following files:
1.TCA.454Reads.fastq in the 16S_seqdata folder. (Note: The pipeline_core.py no longer takes a file with the extension .qual as an argument.
If this is an issue, please use a qual to fastq converter.)nifH_s1.fa and nifH_s2.fa. 16S_rundata.txt, a tab-delimited file containing a list of sample name, and forward and reverse primers
for each barcode in each region. Note the header line must kept unchanged. gene_option.txt, specifies the parameters used for each program if different from the default.
The section "[general]" specifies parameters used for all genes of interest.
The section starts with "[gene]" can be used to override default parameters and those specified in the "[general]" section for that gene. framebot_options.txt and 16s_options.txt. The command option file should contain the following information in order, one item per line:
gene_name, basedir, workdir, user_email, status_file, result_tar and mail_file.framebot_commands.txt, framebot_cluster_commands.txt. The command file lists the command to be executed in order.
Each line contains a tab-separated list containing a command name and the parameters used for that command.
See the complete list of commands in fgp_wrapper.py.Download the RDPTools and Fungene Pipeline scripts into your local directory.
Make the directory output_dir. This directory should be empty before you start the script.
Make an options file. You can use one of the example files as a template; just make sure to adjust the paths accordingly. The file should be in the following format
gene_name
/path/to/output_dir/basedir
/path/to/output_dir/workdir
user_email
/path/to/output_dir/status_file
/path/to/output_dir/result_tar
/path/to/output_dir/mail_fileMake a command file. There are several command files in the examplefiles directory to use as templates. Once you are familiar with the pipeline workflow, you can start making your own command files.
Run the Fungene Pipeline using the following format.
python /path/to/fungene_pipeline/fgp_wrapper.py options_file.txt command_file.txt input_file
If you are using multiple input files, you can separate them by commas or use *.ext to use all files with the same extension. All of the results will be in the output_dir folder.
Here is an example command to run Initial Process, Chimera Check, Alignment and Clustering using fgp_wrapper.py.
Modify the file 16S_options.txt with the correct path to the output directory on your local machine and your email address before run the command:
/path/to/fungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/16S_options.txt /path/to/fungene_pipeline/examplefiles/init_cluster_commands.txt
/path/to/fungene_pipeline/examplefiles/1.TCA.454Reads.fastqAn example command to run FrameBot using fgp_wrapper.py. Modify the file framebot_options.txt with the correct path
to the output directory on your local machine and your email address before run the command:
/path/to/fungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/framebot_options.txt /path/to/fungene_pipeline/examplefiles/framebot_commands.txt
/path/to/fungene_pipeline/examplefiles/nifH_s1.fa /path/to/fungene_pipeline/examplefiles/nifH_s2.fa An example command that runs Chimera Check, FrameBot, and Clustering using fgp_wrapper.py.
/path/tofungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/framebot_options.txt /path/to/fungene_pipeline/examplefiles/framebot_cluster_commands.txt
/path/to/fungene_pipeline/examplefiles/nifH_s1.fa /path/to/fungene_pipeline/examplefiles/nifH_s2.faAn example command that runs ChimeraCheck using fgp_wrapper.py.
/path/tofungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/chimeracheck_option.txt /path/to/fungene_pipeline/examplefiles/chimeracheck_command.txt
/path/to/fungene_pipeline/examplefiles/1.TCA.454Reads.fnaconfig_skel.ini
Configuration file containing path of the program and resource files.
resources
Contains the alignment models and reference database for each gene
fgp_wrapper.py
Runs commands listed in a command file for one input sequence file.
parseErrorAnalysis.py
Generates summary output file for the Defined Community Analysis tool.
pipeline.py
Takes one sequence file (and optional quality file), runs the following commands in order, Initial Process, Chimera Check, Defined Community Analysis (mock control sample only), FrameBot (protein reads only), Alignment, Clustering, Diversity Analysis(Shanno and Chao), Rarefaction.
pipeline_core.py
Contains a set of basic functions to run each individual commands called by other python scripts
pipeline_wrapper.sh
A shell script wrapper that runs fgp_wrapper.py
seq_trimmer_model.py
Slices a set of alignment sequences.
titanium_options.py
Parses a gene option file. Used by other scripts.
titanium_run_processor.py
Takes a directory of sequence data files and a run descriptor file. Runs Initial Process and a listed of commands called by pipeline.py.
examplefiles
Contains the sample data files and example command and option files used by the Usage example.