forked from jueshengong/psytrans
sylvainforet/psytrans
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
master
Could not load branches
Nothing to show
Could not load tags
Nothing to show
{{ refName }}
default
Name already in use
A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code
-
Clone
Use Git or checkout with SVN using the web URL.
Work fast with our official CLI. Learn more about the CLI.
- Open with GitHub Desktop
- Download ZIP
Sign In Required
Please sign in to use Codespaces.
Launching GitHub Desktop
If nothing happens, download GitHub Desktop and try again.
Launching GitHub Desktop
If nothing happens, download GitHub Desktop and try again.
Launching Xcode
If nothing happens, download Xcode and try again.
Launching Visual Studio Code
Your codespace will open once ready.
There was a problem preparing your codespace, please try again.
This branch is 15 commits ahead, 27 commits behind jueshengong:master.
NAME psytrans.py Parasite & Symbiont Transcriptome Separation SYNOPSIS python psytrans.py [QUERIES] [-H FILE] [-S FILE] [OPTIONS] python psytrans.py [QUERIES] [-b BLASTRESULTSFILE] [OPTIONS] DESCRIPTION psytrans.py separates the sequences of a host species from those of its main symbiont(s) or parasite(s) based on Support Vector Machine classification. The program takes as input a file in fasta format with the sequences to be classified. The program also requires a file with sequences of a species related to the host, and a file with sequences related to the symbiont (or parasite). The queries will be compared to these two files using BLASTX. Alternatively, the user can provide the output of pre-computed BLASTX searches (in tabular format: -outfmt 6 or 7). The classification is then carried out using the command line tools from libsvm. DEPENDENCIES psytrans requires makeblastdb and blastx from the NCBI blast+ distribution, unless the user provides pre-computed blast results. psytrans also requires a few command line utilities from libsvm: svm-scale, svm-train and svm-predict OPTIONS Generic Program Information -h, --help Print a usage message briefly summarizing the command-line options. Global options -R, --restart Restart the script from the last checkpoint. -p, --nbThreads Number of threads to use for the blast searches and for the SVM training. -V, --verbosemode Runs the script in verbose mode. -t, --tempDir Specify the name of the temporary directory. -X, --clearTemp Clears all temporary data in the temporary directory upon completion. -z, --stopAfter Choices:['db','runBlast','parseBlast','kmers','SVM'] This option allows the user to choose whether the process should stop, once the process has completed a specific stage. db refers to the database creation stage; runBlast refers to the BLAST search stage; parseBlast refers to the separation of unambiguous and ambiguous sequence stage; kmers refers to the preparation of SVM input stage; SVM refers to the SVM training and testing stage. Preparation of training set options -e, --maxBestEvalue Set the maximum value for the best e-value to be used to classify unambiguous sequences. -n, --numberOfSeq Set the maximum number of training & testing sequences. Kmer parameters -c, --minWordSize Set the minimum value of DNA word length. -k, --maxWordSize Set the maximum value of DNA word length. EXAMPLE You start with an assembly containing a mixture of sequences from a host A and a symbiont (or parasite) B: host_and_symb.fasta You also provide a file with proteins from a species related to the host: related_host_proteins.fasta and a file with proteins from a species related to the symbiont: related_symb_proteins.fasta You can then start the Psytrans process as follows: python psytrans.py host_and_symb.fasta -H related_host_proteins.fasta -S related_symb_proteins.fasta Wait a few hours (depending on the number of sequences), and in the current directory you will find a new file starting with the prefix `host_' and another file starting with the prefix `symb_', corresponding to the sequences classified as host or symbiont (or parasite) respectively. To run the program using 8 threads and using /home/user/tmp as a temporary directory, use the following command: python psytrans.py host_and_symb.fasta -H related_host_proteins.fasta -S related_symb_proteins.fasta -p 8 -t /home/user/tmp AUTHOR Written by Sylvain Forêt and Jue-Sheng Ong. REPORTING BUGS Report bugs at sylvain.foret@anu.edu.au Psytrans repository <https://github.com/sylvainforet/psytrans> COPYRIGHT Copyright © 2014 Sylvain Forêt & Jue-Sheng Ong. psytrans is a free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 3 or later. For more information about these matters see http://www.gnu.org/licenses/.
About
Parasite Symbiont Transcriptome Separation
Resources
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published
Languages
- Python 100.0%