COnTROT (COmprehensive Transcriptomic ORganizational Tool) is a program that will download and organize all expression data in GEO related to a search result, commonly an organism.
COnTROT (COmprehensive Transcriptomic ORganizational Tool) is a program that will download and organize all expression data in GEO related to a search result. This will identify and download GEO GDS, GSE, GSM, and GPL directories and files from NCBI FTP from a GDS search result at NCBI. Then the series data will be organized to retain matches to any gene annotation present in the GenBank file provided. The data will be organized, mean centered, and then joined using the gene annotation into a single text file that can be easily manipulated or opened in Excel.
The results will be two files: one with the data mean centered and the other with no mean centering.
The user must provide the GenBank file to use for annotation from NCBI.
COnTORT will request the search term and use that to search NCBI GEO and download the NCBI GEO results.
Note that COnTORT can only download and combine normalized and processed data imported into NCBI GEO.
COnTORT has been tested on Linux (Ubuntu and CentOS), MacOS (>10.13), and Windows 10.
- The GenBank (.gbff) for your organism, downloaded from NCBI.
You are encouraged to create a new directory each time you run this script.
You can install using pip and then run:
pip install contort contort
You can download the git repository and run the original scripts:
git clone https://github.com/GLBRC/contort.git python contort.py
- python 3
- Python modules argparse, Bio, ftplib, functools, GEOparse, os, pandas, re, shutil, sys, subprocess, sys, tkinter, time, urllib
COnTORT_organized_transcriptomic_data.txt is the primary output.
Primary output is a single text file containing the gene annotations on the first five columns and the mean centered expression data present in the remaining columns. The first row contains the headers references the specific GEO IDs for each experiment. Note that annotations no present in the GenBank file are listed with "N/A".
Locus_Tag Old_Locus_Tag Gene_Name Gene_Synonyms Product GSM_ID_1 GSM_ID_2 RSP_0002 N/A spbB N/A H-NS 12.0 4.0 There will be two files: one where the results are mean-centered for each experiment and one where no mean-centering is performed.
Subdirectories are created for all the files and to organize the directory:
- geo - the downloaded GDS, GSE, GSM and GPL directories - GEOannotate_results - the results of running GEOparse to organize the annotation and data - GeneOrf_match_output - the results of matching the GEOparse results to the gene IDs from the GFF - mean_centered_results - the mean centered expression data for each experiment - FTP_files - files used to download the data from GEO via FTP - log_files - all log files from each step as well as other saved files
Outline of steps & commands used in pipeline:
runFindGEOAddresses( GDSfile ):
Parse GEOfile Opens and parses the GDSfile result txt file from the search term provided by the user. Creates new files: - GEO_FTP_Addresses.txt - all GDS, GSE, GSM, GPL addresses in the file - GEO_FTP_directories.txt - GDS, GSE, GSM, GPL directories that will be downloaded
run_is_ftp_dir( ftp_handle, name, guess_by_extension=True ):
QC for FTP Determines if an item listed on the FTP server is a directory or not by looking for a "." in the fourth position. If it has that, it is nearly always a file and not a directory.
run_make_parent_dir( fpath ):
Make directories to match the FTP Creates the directories in the local directory to match the FTP directories
run_download_FTP_file( ftp_handle, name, dest, overwrite ):
Copy the FTP files to the local directory Copy FTP files into the respective directories on the local directory
run_mirror_ftp_dir( ftp_handle, name, overwrite, guess_by_extension ):
Replicate the directories Replicates a direcotry from the FTP server onto the local drive recusively
download_ftp_tree( ftp_handle, path, destination, overwrite=False, guess_by_extension=True ):
Performs the actions to download files from the NCBI FTP Perform the actions Downloads an entire directory tree from an ftp server to the local destination Will NOT overwrite files if present in the local directory
Default FTP Settings for NCBI GEO:
server = 'ftp.ncbi.nlm.nih.gov' user = 'anonymous' password = '' destination = user input sources of files = from the runFindGEOAddresses module
Organize the GEO series files This first finds and copies all soft.gz files for all GSE (series) data in the GEO download from the previous steps. Using GEOparse, the metadata for each gene is collected and concatentated with the normalized data present for each series. The new files are written for downstream steps and the copied soft.gz files are deleted.
gffMatch( GBFF ):
Match the gene annotations from the GenBank file to the organized expression data Using dictionaries created from the GenBank file for the orgainsm, this script will search for matches to the gene annotation in the GenBank file and retain only those data with matches. This will make new files for each GEOquery output with columns representing gene annotations and then the log2 normalized data from the GEO series files. The data are then mean centered and joined together with the gene annotations annotation as the key. All blanks are retained for consistency. This file is written and can be used in Excel or R for further analysis.
cleanUp( cwd ):
Clean up the directory Organize the files into folders for a cleaner directory
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