You can find the AthaMap data sets on this wiki page. Data sets were obtained from the original AthaMap website.
This repository contains scripts associated with the AthaMap database and related transcription factor analyses. Most scripts are included for documentation purposes and might not be helpful beyond the described purpose.
This script takes different PWMs that belong to the same transcription factor and calculates an average value for individual positions. The motifs are reduced to the smalles suppported size to enable a sensitive analysis.
Usage
python3 PWM_merger.py --in <FOLDER> --info <FILE> --out <FOLDER>
Mandatory:
--in STR Input folder with PWM files
--info STR Info table file
--out STR Output folder for PWM files
--in specifies the input folder that contains PWM files. Text files (.txt) in this folder will be processed if they are mentioned in the info table (--info).
--info specifies an information input table that connects different PWMs of the same transcription factor. The transcritpion factor ID is given in the first column. The PWM ID is given in the fourth column.
--out specifies the output folder. This folder will be created if it does not exist already. Output files will be placed in this folder.
This script screens a given genome sequence for all occurrences of TF binding sites based on the provided PWM.
Usage
python3 PWM_screen.py --pwm <FILE> --seq <FILE> --out <FILE>
Mandatory:
--pwm STR Input PWM file
--seq STR Input FASTA file
--out STR Output file
--pwm specifies the PWM input file (.txt) that provides the information for the identification of TF binding sites.
--seq specifies the FASTA input file that contains the sequences that will be screened for TF binding sites.
--out specifies the output file (.txt) that lists all identified TF binding sites.
This script compares the co-expression of TFs with their target genes against co-expression with a random set of genes.
Usage1
python3 cis2coexp.py --cis <FILE> --exp <FILE> --ref <STR> --out <FILE>
Usage2
python3 cis2coexp.py --cisdir <FOLDER> --exp <FILE> --reffile <FILE> --out <FILE>
Mandatory1:
--cis STR Input target gene file
--exp STR Input expression file
--ref STR AGI of TF
--out STR Output file
Mandatory2:
--cisdir STR Folder containing input target gene files
--exp STR Input expression file
--reffile STR File containing AGIs of TFs
--out STR Output file
Optional:
--cutoff FLOAT Mininmal score cutoff
--cis specifies the target gene input file.
--exp specifies the gene expression input file.
--ref specifies the Arabidopsis Gene Identifier (AGI) of the analzyed TF.
--out specifies the output file.
--cisdir specifies a folder containing the target gene input files.
--reffile specifies a file containing the AGIs of the analyzed TFs.
--cutoff specifies the minimal score that should be considered.
This script allows the transfer of cis-regulatory elements annotated in AthaMap based on the Arabidopsis thaliana genome sequence TAIR8 to TAIR10.
Usage
python3 pos_transfer.py --in <FILE> --tair10 <FILE> --tair8 <FILE> --out <FILE>
Mandatory:
--in STR Input cis-regulatory element file
--tair10 STR Input TAIR10 FASTA file
--tair8 STR Input TAIR8 FASTA file
--out STR Output cis-regulatory element file
--in specifies the input file that contains information about the positions of cis-regulatory elements based on TAIR8. This file can be downloaded from AthaMap.
--tair10 specifies the Arabidopsis thaliana genome sequence TAIR10 FASTA file.
--tair8 specifies the Arabidopsis thaliana genome sequence TAIR8 FASTA file.
--out specifies the output file that contains information about the positions of cis-regulatory elements based on TAIR10.
This repository.