Some potentially useful scripts.
If you use any of the scripts in this repository please cite it as follows:
Parker, D.J. 2018. Useful_scripts. GitHub repository: https://github.com/DarrenJParker/Useful_scripts/
NOTE: help messages can be displayed for all scripts by specifying -h (i.e. python [name of script] -h) . All scripts written in python3.4 or higher.
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fasta_file_tidier.py | Takes a fasta file, orders sequences by size, and renames them sequentially. Also filters out small contigs if required.
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Kalli_to_edgeR.py | Takes a directory of Kallisto produced directories a single csv file for use in EdgeR (or similar), along with a stat file.
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HTSeq accessory scripts
- Maker_gff_to_HTseq_gff.py | Takes a gff produced by Maker2 and converts it for use in HTseq.
- HTSeq_to_edgeR.py | Takes a directory of read count files from HTseq and produces a single csv file for use in EdgeR (or similar), along with a stat file.
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gff_feature_lengths.py | Gets lengths of features in a gff file, summed by a parent ID.
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gff_name_updater.py | Updates the contig names of gff file made on one fasta file with those in a new fasta file (e.g. a renamed subset of the original file)
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gff_to_topGO.py | extracts GO terms from a gff file for use in TopGO