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@ -53,20 +53,18 @@ Input a spreadsheet with ten digit codes in the first column and the genus and s
### assess_transcriptomes.py: ### assess_transcriptomes.py:
Written March 2023 by Elinor (esterner27@gmail.com) to plot length, coverage and GC of assembled transcripts Written March 2023 by Elinor (esterner27@gmail.com) to plot length, coverage and GC of assembled transcripts
**Purpose** Rename rnaSpades output to new names in the txt file, then iterate through them all and gather GC, length and coverage. With that data, it plots R scripts **Purpose** This script will iterate through all assembled files (named as 10 digit code plus assembledTranscripts) with and gather GC, length and coverage. With that data, it plots R scripts
**Input** **Input**
Directory of directories output by rnaSpades OR folder called Renamed_assembled_files of previously renamed files (if this is the case, put `-r` or --renamed in the command line) folder of renamed assemblies (if this is the case, put `-i` or --input in the command line)
txt file of LKH number and new names formatted like this: LKHxxx\tLKHxxx-10_digit_code\tdescriptor_of_taxon tsv file of ten digit code and taxon info (lifestage, species, etc) formatted like this: 10_digit_code\tdescriptor_of_taxon
R script plot_assemblies.R, which is called from within this python script R script plot_assemblies.R, which is called from within this python script
**Usage** **Usage**
To run if your rnaSpades output is **not** renamed yet: To run:
>`python assess_transcriptomes.py --raw <pathway to directory of spades output>` >`python assess_transcriptomes.py --input <pathway to directory of renamed assemblies>`
To run if your files are already renamed:
>`python assess_transcriptomes.py --renamed <pathway to directory of renamed assemblies>`
**Output** csv file of length, GC, coverage of each transcript, and multiple R plots, faceted by taxon and a csv file of data. It plots GC by length, and distributions of coverage, length and GC content across the whole transcript **Output** csv file of length, GC, coverage of each transcript, and multiple R plots, faceted by taxon and a csv file of data. It plots GC by length, and distributions of coverage, length and GC content across the whole transcript