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Godwin Ani 2024-01-12 09:54:54 -05:00 committed by GitHub
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Utilities/For_Assemblies/assess_transcriptomes.py
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'''
Written March 2023 by Elinor (esterner27@gmail.com) to plot length, coverage and GC of assembled transcripts
This script will iterate through all assembled files (named as 10 digit code _assembledTranscripts) with and gather GC, length and coverage. With that data, it plots R scripts
Input:
Folder called Renamed_assembled_files of previously renamed files (if this is the case, put -r or --renamed in the command line)
#Author, date: Elinor Sterner(esterner27@gmail.com), March 2023. Last updated Nov 27th 2023
#Motivation: To describe transcriptomes.
#Intent: Plot length, coverage and GC of assembled transcripts with stats generated.
#Dependencies: Python3
#Inputs: Folder called Renamed_assembled_files of previously renamed files (if this is the case, put -r or --renamed in the command line)
tsv file of LKH number and new names formatted like this: 10_digit_code\tdescriptor_of_taxon called new_names.tsv
To run:
python assess_transcriptomes.py -input <pathway to directory of spades output>
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
#Outputs: A spreadsheet containing the length, GC, and coverage of each transcript.
#Example: python assess_transcriptomes.py -input <pathway to directory of spades output>
'''
import os
import sys