From a7acdd26be372775b8526dd53574a26b2210b800 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Fri, 12 Jan 2024 09:54:54 -0500 Subject: [PATCH] Update headers --- .../For_Assemblies/assess_transcriptomes.py | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/Utilities/For_Assemblies/assess_transcriptomes.py b/Utilities/For_Assemblies/assess_transcriptomes.py index 410d111..5b96759 100644 --- a/Utilities/For_Assemblies/assess_transcriptomes.py +++ b/Utilities/For_Assemblies/assess_transcriptomes.py @@ -1,17 +1,12 @@ ''' -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 - -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 ''' import os import sys