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Update assess_transcriptomes.py

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ElinorSterner 2023-04-05 15:53:14 -04:00 committed by GitHub
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Utilities/For_Assemblies/assess_transcriptomes.py
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@ -23,7 +23,7 @@ from Bio import SeqIO
def script_help():
print('\nThis script grabs and plots GC, length and coverage of transcriptomes. \n\nInput:\ntxt file of tab separated LKH number, ten digit code and taxon info (taxonomy, lifestage, etc).\nAND\nfolder of the folders output by spades named with LKH number \n(LKH999 or WTALKH999)\nOR\ndirectory of renamed assemblies in this format: ten_digit_code_assembledTranscripts.fasta\n\nOutput is multiple R plots, faceted by taxon and a csv file of data. \n\nIt plots GC by length, and distributions of coverage, length and GC.\n\n To run: \n\n\tpython assess_transcriptomes.py <pathway to directory of spades output>\n\nOptional parameters:\n\n-r or --renamed if your assemblies are already renamed to this format: ten_digit_code_assembledTranscript.fasta\n\n-h or --help for this message\n\n')
print('\nThis script grabs and plots GC, length and coverage of transcriptomes. \n\nInput:\ntxt file of tab separated LKH number, ten digit code and taxon info (taxonomy, lifestage, etc).\nAND\nfolder of the folders output by spades named with LKH number \n(LKH999 or WTALKH999)\nOR\ndirectory of renamed assemblies in this format: ten_digit_code_assembledTranscripts.fasta\n\nOutput is multiple R plots, faceted by taxon and a csv file of data. \n\nIt plots GC by length, and distributions of coverage, length and GC.\n\n To run: \n\n\tpython assess_transcriptomes.py <pathway to directory of spades output>\n\n-r or --renamed if your assemblies are already renamed to this format: ten_digit_code_assembledTranscript.fasta/nand this command if they are not yet named: --raw <path to directory of spades output folders>\n\n-h or --help for this message\n\n')
def get_args():
#this parses user arguments. Checks if the files are renamed already or not (--renamed or --raw), and gets the directory of those files.