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127 lines
4.5 KiB
Python
127 lines
4.5 KiB
Python
'''
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#Author, date: Elinor Sterner(esterner27@gmail.com), March 2023. Last updated Nov 27th 2023
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#Motivation: To describe transcriptomes.
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#Intent: Plot length, coverage and GC of assembled transcripts with stats generated.
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#Dependencies: Python3
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#Inputs: Folder called Renamed_assembled_files of previously renamed files (if this is the case, put -r or --renamed in the command line)
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tsv file of LKH number and new names formatted like this: 10_digit_code\tdescriptor_of_taxon called new_names.tsv
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#Outputs: A spreadsheet containing the length, GC, and coverage of each transcript.
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#Example: python assess_transcriptomes.py -input <pathway to directory of spades output>
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'''
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import os
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import sys
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from pathlib import Path
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import sys
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from Bio.SeqUtils import GC
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from Bio import SeqIO
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def script_help():
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print('\nThis script grabs and plots GC, length and coverage of transcriptomes. \n\nInput:\ntsv file of tab separated ten digit code and taxon info (taxonomy, lifestage, etc).\nAND\n\ndirectory of assemblies renamed 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 -i <pathway to directory of assemblies>\n\nRun -h or --help for this message\n\n')
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def get_args():
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#this parses user arguments. Checks if the files are renamed already or not (--renamed or --raw), and gets the directory of those files.
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if('--help' in sys.argv or '-h' in sys.argv):#check for help function in command line
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script_help()
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exit()
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if ('--input'in sys.argv or '-i' in sys.argv):#check for renamed parameter
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renamed = True
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try:
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if('--input' in sys.argv):
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input_dir = sys.argv[sys.argv.index('--input') + 1]
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else:
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input_dir = sys.argv[sys.argv.index('-i') + 1]
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except IndexError:
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print('\nSomething went wrong went parsing the arguments. Did you input a directory of assemblies?\n')
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make_dirs(input_dir)
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def make_dirs(input_dir):
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Path(f'plots').mkdir(parents=True, exist_ok=True)#makes output folder for r plots
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assess_transcriptomes(input_dir)#skip renaming funtion if theyre already renamed
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def assess_transcriptomes(input_dir):
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#iterate through renamed fasta files
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for file in os.listdir(input_dir):
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if file.endswith('fasta'):
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print(f'gathering data from {file}..\n')
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data = []#initiate list of data per LKH
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records = list(SeqIO.parse(f'{input_dir}/{file}', 'fasta'))#parse the fasta files
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taxon_info = get_taxon_info(file)#send to get_taxon_info function
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#parse output from that function
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ten_digit_code = taxon_info[0]
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taxon = taxon_info[1]
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# extract all data for each transcript
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for record in records:
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gc = GC(record.seq)
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length = len(record.seq)
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iden = record.id
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cov = record.id.split('_')[5]
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transcript_data = f'{iden}, {length}, {gc}, {cov}, {ten_digit_code}, {taxon}'#list of data per transcriptome
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data.append(transcript_data)#data for each LKH
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all_data.update({file.split('_assembledTranscripts')[0]: data})#make dict of ten digit code: all information
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write_to_file()
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def get_taxon_info(file):#parse the info in the new_names.tsv file to get info on the taxon
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with open('new_names.tsv', 'r') as o:
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cell_info = o.readlines()
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for line in cell_info:
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if '_'.join(file.split('_')[0:3]) in line:
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ten_digit_code = line.split('\t')[0]
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taxon = line.split('\t')[1]
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try:
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return ten_digit_code, taxon
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except UnboundLocalError:
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print(f'no taxon information in new_names.tsv for {file}')
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print('done getting taxon info from new_names.tsv')
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def write_to_file():
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with open('assembly_assessment.csv', 'w') as o:#create output csv
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print('writing data to assembly_assessment.csv\n')
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o.write('seqID, length, GC, cov, ten_digit_code, taxon_info\n')#write header
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for lkh, data in all_data.items():
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for transcript in data:
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o.write(f'{transcript.strip()}\n')#write each line
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plot_assessment()
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def plot_assessment():
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print('Plotting your data\n')
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os.system('Rscript plot_assemblies.R')
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for file in os.listdir():
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if file.endswith('.png') or file.endswith('.pdf'):
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os.system(f'mv {file} plots/{file}')
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print('\n\n\n\nDone! All your plots are saved to the folder called plots\n\n')
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if __name__ == '__main__':
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all_data = {}
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try:
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f = open("new_names.tsv")
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except FileNotFoundError:
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print('\n\n Did you include a tsv file of your cells? It should be called new_names.tsv and formatted like this: 10_digit_code\tdescriptor_of_taxon\n\n')
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exit()
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else:
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get_args()
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