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v1.7.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,264 @@ | ||
| #!/usr/bin/env python3 | ||
| import argparse | ||
| import os | ||
| import shutil | ||
| import sys | ||
| from argparse import RawTextHelpFormatter | ||
| from pathlib import Path | ||
|
|
||
| from loguru import logger | ||
| from plot import create_single_plot | ||
| from pycirclize.parser import Genbank | ||
| from util import get_version | ||
|
|
||
|
|
||
| def get_input(): | ||
| """gets input for pharokka_plotter.py | ||
| :return: args | ||
| """ | ||
| parser = argparse.ArgumentParser( | ||
| description="pharokka_multiplotter.py: pharokka plotting function for muliple phages", | ||
| formatter_class=RawTextHelpFormatter, | ||
| ) | ||
| parser.add_argument( | ||
| "-g", | ||
| "--genbank", | ||
| action="store", | ||
| required=True, | ||
| help="Input genbank file from Pharokka.", | ||
| ) | ||
| parser.add_argument( | ||
| "-o", | ||
| "--outdir", | ||
| action="store", | ||
| help="Pharokka output directory.", | ||
| required=True, | ||
| ) | ||
| parser.add_argument( | ||
| "-f", "--force", help="Overwrites the output plot file.", action="store_true" | ||
| ) | ||
| parser.add_argument( | ||
| "--label_hypotheticals", | ||
| help="Flag to label hypothetical or unknown proteins. By default these are not labelled.", | ||
| action="store_true", | ||
| ) | ||
| parser.add_argument( | ||
| "--remove_other_features_labels", | ||
| help="Flag to remove labels for tRNA/tmRNA/CRISPRs. By default these are labelled. \nThey will still be plotted in black.", | ||
| action="store_true", | ||
| ) | ||
| parser.add_argument( | ||
| "--title_size", | ||
| action="store", | ||
| default="20", | ||
| help="Controls title size. Must be an integer. Defaults to 20.", | ||
| ) | ||
| parser.add_argument( | ||
| "--label_size", | ||
| action="store", | ||
| default="8", | ||
| help="Controls annotation label size. Must be an integer. Defaults to 8.", | ||
| ) | ||
| parser.add_argument( | ||
| "--interval", | ||
| action="store", | ||
| default="5000", | ||
| help="Axis tick interval. Must be an integer. Must be an integer. Defaults to 5000.", | ||
| ) | ||
| parser.add_argument( | ||
| "--truncate", | ||
| action="store", | ||
| default="20", | ||
| help="Number of characters to include in annoation labels before truncation with ellipsis. \nMust be an integer. Defaults to 20.", | ||
| ) | ||
| parser.add_argument( | ||
| "--dpi", | ||
| action="store", | ||
| default="600", | ||
| help="Resultion (dots per inch). Must be an integer. Defaults to 600.", | ||
| ) | ||
| parser.add_argument( | ||
| "--annotations", | ||
| action="store", | ||
| default="1", | ||
| help="Controls the proporition of annotations labelled. Must be a number between 0 and 1 inclusive. \n0 = no annotations, 0.5 = half of the annotations, 1 = all annotations. \nDefaults to 1. Chosen in order of CDS size.", | ||
| ) | ||
| parser.add_argument( | ||
| "-t", "--plot_title", action="store", default="Phage", help="Plot name." | ||
| ) | ||
| parser.add_argument( | ||
| "--label_ids", | ||
| action="store", | ||
| default="", | ||
| help="Text file with list of CDS IDs (from gff file) that are guaranteed to be labelled.", | ||
| ) | ||
| args = parser.parse_args() | ||
| return args | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| args = get_input() | ||
| # preamble | ||
| logger.add(lambda _: sys.exit(1), level="ERROR") | ||
| logger.info(f"Starting Pharokka v{get_version()}") | ||
| logger.info("Running pharokka_multiplotter.py to plot your phages.") | ||
| logger.info("Command executed: {}", args) | ||
| logger.info("Repository homepage is https://github.com/gbouras13/pharokka") | ||
| logger.info("Written by George Bouras: george.bouras@adelaide.edu.au") | ||
| logger.info("Checking your inputs.") | ||
|
|
||
| try: | ||
| int(args.interval) | ||
| except: | ||
| logger.error( | ||
| f"--interval {args.interval} specified is not an integer. Please check your input and try again." | ||
| ) | ||
|
|
||
| try: | ||
| int(args.label_size) | ||
| except: | ||
| logger.error( | ||
| f"--label_size {args.label_size} specified is not an integer. Please check your input and try again." | ||
| ) | ||
|
|
||
| try: | ||
| int(args.title_size) | ||
| except: | ||
| logger.error( | ||
| f"--title_size {args.title_size} specified is not an integer. Please check your input and try again." | ||
| ) | ||
|
|
||
| try: | ||
| int(args.dpi) | ||
| except: | ||
| logger.error( | ||
| f"--dpi {args.dpi} specified is not an integer. Please check your input and try again." | ||
| ) | ||
|
|
||
| try: | ||
| float(args.annotations) | ||
| except: | ||
| logger.error( | ||
| f"--annotations {args.annotations} specified is not a float. Please check your input and try again." | ||
| ) | ||
|
|
||
| if args.force == True: | ||
| if os.path.exists(args.outdir) == True: | ||
| logger.info(f"Removing {args.outdir} as --force was specified.") | ||
| shutil.rmtree(args.outdir) | ||
| else: | ||
| logger.warning( | ||
| f"--force was specified even though the output plot directory {args.outdir} does not already exist." | ||
| ) | ||
| logger.warning("Continuing") | ||
| else: | ||
| if os.path.exists(args.outdir) == True: | ||
| logger.error( | ||
| f"Output directoey {args.outdir} already exists and force was not specified. Please specify -f or --force to overwrite the output directory." | ||
| ) | ||
|
|
||
| # instantiate outdir | ||
| if Path(args.outdir).exists() is False: | ||
| Path(args.outdir).mkdir(parents=True, exist_ok=True) | ||
|
|
||
| # check label_ids | ||
|
|
||
| # list of all IDs that need to be labelled from file | ||
| label_force_list = [] | ||
|
|
||
| if args.label_ids != "": | ||
| logger.info( | ||
| f"You have specified a file {args.label_ids} containing a list of CDS IDs to force label." | ||
| ) | ||
| # check if it is a file | ||
| if os.path.isfile(args.label_ids) == False: | ||
| logger.error(f"{args.label_ids} was not found.") | ||
| # check if it contains text | ||
| try: | ||
| # Open the file in read mode | ||
| with open(Path(args.label_ids), "r") as file: | ||
| # Read the first character | ||
| first_char = file.read(1) | ||
|
|
||
| # read all the labels | ||
| with open(Path(args.label_ids)) as f: | ||
| ignore_dict = {x.rstrip().split()[0] for x in f} | ||
| # label force list | ||
| label_force_list = list(ignore_dict) | ||
|
|
||
| except FileNotFoundError: | ||
| logger.warning( | ||
| f"{args.label_id} contains no text. No contigs will be ignored" | ||
| ) | ||
|
|
||
| logger.info("All files checked.") | ||
|
|
||
| # single threaded plots | ||
| threads = 1 | ||
|
|
||
| gbk = Genbank(args.genbank) | ||
|
|
||
| # gets all contigs and seqs | ||
| gb_seq_dict = gbk.get_seqid2seq() | ||
|
|
||
| gb_size_dict = gbk.get_seqid2size() | ||
|
|
||
| contig_count = len(gb_seq_dict) | ||
|
|
||
| # gets all features - will get all regardless of type (tRNA etc from pharokka) | ||
| gb_feature_dict = gbk.get_seqid2features() | ||
|
|
||
| # check label_ids | ||
| # list of all IDs that need to be labelled from file | ||
| label_force_list = [] | ||
|
|
||
| label_ids = args.label_ids | ||
|
|
||
| if label_ids != "": | ||
| logger.info( | ||
| f"You have specified a file {label_ids} containing a list of CDS IDs to force label." | ||
| ) | ||
| # check if it is a file | ||
| if Path(label_ids).exists() is False: | ||
| logger.error(f"{label_ids} was not found.") | ||
| # check if it contains text | ||
| try: | ||
| # Open the file in read mode | ||
| with open(Path(label_ids), "r") as file: | ||
| # Read the first character | ||
| # will error if file is empty | ||
| first_char = file.read(1) | ||
|
|
||
| # read all the labels | ||
| with open(Path(label_ids)) as f: | ||
| ignore_dict = {x.rstrip().split()[0] for x in f} | ||
| # label force list | ||
| label_force_list = list(ignore_dict) | ||
|
|
||
| except FileNotFoundError: | ||
| logger.warning(f"{label_ids} contains no text. No contigs will be ignored") | ||
|
|
||
| # if there is 1 contig, then all the parameters will apply | ||
|
|
||
| for contig_id, contig_sequence in gb_seq_dict.items(): | ||
| logger.info(f"Plotting {contig_id}") | ||
|
|
||
| create_single_plot( | ||
| contig_id, | ||
| contig_sequence, | ||
| contig_count, | ||
| gb_size_dict, | ||
| gb_feature_dict, | ||
| gbk, | ||
| int(args.interval), | ||
| float(args.annotations), | ||
| int(args.title_size), | ||
| args.plot_title, | ||
| int(args.truncate), | ||
| args.outdir, | ||
| int(args.dpi), | ||
| float(args.label_size), | ||
| args.label_hypotheticals, | ||
| args.remove_other_features_labels, | ||
| label_force_list, | ||
| ) |
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