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d59c79b149
These are PTL1 scripts from ACL on Feb8. NOTE: These are WITHOUT databases..... these are at (Katzlab only) link here https://drive.google.com/drive/folders/10n1GdTJqEOBg1nGA1hjxNHgaNZgmbwb5
217 lines
8.5 KiB
Python
217 lines
8.5 KiB
Python
#!/usr/bin/env python3.5
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##__Updated__: 19_09_2017
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##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
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##__Usage__: python 1g_RenameCDS.py --help
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from Bio import SeqIO
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from Bio.SeqUtils import GC
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import argparse, os, sys, time
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from argparse import RawTextHelpFormatter,SUPPRESS
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#----------------------------- Colors For Print Statements ------------------------------#
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class color:
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PURPLE = '\033[95m'
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CYAN = '\033[96m'
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DARKCYAN = '\033[36m'
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ORANGE = '\033[38;5;214m'
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BLUE = '\033[94m'
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GREEN = '\033[92m'
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YELLOW = '\033[93m'
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RED = '\033[91m'
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BOLD = '\033[1m'
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UNDERLINE = '\033[4m'
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END = '\033[0m'
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#------------------------------- Main Functions of Script --------------------------------#
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###########################################################################################
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###--------------------- Parses and Checks Command-Line Arguments ----------------------###
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###########################################################################################
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def check_args():
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parser = argparse.ArgumentParser(description=
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color.BOLD + '\n\nThis script is intended to extract '+color.RED+'Annotated '+\
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color.PURPLE+'ORFS\n'+color.END+color.BOLD+'from a provided Genbank formatted file.'\
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+usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter)
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required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END)
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required_arg_group.add_argument('--input_file','-in', action='store',
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help=color.BOLD+color.GREEN+' Fasta file with CDSs\n'+color.END)
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required_arg_group.add_argument('--output_dir','-o', action='store',
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help=color.BOLD+color.GREEN+' Output directory\n'+color.END)
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optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
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optional_arg_group.add_argument('--source','-s', action='store', default='GenBank',
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help=color.BOLD+color.GREEN+' Data Source of CDSs (default = "GenBank")\n'+color.END)
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optional_arg_group.add_argument('--list_source','-lsrc', action='store_true',
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help=color.BOLD+color.GREEN+' Lists supported data sources\n'+color.END)
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optional_arg_group.add_argument('-author', action='store_true',
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help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END)
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if len(sys.argv[1:]) == 0:
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print (parser.description)
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print ('\n')
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sys.exit()
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args = parser.parse_args()
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more_info = return_more_info(args)
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if more_info != None:
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print (parser.description)
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print (more_info)
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sys.exit()
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args.folder = args.output_dir + '/' + args.input_file.split('/')[-1][:10]
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return args
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###########################################################################################
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###------------------------------- Script Usage Message --------------------------------###
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###########################################################################################
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def usage_msg():
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return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 1g_RenameCDS.py'\
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' --input_file ../Stentor_coeruleus.WGS.CDS.Prep/Stentor_coeruleus.WGS.CDS.fasta --source'\
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' GenBank'+color.END)
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##########################################################################################
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###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------###
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##########################################################################################
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def return_more_info(args):
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acceptable_sources = ['in-house', 'in-lab', 'GenBank', 'gb', 'NCBI']
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author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\
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' maurerax@gmail.com\n\n'+color.END)
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if args.author == True:
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return author
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if args.list_source == True:
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print (color.BOLD+color.RED+'\nThese are the currently supported data sources.\n'+color.END)
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print (color.BOLD+color.ORANGE+'\n'.join(acceptable_sources)+'\n\n'+color.END)
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sys.exit()
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if args.source.lower() not in [i.lower() for i in acceptable_sources]:
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print (color.BOLD+color.RED+'\nUnsupported source was provided.\n\nEnsure that '\
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'you are providing a valid data source (see below).\n'+color.END)
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print (color.BOLD+color.ORANGE+'\n'.join(acceptable_sources)+'\n'+color.END)
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sys.exit()
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if args.input_file != None:
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if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])):
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
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'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
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' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
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sys.exit()
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###########################################################################################
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###--------------------------- Does the Inital Folder Prep -----------------------------###
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###########################################################################################
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def prep_folders(args):
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if os.path.isdir(args.folder) != True:
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os.system('mkdir '+args.folder)
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os.system('cp '+args.input_file+' '+args.folder)
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args.input_file = args.folder+'/'+args.input_file.split('/')[-1]
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if os.path.isdir(args.folder+'/Original') != True:
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os.system('mkdir '+args.folder+'/Original')
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os.system('cp '+args.input_file+' '+args.folder+'/Original/')
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###########################################################################################
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###------------- Renames Protein-Coding CDS Sequences to Standard Format ---------------###
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###########################################################################################
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def renamed_GenomeCDS(args):
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print (color.BOLD+'\n\nPrepping to rename '+color.GREEN+args.input_file.split('/')[-1]+\
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color.END+color.BOLD+"'s CDS sequences"+color.END)
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inFasta = sorted((i for i in SeqIO.parse(args.input_file,'fasta')),key=lambda seq_rec: -len(seq_rec.seq))
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renamed_seqs = []
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seq_code_dict = {}
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count = 1
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for seq_rec in inFasta:
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seq_code_dict.setdefault(seq_rec.description,[]).append('Contig_'+str(count)+'_Len'+str(len(seq_rec.seq)))
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seq_code_dict[seq_rec.description].append(str(seq_rec.seq).upper())
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renamed_seqs.append('>Contig_' + str(count) + '_Len' + str(len(seq_rec.seq)) + '\n' + str(seq_rec.seq).upper())
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count += 1
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## keeps only CDSs that are greater than 30 bp (10 AA --> This is a cut-off in the
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## phylogenomic pipeline too!)
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renamed_seqs = [i for i in renamed_seqs if len(i.split('\n')[-1]) > 30]
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print (color.BOLD+'\n\nFor '+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+\
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color.BOLD+', '+color.RED+str(len(renamed_seqs))+' CDS sequences\n'+color.END+color.BOLD+
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'were renamed while preserving the '+color.ORANGE+args.source+color.END+color.BOLD+' formatting'\
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+color.END+'\n')
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with open(args.input_file.replace('.fasta','.Prepped.fasta'),'w+') as w:
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w.write('\n'.join(renamed_seqs))
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with open(args.input_file.split('/')[-1].replace('.fasta','.SeqCodes.tsv'),'w+') as w:
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w.write('Original Name\tNew Name\tSeq Length\t Seq GC\n')
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for k, v in seq_code_dict.items():
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w.write(k+'\t'+v[0]+'\t'+str(len(v[1]))+'\t'+str(GC(v[1]))+'\n')
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###########################################################################################
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###--------------------- Cleans up the Folder and Moves Final Files --------------------###
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###########################################################################################
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def clean_up(args):
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# os.system('rm '+args.input_file)
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os.system('mv ' + args.input_file.split('/')[-1].replace('.fasta','.SeqCodes.tsv') + ' ' + args.folder + '/Original/')
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os.system('mv ' + args.input_file + ' ' + args.folder + '/Original/')
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###########################################################################################
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###-------------------------------- Next Script Message --------------------------------###
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###########################################################################################
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def next_script(args):
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print (color.BOLD+'\nLook for '+color.DARKCYAN+args.input_file.split('/')[-1].replace('.fasta','.Renamed.fasta')\
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+'.fasta'+color.END+color.BOLD+'\nin the '+color.ORANGE+args.folder.split('/')[-1]+\
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' Folder\n\n'+color.END+color.BOLD)
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print ('Next Script(s) are:\n\n'+color.PURPLE+'2g_GCodeEval.py'+color.END+color.BOLD\
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+' (if Genetic Code is '+color.RED+'Unknown'+color.END+color.BOLD+')\n\nOtherwise:\n\n'+\
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color.PURPLE+'3g_GCodeTranslate.py\n\n'+color.END)
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##########################################################################################
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###----------------------------- Calls on Above Functions -----------------------------###
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##########################################################################################
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def main():
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args = check_args()
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prep_folders(args)
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renamed_GenomeCDS(args)
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clean_up(args)
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next_script(args)
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main() |