mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 07:10:25 +08:00
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
374 lines
19 KiB
Python
374 lines
19 KiB
Python
#!/usr/bin/env python3.5
|
|
|
|
##__Updated__: 20_09_2017
|
|
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
|
|
##__Usage__: python 5g_FinalizeName.py --help
|
|
|
|
##################################################################################################
|
|
## This script is intended to rename the outputs of the FilterPartials script ##
|
|
## to a given 10-character that is used in the Katz lab Phylogenomic Tree building methods ##
|
|
## ##
|
|
## Prior to running this script, ensure the following: ##
|
|
## ##
|
|
## 1. You have assembled your transcriptome and COPIED the 'assembly' file ##
|
|
## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ##
|
|
## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ##
|
|
## 3. Removed SSU/LSU sequences from your Fasta File ##
|
|
## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ##
|
|
## 5. Classified the Non-Strongly Prokaryotic sequences into OGs ##
|
|
## 6. You either know (or have inferred) the genetic code of the organism ##
|
|
## 7. You have translated the sequences and checked for the data in the RemovePartials folder ##
|
|
## 8. Partial sequences have been removed from the transcriptomic data sets ##
|
|
## ##
|
|
## COMMAND Example Below ##
|
|
## Extra Notes at Bottom of Script ##
|
|
## ##
|
|
## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
|
|
## ##
|
|
## Next Script(s) to Run: ##
|
|
## NONE! You're FINISHED! :D ##
|
|
## ##
|
|
##################################################################################################
|
|
|
|
import argparse, os, sys
|
|
from argparse import RawTextHelpFormatter,SUPPRESS
|
|
|
|
#----------------------- Solely to Make Print Statements Colorful -----------------------#
|
|
|
|
class color:
|
|
PURPLE = '\033[95m'
|
|
CYAN = '\033[96m'
|
|
DARKCYAN = '\033[36m'
|
|
ORANGE = '\033[38;5;214m'
|
|
BLUE = '\033[94m'
|
|
GREEN = '\033[92m'
|
|
YELLOW = '\033[93m'
|
|
RED = '\033[91m'
|
|
BOLD = '\033[1m'
|
|
UNDERLINE = '\033[4m'
|
|
END = '\033[0m'
|
|
|
|
|
|
#------------------------------- Main Functions of Script --------------------------------#
|
|
|
|
###########################################################################################
|
|
###--------------------- Parses and Checks Command-Line Arguments ----------------------###
|
|
###########################################################################################
|
|
|
|
def check_args():
|
|
|
|
parser = argparse.ArgumentParser(description=
|
|
color.BOLD + '\n\nThis script is intended to '+color.RED+'Rename '+color.END\
|
|
+color.BOLD+'the core set of '+color.PURPLE+'ORFS\n'+color.END+color.BOLD+'with a valid '\
|
|
+color.RED+'10-character code'+color.END+color.BOLD+' for use in the KatzLab\nPhylogenomic Pipeline'\
|
|
+usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter)
|
|
|
|
required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END)
|
|
|
|
required_arg_group.add_argument('--input_file','-in', action='store',
|
|
help=color.BOLD+color.GREEN+' One of the Fasta files that is to be renamed\n'+color.END)
|
|
required_arg_group.add_argument('--name','-n', action='store',
|
|
help=color.BOLD+color.GREEN+' A valid 10-Character code for updating the data\n'+color.END)
|
|
|
|
|
|
optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
|
|
|
|
optional_arg_group.add_argument('-author', action='store_true',
|
|
help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END)
|
|
|
|
if len(sys.argv[1:]) == 0:
|
|
print (parser.description)
|
|
print ('\n')
|
|
sys.exit()
|
|
|
|
args = parser.parse_args()
|
|
|
|
quit_eval = return_more_info(args)
|
|
if quit_eval > 0:
|
|
print ('\n')
|
|
sys.exit()
|
|
|
|
args.all_output_folder = '/'.join(args.input_file.split('/')[:-3])
|
|
|
|
args.r2g_aa = args.all_output_folder + '/ReadyToGo/ReadyToGo_AA/'
|
|
args.r2g_ntd = args.all_output_folder + '/ReadyToGo/ReadyToGo_NTD/'
|
|
args.r2g_tsv = args.all_output_folder + '/ReadyToGo/ReadyToGo_TSV/'
|
|
args.r2g_xml = args.all_output_folder + '/ReadyToGo/ReadyToGo_XML/'
|
|
|
|
args.xml_out = args.input_AA.split('/')[-1]+'_1e-10keepall_BlastOutall.oneHit'
|
|
|
|
check_code(args)
|
|
|
|
return args
|
|
|
|
|
|
###########################################################################################
|
|
###------------------------------- Script Usage Message --------------------------------###
|
|
###########################################################################################
|
|
|
|
def usage_msg():
|
|
return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 5g_FinalizeName.py'\
|
|
' --input_file ../Stentor_coeruleus.WGS.CDS.Prep/Stentor_coeruleus.WGS.CDS.Renamed.Universal.AA.fasta'\
|
|
' --name Sr_ci_Scer'+color.END)
|
|
|
|
|
|
##########################################################################################
|
|
###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------###
|
|
##########################################################################################
|
|
|
|
def return_more_info(args):
|
|
|
|
valid_args = 0
|
|
|
|
author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\
|
|
' maurerax@gmail.com\n\n'+color.END)
|
|
|
|
if args.author == True:
|
|
print (author)
|
|
valid_args += 1
|
|
|
|
if args.input_file.endswith('AA.fasta'):
|
|
args.input_NTD = args.input_file.replace('AA.fasta','NTD.fasta')
|
|
args.input_AA = args.input_file
|
|
args.input_TSV = args.input_file.replace('.AA.fasta','_allOGCleanresults.tsv')
|
|
|
|
elif args.input_file.endswith('NTD.fasta'):
|
|
args.input_NTD = args.input_file
|
|
args.input_AA = args.input_file.replace('NTD.fasta','AA.fasta')
|
|
args.input_TSV = args.input_file.replace('.NTD.fasta','_allOGCleanresults.tsv')
|
|
|
|
if os.path.isfile(args.input_NTD) != True:
|
|
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Nucleotide '\
|
|
'Fasta file ('+color.DARKCYAN+args.input_NTD.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
|
|
' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
|
|
valid_args += 1
|
|
|
|
if os.path.isfile(args.input_AA) != True:
|
|
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Protein '\
|
|
'Fasta file ('+color.DARKCYAN+args.input_AA.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
|
|
' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
|
|
valid_args += 1
|
|
|
|
if os.path.isfile(args.input_TSV) != True:
|
|
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Nucleotide '\
|
|
'Fasta file ('+color.DARKCYAN+args.input_TSV.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
|
|
' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
|
|
valid_args += 1
|
|
|
|
return valid_args
|
|
|
|
###########################################################################################
|
|
###-------------------- Double Checks Format for 10-Character Code ---------------------###
|
|
###########################################################################################
|
|
|
|
def check_code(args):
|
|
|
|
check_name = args.name.split('_')
|
|
|
|
if len(args.name) != 10:
|
|
print (color.BOLD+'\n\nNew Species Prefix is not 10 characters long\n\n')
|
|
print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\
|
|
'Am_ar_Ehis\n\n'+color.END)
|
|
sys.exit()
|
|
|
|
elif args.name.count('_') != 2:
|
|
print (color.BOLD+'\n\nCheck the format of your Species Prefix!\n\n')
|
|
print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\
|
|
'Am_ar_Ehis\n\n'+color.END)
|
|
sys.exit()
|
|
|
|
if len(check_name[0]) == 2 and len(check_name[1]) == 2 and len(check_name[2]) == 4:
|
|
print (color.BOLD+"\n\nRenaming "+color.ORANGE+args.input_file.split('/')[-1]\
|
|
.split('_Filtered')[0]+color.END+color.BOLD+"'s files\nusing the following 10-character "\
|
|
"code: "+color.CYAN+args.name+color.END+'\n')
|
|
|
|
else:
|
|
print (color.BOLD+'\n\nCheck the format of your Species Prefix!\n\n')
|
|
print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\
|
|
'Am_ar_Ehis\n\n'+color.END)
|
|
sys.exit()
|
|
|
|
|
|
##########################################################################################
|
|
###------------------------- Creates Folders For Storing Data -------------------------###
|
|
##########################################################################################
|
|
|
|
def prep_folders(args):
|
|
|
|
if os.path.isdir(args.all_output_folder + '/ReadyToGo/') != True:
|
|
os.system('mkdir ' + args.all_output_folder + '/ReadyToGo')
|
|
|
|
if os.path.isdir(args.all_output_folder + '/ReadyToGo/ReadyToGo_NTD/') != True:
|
|
os.system('mkdir '+args.r2g_ntd)
|
|
if os.path.isdir(args.all_output_folder + '/ReadyToGo/ReadyToGo_AA/') != True:
|
|
os.system('mkdir '+args.r2g_aa)
|
|
if os.path.isdir(args.all_output_folder + '/ReadyToGo/ReadyToGo_TSV/') != True:
|
|
os.system('mkdir '+args.r2g_tsv)
|
|
if os.path.isdir(args.all_output_folder + '/ReadyToGo/ReadyToGo_XML/') != True:
|
|
os.system('mkdir '+args.r2g_xml)
|
|
|
|
|
|
###########################################################################################
|
|
###----------- Renames the NTD and AA CDSs with the Given 10-Character Code ------------###
|
|
###########################################################################################
|
|
|
|
def rename_paralogs(args):
|
|
|
|
home_folder = '/'.join(args.input_AA.split('/')[:-2]) + '/'
|
|
|
|
print('HOME ' + home_folder)
|
|
|
|
print (color.BOLD+'\nRenaming Translated (Protein) '+color.PURPLE+'ORFs\n'+color.END)
|
|
renamed_Final_Prots = open(args.input_AA).read().replace('>','>'+args.name+'_')
|
|
|
|
print (color.BOLD+'\nRenaming Nucleotide '+color.PURPLE+'ORFs\n'+color.END)
|
|
renamed_Final_Nucs = open(args.input_NTD).read().replace('>','>'+args.name+'_')
|
|
|
|
|
|
print (color.BOLD+'\nUpdating CDS Names in the Spreadsheet'+color.END)
|
|
if '\n\n' in open(args.input_TSV).read():
|
|
renamed_Final_tsv = open(args.input_TSV).read().rstrip('\n')\
|
|
.replace('\n\n','\n'+args.name+'_')
|
|
else:
|
|
renamed_Final_tsv = open(args.input_TSV).read().rstrip('\n')\
|
|
.replace('\n','\n'+args.name+'_')
|
|
|
|
with open(home_folder + args.input_AA.split('/')[-1],'w+') as w:
|
|
w.write(renamed_Final_Prots)
|
|
|
|
with open(home_folder + args.input_NTD.split('/')[-1],'w+') as x:
|
|
x.write(renamed_Final_Nucs)
|
|
|
|
with open(home_folder + args.input_TSV.split('/')[-1],'w+') as y:
|
|
y.write(renamed_Final_tsv)
|
|
|
|
|
|
###########################################################################################
|
|
###--------------------------------- Header/Tail Lines ---------------------------------###
|
|
###########################################################################################
|
|
|
|
def header_tail():
|
|
header = '<?xml version="1.0"?>\n<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n'\
|
|
'<BlastOutput>\n <BlastOutput_program>blastp</BlastOutput_program>\n <BlastOutput_version>BLASTP 2.2.29+</BlastOutput_version>\n'\
|
|
' <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>\n'\
|
|
' <BlastOutput_db>../OGBlastDB/renamed_aa_seqs_OrthoMCL-5_12653.fasta</BlastOutput_db>\n <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n'
|
|
|
|
tail = '</BlastOutput_iterations>\n</BlastOutput>'
|
|
return header, tail
|
|
|
|
|
|
###########################################################################################
|
|
###------------------------------- TSV to XML Conversion -------------------------------###
|
|
###########################################################################################
|
|
|
|
def convert_TSV_data(args):
|
|
|
|
home_folder = '/'.join(args.input_AA.split('/')[:-2])
|
|
|
|
TSVforConvert = home_folder+ '/' + args.input_TSV.split('/')[-1]
|
|
|
|
inTSV = [line.rstrip('\n') for line in open(TSVforConvert).readlines() if line != '\n']
|
|
|
|
iterations = []
|
|
|
|
for n in range(len(inTSV)):
|
|
if n == 0:
|
|
iterations.append(' <BlastOutput_query-def>'+inTSV[n].split('\t')[0]+'</BlastOutput_query-def>\n <BlastOutput_query-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</BlastOutput_query-len>\n'\
|
|
' <BlastOutput_param>\n <Parameters>\n <Parameters_matrix>BLOSUM62</Parameters_matrix>\n <Parameters_expect>1e-10</Parameters_expect>\n'\
|
|
' <Parameters_gap-open>11</Parameters_gap-open>\n <Parameters_gap-extend>1</Parameters_gap-extend>\n <Parameters_filter>F</Parameters_filter>\n'\
|
|
' </Parameters>\n </BlastOutput_param>\n<BlastOutput_iterations>\n<Iteration>\n <Iteration_iter-num>1</Iteration_iter-num>\n <Iteration_query-ID>Query_1</Iteration_query-ID>\n'\
|
|
' <Iteration_query-def>'+inTSV[n].split('\t')[0]+'</Iteration_query-def>\n <Iteration_query-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Iteration_query-len>\n'\
|
|
'<Iteration_hits>\n<Hit>\n <Hit_num>1</Hit_num>\n <Hit_id>Fake_Entry</Hit_id>\n <Hit_def>'+inTSV[n].split('\t')[1]+'</Hit_def>\n <Hit_accession>Fake_Accession</Hit_accession>\n'\
|
|
' <Hit_len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Hit_len>\n <Hit_hsps>\n <Hsp>\n <Hsp_num>1</Hsp_num>\n <Hsp_bit-score>1234</Hsp_bit-score>\n'\
|
|
' <Hsp_score>'+inTSV[n].split('\t')[-1]+'</Hsp_score>\n <Hsp_evalue>'+inTSV[n].split('\t')[-2]+'</Hsp_evalue>\n <Hsp_query-from>'+inTSV[n].split('\t')[-4]+'</Hsp_query-from>\n'\
|
|
' <Hsp_query-to>'+inTSV[n].split('\t')[-3]+'</Hsp_query-to>\n <Hsp_hit-from>'+inTSV[n].split('\t')[-4]+'</Hsp_hit-from>\n <Hsp_hit-to>'+inTSV[n].split('\t')[-3]+'</Hsp_hit-to>\n'\
|
|
' <Hsp_query-frame>0</Hsp_query-frame>\n <Hsp_hit-frame>0</Hsp_hit-frame>\n <Hsp_identity>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_identity>\n'\
|
|
' <Hsp_positive>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_positive>\n <Hsp_gaps>0</Hsp_gaps>\n <Hsp_align-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_align-len>\n'\
|
|
' <Hsp_qseq></Hsp_qseq>\n <Hsp_hseq></Hsp_hseq>\n <Hsp_midline></Hsp_midline>\n </Hsp>\n </Hit_hsps>\n</Hit>\n'\
|
|
'\n</Iteration_hits>\n <Iteration_stat>\n <Statistics>\n <Statistics_db-num>379660</Statistics_db-num>\n <Statistics_db-len>197499634</Statistics_db-len>\n'\
|
|
' <Statistics_hsp-len>123</Statistics_hsp-len>\n <Statistics_eff-space>184705217500</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n'\
|
|
' <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n </Statistics>\n </Iteration_stat>\n</Iteration>\n')
|
|
else:
|
|
iterations.append('<Iteration>\n <Iteration_iter-num>'+str(n+1)+'</Iteration_iter-num>\n <Iteration_query-ID>Query_'+str(n+1)+'</Iteration_query-ID>\n'\
|
|
' <Iteration_query-def>'+inTSV[n].split('\t')[0]+'</Iteration_query-def>\n <Iteration_query-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Iteration_query-len>\n'\
|
|
'<Iteration_hits>\n<Hit>\n <Hit_num>1</Hit_num>\n <Hit_id>Fake_Entry</Hit_id>\n <Hit_def>'+inTSV[n].split('\t')[1]+'</Hit_def>\n <Hit_accession>Fake_Accession</Hit_accession>\n'\
|
|
' <Hit_len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Hit_len>\n <Hit_hsps>\n <Hsp>\n <Hsp_num>1</Hsp_num>\n <Hsp_bit-score>1234</Hsp_bit-score>\n'\
|
|
' <Hsp_score>'+inTSV[n].split('\t')[-1]+'</Hsp_score>\n <Hsp_evalue>'+inTSV[n].split('\t')[-2]+'</Hsp_evalue>\n <Hsp_query-from>'+inTSV[n].split('\t')[-4]+'</Hsp_query-from>\n'\
|
|
' <Hsp_query-to>'+inTSV[n].split('\t')[-3]+'</Hsp_query-to>\n <Hsp_hit-from>'+inTSV[n].split('\t')[-4]+'</Hsp_hit-from>\n <Hsp_hit-to>'+inTSV[n].split('\t')[-3]+'</Hsp_hit-to>\n'\
|
|
' <Hsp_query-frame>0</Hsp_query-frame>\n <Hsp_hit-frame>0</Hsp_hit-frame>\n <Hsp_identity>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_identity>\n'\
|
|
' <Hsp_positive>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_positive>\n <Hsp_gaps>0</Hsp_gaps>\n <Hsp_align-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_align-len>\n'\
|
|
' <Hsp_qseq></Hsp_qseq>\n <Hsp_hseq></Hsp_hseq>\n <Hsp_midline></Hsp_midline>\n </Hsp>\n </Hit_hsps>\n</Hit>\n'\
|
|
'\n</Iteration_hits>\n <Iteration_stat>\n <Statistics>\n <Statistics_db-num>379660</Statistics_db-num>\n <Statistics_db-len>197499634</Statistics_db-len>\n'\
|
|
' <Statistics_hsp-len>123</Statistics_hsp-len>\n <Statistics_eff-space>184705217500</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n'\
|
|
' <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n </Statistics>\n </Iteration_stat>\n</Iteration>\n')
|
|
|
|
return iterations
|
|
|
|
|
|
###########################################################################################
|
|
###--------------------------- Writes Out the Fake XML File ----------------------------###
|
|
###########################################################################################
|
|
|
|
def write_Fake_XML(args):
|
|
|
|
home_folder = '/'.join(args.input_AA.split('/')[:-2]) + '/'
|
|
|
|
print (color.BOLD+'\n\nConverting '+color.ORANGE+args.name+'_XX_'+args.input_TSV.split('/')[-1]\
|
|
+color.END+color.BOLD+' to XML format\n'+color.END)
|
|
|
|
header, tail = header_tail()
|
|
|
|
iterations = convert_TSV_data(args)
|
|
|
|
with open(home_folder+args.xml_out,'w+') as w:
|
|
w.write(header)
|
|
w.write(''.join(iterations))
|
|
w.write(tail)
|
|
|
|
##########################################################################################
|
|
###-------------------- Cleans up the Folder and Moves Final Files --------------------###
|
|
##########################################################################################
|
|
def clean_up(args):
|
|
|
|
final_folder = '/'.join(args.input_file.split('/')[:-2]) + '/'
|
|
|
|
os.system('rm '+args.input_AA)
|
|
os.system('rm '+args.input_NTD)
|
|
os.system('rm '+args.input_TSV)
|
|
|
|
os.system('cp '+final_folder+'*Renamed.*.AA.fasta '+args.r2g_aa)
|
|
os.system('cp '+final_folder+'*Renamed.*.NTD.fasta '+args.r2g_ntd)
|
|
os.system('cp '+final_folder+'*.Renamed.*_allOGCleanresults.tsv '+args.r2g_tsv)
|
|
os.system('cp '+final_folder+'*oneHit '+args.r2g_xml)
|
|
|
|
###########################################################################################
|
|
###-------------------------------- Next Script Message --------------------------------###
|
|
###########################################################################################
|
|
|
|
def next_script(args):
|
|
|
|
print (color.BOLD+'\nThere is no next script! The final '+color.ORANGE+args.xml_out\
|
|
.split('_XX')[0]+color.END+color.BOLD+' files can be\nfound in the '+color.RED+\
|
|
args.xml_out.split('_XX_')[-1].split('.Renamed')[0]+'.Prep'+color.END+color.BOLD+' and '\
|
|
+color.RED+'ReadyToGo folders'+color.END+color.BOLD+' and are ready\n'\
|
|
'for the KatzLab Phylogenomic Tree-Building Steps!\n\n'+color.END)
|
|
|
|
##########################################################################################
|
|
###--------------- Checks Command Line Arguments and Calls on Functions ---------------###
|
|
##########################################################################################
|
|
|
|
def main():
|
|
|
|
args = check_args()
|
|
|
|
prep_folders(args)
|
|
|
|
rename_paralogs(args)
|
|
|
|
write_Fake_XML(args)
|
|
|
|
clean_up(args)
|
|
|
|
next_script(args)
|
|
|
|
main() |