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PTL1/Transcriptomes/Scripts/CheckSetup.py
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194
PTL1/Transcriptomes/Scripts/CheckSetup.py
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import os, sys, re
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from Bio import SeqIO
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def check_transcripts(params):
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taxa = []
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if os.path.isdir(params.assembled_transcripts):
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for file in os.listdir(params.assembled_transcripts):
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if file[10:] == '_assembledTranscripts.fasta':
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taxa.append(file[:10])
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for rec in SeqIO.parse(params.assembled_transcripts + '/' + file, 'fasta'):
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if 'node_' not in rec.id.lower() or '_length_' not in rec.id.lower() or '_cov_' not in rec.id.lower():
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print('\nERROR: The sequence record ' + rec.id + ' from taxon ' + file[:10] + ' is incorrectly formatted. All sequence names must have be formatted in the style of rnaSpades output (with a NODE ID, length, and coverage)\n')
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exit()
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elif 'DS_Store' not in file:
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print('\nERROR: The file ' + file + ' in the give folder of assembled transcripts is incorrectly formatted. The files must start with a ten digit taxon identifier and then be named like Am_tu_Hp01_assembledTranscripts.fasta\n')
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exit()
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else:
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print('\nERROR: Assembled transcripts folder could not be found. Please ensure the given path is correct.\n')
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exit()
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return taxa
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def check_databases(params):
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if os.path.isdir(params.databases):
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if os.path.isdir(params.databases + '/db_BvsE'):
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if not os.path.isfile(params.databases + '/db_BvsE/eukout.dmnd'):
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print('\nERROR: eukout.dmnd could not be found in the Databses/db_BvsE folder')
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exit()
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if not os.path.isfile(params.databases + '/db_BvsE/micout.dmnd'):
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print('\nERROR: micout.dmnd could not be found in the Databses/db_BvsE folder')
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exit()
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if not os.path.isfile(params.databases + '/db_BvsE/SSULSUdb.nhr'):
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print('\nERROR: SSULSUdb.nhr could not be found in the Databses/db_BvsE folder')
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exit()
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if not os.path.isfile(params.databases + '/db_BvsE/SSULSUdb.nin'):
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print('\nERROR: SSULSUdb.nin could not be found in the Databses/db_BvsE folder')
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exit()
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if not os.path.isfile(params.databases + '/db_BvsE/SSULSUdb.nsq'):
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print('\nERROR: SSULSUdb.nsq could not be found in the Databses/db_BvsE folder')
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exit()
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else:
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print('\nERROR: The db_BvsE folder could not be found in the databases folder.\n')
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exit()
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if os.path.isdir(params.databases + '/db_OG'):
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fasta = [file for file in os.listdir(params.databases + '/db_OG') if file.endswith('.fasta')]
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dmnd = [file for file in os.listdir(params.databases + '/db_OG') if file.endswith('.dmnd')]
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if len(fasta) == 0:
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print('\nERROR: No Hook fasta file found in the Databases/db_OG folder\n')
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exit()
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elif len(fasta) > 1:
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print('\nERROR: More than one Hook fasta file found in the Databases/db_OG folder. Please delete all except for the correct file.\n')
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exit()
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else:
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for rec in SeqIO.parse(params.databases + '/db_OG/' + fasta[0], 'fasta'):
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try:
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og_number = re.split('OG.{1}_', rec.id)[-1][:6]
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og_prefix = rec.id.split(og_number)[-2][-4:]
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og = og_prefix + og_number
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if rec.id[-10:] != og:
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print('\nError: The sequence name ' + rec.id + ' in the given Hook database fasta file is incorrectly formatted. Each sequence ID should start with a ten-digit taxon identifier and end with a ten-digit gene family identifier (which must start with OGX_, with "X" being any digit. E.g. Op_me_Hsap_0_OG6_110767)\n')
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exit()
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except IndexError:
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print('\nError: The sequence name ' + rec.id + ' in the given Hook database fasta file is incorrectly formatted. Each sequence ID should start with a ten-digit taxon identifier and end with a ten-digit gene family identifier (which must start with OGX_, with "X" being any digit. E.g. Op_me_Hsap_0_OG6_110767)\n')
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exit()
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if len(dmnd) == 0:
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print('\nERROR: No Hook Diamond database (.dmnd) file found in the Databases/db_OG folder.\n')
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exit()
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elif len(dmnd) > 1:
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print('\nERROR: No Hook Diamond database (.dmnd) file found in the Databases/db_OG folder. Please delete all except for the correct file.\n')
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exit()
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else:
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print('\nERROR: The db_OG folder could not be found in the databases folder.\n')
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exit()
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if os.path.isdir(params.databases + '/db_StopFreq'):
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if not os.path.isfile(params.databases + '/db_StopFreq/RepEukProts.dmnd'):
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print('\nERROR: The RepEukProts.dmnd file could not be found in the Databases/db_StopFreq folder.\n')
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else:
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print('\nERROR: The db_StopFreq folder could not be found in the databases folder.\n')
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exit()
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else:
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print('\nERROR: Databases folder could not be found. Please ensure the given path is correct.\n')
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exit()
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def check_conspecifics(params, transcript_taxa):
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if params.xplate_contam:
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if params.conspecific_names != None:
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if os.path.isfile(params.conspecific_names):
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lines = [line for line in open(params.conspecific_names)]
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seen_taxa = []
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for line in lines:
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if len(line.split('\t')) > 0 and not len(line.split('\t')) > 2:
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taxon = line.split('\t')[0]
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if taxon not in seen_taxa:
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seen_taxa.append(taxon)
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else:
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print('\nERROR: The taxon ' + taxon + ' is listed in the conspecific names file twice. Please make sure this file is correct.\n')
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exit()
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if taxon not in transcript_taxa:
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print('\nERROR: The taxon ' + taxon + ' is listed in the conspecific names file but there is no assembled transcripts file that corresponds to this taxon.\n')
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exit()
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else:
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print('\nERROR: Unclear how to parse the line ' + line + ' in the given conspecific names file. This file should have two tab-separated columns.\n')
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exit()
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missing = [tax for tax in transcript_taxa if tax not in seen_taxa]
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if len(missing) > 0:
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print('\nERROR: The following taxa have assembled transcripts but are not listed in the conspecific names file:' + '\n\t'.join(missing) + '\n')
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exit()
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else:
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print('\nERROR: The given file of conspecific names (' + params.conspecific_names + ') could not be found.\n')
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exit()
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else:
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print('\nERROR: If running cross-plate contamination, a file with conspecific names is required.\n')
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exit()
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def check_gcodes(params, transcript_taxa):
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valid_codes = ['bleph','blepharisma','chilo','chilodonella','condy', 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal','taa','tag','tga','mesodinium']
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if params.genetic_code != None:
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if os.path.isfile(params.genetic_code):
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lines = [line for line in open(params.genetic_code)]
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seen_taxa = []
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for line in lines:
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if len(line.split('\t')) > 0 and not len(line.split('\t')) > 2:
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taxon = line.split('\t')[0]
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if taxon not in seen_taxa:
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seen_taxa.append(taxon)
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else:
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print('\nERROR: The taxon ' + taxon + ' is listed in the genetic codes file twice. Please make sure this file is correct.\n')
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exit()
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if taxon not in transcript_taxa:
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print('\nERROR: The taxon ' + taxon + ' is listed in the genetic codes file but there is no assembled transcripts file that corresponds to this taxon.\n')
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exit()
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if line.split('\t')[1].strip().lower() not in valid_codes:
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print('\nERROR: The code ' + line.split('\t')[1].strip() + ' is not a valid genetic code. Make sure you input only accepted genetic codes and that the genetic codes file is properly formatted.\n')
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exit()
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else:
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print('\nERROR: Unclear how to parse the line ' + line + ' in the given genetic codes file. This file should have two tab-separated columns.\n')
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exit()
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missing = [tax for tax in transcript_taxa if tax not in seen_taxa]
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if len(missing) > 0:
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print('\nERROR: The following taxa have assembled transcripts but are not listed in the genetic codes names file:' + '\n\t'.join(missing) + '\n')
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exit()
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else:
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if params.genetic_code.lower() not in valid_codes:
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print('\nERROR: The code ' + params.genetic_code + ' is not a valid genetic code. Make sure you input only accepted genetic codes and that the genetic codes file is properly formatted.\n')
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exit()
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else:
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print('\nERROR: An input genetic code is required.\n')
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exit()
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def run(params):
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print('\nChecking the input files and scripts setup...\n')
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transcript_taxa = check_transcripts(params)
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check_databases(params)
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check_conspecifics(params, transcript_taxa)
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check_gcodes(params, transcript_taxa)
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print('\nAll checks passed!\n')
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@ -2,6 +2,7 @@
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import os, sys, re
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import shutil
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import argparse
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import CheckSetup
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def get_args():
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@ -28,6 +29,9 @@ def get_args():
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#running the first script on all the bare files
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def script_one(args, ten_digit_codes):
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CheckSetup.run(args)
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for file in os.listdir(args.assembled_transcripts):
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if file[10:] == '_assembledTranscripts.fasta' and file[:10] in ten_digit_codes:
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os.system('python 1a_TranscriptLengthFilter.py --input_file ' + args.assembled_transcripts + '/' + file + ' --output_file ' + args.output + '/Output/' + file[:10] + ' --minLen ' + str(args.minlen) + ' --maxLen ' + str(args.maxlen) + ' --spades') #SPADES ARGUMENT??
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