def divide_values(file, ref_scores):
"""divide each BSR value in a row by that row's maximum value"""
errors = []
outdata = []
with open(file) as infile:
firstLine = infile.readline()
FL_F=firstLine.split()
outfile = open("BSR_matrix_values.txt", "w")
outfile.write('\t'.join([str(item) for item in FL_F])+"\n")
for line in infile:
fields=line.split()
all_fields=list(fields)
try:
fields=list(map(float, all_fields[1:]))
except:
raise TypeError("abnormal number of fields observed")
values= []
for x in fields:
try:
values.append(float(x)/float(ref_scores.get(all_fields[0])))
except:
"""if a mismatch error in names encountered, change values to 0"""
errors.append(all_fields[0])
values.append(float("0"))
sort_values=['%.2f' % elem for elem in values]
outfile.write('\t'.join([str(item) for item in sort_values])+"\n")
outdata.append(values)
outfile.close()
if len(errors)>0:
nr=[x for i, x in enumerate(errors) if x not in errors[i+1:]]
logging.logPrint("The following genes had no hits in datasets or are too short, values changed to 0, check names and output:%s" % "\n".join(nr))
return outdata
def translate_genes(genes,outfile,min_len):
"""translate nucleotide into peptide with BioPython"""
output = []
output_handle = open(outfile, "w")
too_short = []
with open(genes) as infile:
for record in SeqIO.parse(infile, "fasta"):
try:
min_pep_len=int(min_len)
"""Should I trim these sequences back to be multiples of 3?"""
if (len(record.seq)/3.0).is_integer():
pep_seq=record.seq.translate(to_stop=True, table=11)
elif ((len(record.seq)-1)/3.0).is_integer():
pep_seq=record.seq[:-1].translate(to_stop=True, table=11)
elif ((len(record.seq)-2)/3.0).is_integer():
pep_seq=record.seq[:-2].translate(to_stop=True, table=11)
elif ((len(record.seq)-3)/3.0).is_integer():
pep_seq=record.seq[:-3].translate(to_stop=True, table=11)
else:
print("Sequence of odd length found and couldn't be trimmed")
if len(pep_seq)>=min_pep_len:
output_handle.write(">"+record.id+"\n")
output_handle.write("".join(pep_seq)+"\n")
output.append(pep_seq)
else:
too_short.append(record.id)
except:
raise TypeError("odd characters observed in sequence %s" % record.id)
output_handle.close()
for record in output:
return str(record)
if len(too_short)>0:
logging.logPrint("The following sequences were too short and will not be processed: %s" % "\n".join(too_short))
def main(directory,id,filter,processors,genes,cluster_method,blast,length,
max_plog,min_hlog,f_plog,keep,filter_peps,filter_scaffolds,prefix,min_pep_length,
intergenics,min_len,dup_toggle):
start_dir = os.getcwd()
ap=os.path.abspath("%s" % start_dir)
dir_path=os.path.abspath("%s" % directory)
"""Here's a check to make sure that there are no conflicting methods"""
if "null" not in genes and "null" not in cluster_method:
logging.logPrint("Choose either genes or de novo clustering method, not both")
sys.exit()
"""Test for use of intergenics with a protein alignment method"""
if intergenics=="T" and blast=="tblastn":
logging.logPrint("Incompatible choices: if incorporating intergenics, choose a nucleotide alignment method")
sys.exit()
elif intergenics == "T" and blast=="blastp":
logging.logPrint("Incompatible choices: if incorporating intergenics, choose a nucleotide alignment method")
sys.exit()
elif intergenics == "T" and blast=="diamond":
logging.logPrint("Incompatible choices: if incorporating intergenics, choose a nucleotide alignment method")
sys.exit()
logging.logPrint("Testing paths of dependencies")
if blast=="blastn" or blast=="tblastn" or blast=="blastp":
ab = subprocess.call(['which', 'blastn'])
if ab == 0:
print("citation: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402")
else:
print("blast isn't in your path, but needs to be!")
sys.exit()
elif blast=="blat":
ac = subprocess.call(['which', 'blat'])
if ac == 0:
print("citation: W.James Kent. 2002. BLAT - The BLAST-Like Alignment Tool. Genome Research 12:656-664")
else:
print("You have requested blat, but it is not in your PATH")
sys.exit()
elif blast=="diamond":
ac = subprocess.call(['which', 'diamond'])
if ac == 0:
print("citation: Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nature methods, 12, 59-60.")
else:
print("You have requested DIAMOND, but it is not in your PATH (as diamond)")
sys.exit()
if "NULL" in prefix:
import datetime
timestamp = datetime.datetime.now()
tmp_rename = str(timestamp.year), str(timestamp.month), str(timestamp.day), str(timestamp.hour), str(timestamp.minute), str(timestamp.second)
rename = "".join(tmp_rename)
if os.path.exists("%s/%s" % (ap,rename)):
print("old temp directory exists (%s/%s). Delete and run again" % (ap,rename))
sys.exit()
else:
os.makedirs("%s/%s" % (ap,rename))
fastadir = ("%s/%s" % (ap,rename))
else:
if os.path.exists("%s/%s" % (ap,prefix)):
print("old temp directory exists (%s/%s). Delete and run again" % (ap,prefix))
sys.exit()
else:
os.makedirs("%s/%s" % (ap,prefix))
fastadir = "%s/%s" % (ap,prefix)
samples = []
for infile in glob.glob(os.path.join(dir_path, '*.fasta')):
name=get_seq_name(infile)
samples.append(name)
try:
os.symlink("%s" % infile, os.path.join(dir_path, os.path.dirname(dir_path)))
except:
copyfile("%s" % infile, "%s/%s.new" % (fastadir,name))
genbank_files = []
for infile in glob.glob(os.path.join(dir_path, '*.gbk')):
name=get_seq_name(infile)
genbank_files.append("1")
"""Do I need to add this to samples as well?"""
if len(samples) == 0 and len(genbank_files) == 0:
print("no usable genome files found, exiting...")
sys.exit()
"""This is the section on de novo clustering"""
if "null" in genes:
if "null" in cluster_method:
print("Clustering method needed if genes aren't provided...exiting")
sys.exit()
else:
pass
rc = subprocess.call(['which', 'prodigal'])
if rc == 0:
print("citation: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119")
else:
print("prodigal is not in your path, but needs to be!")
sys.exit()
if "usearch" in cluster_method:
rc = subprocess.call(['which', 'usearch'])
if rc == 0:
print("citation: Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461")
else:
print("usearch is not in your path, but needs to be!")
sys.exit()
elif "cd-hit" in cluster_method:
if blast == "blastp" or blast == "diamond":
rc = subprocess.call(['which', 'cd-hit'])
else:
rc = subprocess.call(['which', 'cd-hit-est'])
if rc == 0:
print("citation: Li, W., Godzik, A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nuceltodie sequences. Bioinformatics 22(13):1658-1659")
else:
print("cd-hit is not in your path, but needs to be!")
sys.exit()
elif "vsearch" in cluster_method:
if blast == "blastp" or blast == "diamond":
print("vsearch not compatible with proteins, exiting...")
sys.exit()
else:
rc = subprocess.call(['which', 'vsearch'])
if rc == 0:
print("citation: Rognes, T., Flouri, T., Nichols, B., Qunice, C., Mahe, Frederic. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ Preprints. DOI: https://doi.org/10.7287/peerj.preprints.2409v1")
else:
print("vsearch is not in your path, but needs to be!")
sys.exit()
if len(samples) == 0:
pass
else:
logging.logPrint("predicting genes with Prodigal")
"""Only predict genes if there are FASTA files"""
predict_genes(fastadir, processors, intergenics)
logging.logPrint("Prodigal done")
"""This function produces locus tags"""
if len(genbank_files)>0:
logging.logPrint("Converting genbank files")
os.chdir("%s" % fastadir)
genbank_hits = process_genbank_files(dir_path)
else:
genbank_hits = []
if genbank_files == None or len(genbank_files) == 0:
if intergenics == "F":
os.system("cat *genes.seqs > all_gene_seqs.out")
elif intergenics == "T":
os.system("cat *genes.seqs *intergenics.seqs > all_gene_seqs.out")
else:
pass
if filter_scaffolds == "T":
filter_scaffolds_fun("all_gene_seqs.out")
os.system("mv tmp.out all_gene_seqs.out")
else:
pass
else:
"""First combine all of the prodigal files into one file
:First check that there will be prodigal annotations"""
if len(samples)>0:
if intergenics == "F":
os.system("cat *genes.seqs > all_gene_seqs.out.tmp")
elif intergenics == "T":
os.system("cat *genes.seqs *intergenics.seqs > all_gene_seqs.out.tmp")
if filter_scaffolds == "T":
filter_scaffolds_fun("all_gene_seqs.out.tmp")
os.system("mv tmp.out all_gene_seqs.out.tmp")
else:
pass
"""This combines the locus tags with the Prodigal prediction.
If there are no prodigal predictions, then no error is printed"""
if len(samples)>0:
os.system("cat *locus_tags.fasta all_gene_seqs.out.tmp > all_gene_seqs.out")
else:
os.system("cat *locus_tags.fasta > all_gene_seqs.out")
if blast=="blastp" or blast=="diamond":
"""Need to convert the locus tags into peptides here"""
translate_genes("all_gene_seqs.out","all_genes.pep",30)
for infile in glob.glob(os.path.join(fastadir, "*locus_tags.fasta")):
base = os.path.basename(infile)
name = base.replace(".locus_tags.fasta","")
translate_genes(base,"%s.fasta.new_genes.pep" % name,30)
else:
for hit in genbank_hits:
reduced_hit = hit.replace(".gbk","")
"""This is to ensure that genes are aligned back against the genome"""
SeqIO.convert("%s/%s" % (dir_path, hit), "genbank", "%s.fasta.new" % reduced_hit, "fasta")
if "NULL" in cluster_method:
print("Clustering chosen, but no method selected...exiting")
sys.exit()
elif "usearch" in cluster_method:
os.system("mkdir split_files")
if blast == "blastp" or blast == "diamond":
if genbank_hits == None or len(genbank_hits) == 0:
os.system("cat *new_genes.pep > split_files/all_sorted.txt")
else:
os.system("cp all_genes.pep split_files/all_sorted.txt")
else:
os.system("cp all_gene_seqs.out split_files/all_sorted.txt")
os.chdir("split_files/")
logging.logPrint("Splitting FASTA file for use with USEARCH")
split_files("all_sorted.txt")
logging.logPrint("clustering with USEARCH at an ID of %s" % id)
run_usearch_dev(id,processors)
os.system("cat *.usearch.out > all_sorted.txt")
os.system("mv all_sorted.txt %s" % fastadir)
os.chdir("%s" % fastadir)
"""Need to make output either FASTA or PEP"""
data_type = find_data_type("all_sorted.txt")
uclust_cluster(id,data_type)
logging.logPrint("USEARCH clustering finished")
elif "vsearch" in cluster_method:
logging.logPrint("clustering with VSEARCH at an ID of %s, using %s processors" % (id,processors))
run_vsearch(id, processors, "all_gene_seqs.out")
os.system("mv vsearch.out consensus.fasta")
logging.logPrint("VSEARCH clustering finished")
elif "cd-hit" in cluster_method:
logging.logPrint("clustering with cd-hit at an ID of %s, length percentage of %s, using %s processors" % (id,min_len,processors))
if blast == "blastp" or blast == "diamond":
os.system("cat *new_genes.pep > all_gene_seqs.pep")
subprocess.check_call("cd-hit -i all_gene_seqs.pep -o consensus.pep -M 0 -T %s -c %s -s %s > cdhit.cluster 2>&1" % (processors,id,min_len), shell=True)
else:
subprocess.check_call("cd-hit-est -i all_gene_seqs.out -o consensus.fasta -M 0 -T %s -c %s -s %s > cdhit.cluster 2>&1" % (processors,id,min_len), shell=True)
"""need to check for dups here"""
if os.path.exists("consensus.fasta"):
dup_ids = test_duplicate_header_ids("consensus.fasta")
elif os.path.exists("consensus.pep"):
dup_ids = test_duplicate_header_ids("consensus.pep")
else:
print("clustering didn't work. Check input and try again")
sys.exit()
if dup_ids == "True":
pass
elif dup_ids == "False":
print("duplicate headers identified, renaming..")
try:
rename_fasta_header("consensus.fasta", "tmp.txt")
os.system("mv tmp.txt consensus.fasta")
except:
rename_fasta_header("consensus.pep", "tmp.txt")
os.system("mv tmp.txt consensus.pep")
else:
pass
if "tblastn" == blast:
subprocess.check_call("makeblastdb -in consensus.fasta -dbtype nucl > /dev/null 2>&1", shell=True)
translate_genes("consensus.fasta","tmp.pep",min_pep_length)
if filter_peps == "T":
filter_seqs("tmp.pep","consensus.pep")
os.system("rm tmp.pep")
else:
os.system("mv tmp.pep consensus.pep")
clusters = get_cluster_ids("consensus.pep")
blast_against_self_tblastn("tblastn", "consensus.fasta", "consensus.pep", "tmp_blast.out", processors, filter)
elif "blastn" == blast:
subprocess.check_call("makeblastdb -in consensus.fasta -dbtype nucl > /dev/null 2>&1", shell=True)
blast_against_self_blastn("blastn", "consensus.fasta", "consensus.fasta", "tmp_blast.out", filter, processors)
clusters = get_cluster_ids("consensus.fasta")
elif "blat" == blast:
blat_against_self("consensus.fasta", "consensus.fasta", "tmp_blast.out", processors)
clusters = get_cluster_ids("consensus.fasta")
elif "blastp" == blast:
subprocess.check_call("makeblastdb -in consensus.pep -dbtype prot > /dev/null 2>&1", shell=True)
blast_against_self_tblastn("blastp", "consensus.pep", "consensus.pep", "tmp_blast.out", processors, filter)
clusters = get_cluster_ids("consensus.pep")
elif "diamond" == blast:
"""Check this"""
if filter_peps == "T":
filter_seqs("consensus.pep","tmp.pep")
os.system("mv tmp.pep consensus.pep")
else:
pass
subprocess.check_call("diamond makedb --in consensus.pep -d consensus > /dev/null 2>&1", shell=True)
subprocess.check_call("diamond blastp -p 4 -d consensus -f 6 -q consensus.pep -o tmp_blast.out > /dev/null 2>&1", shell=True)
clusters = get_cluster_ids("consensus.pep")
subprocess.check_call("sort -u -k 1,1 tmp_blast.out > self_blast.out", shell=True)
ref_scores=parse_self_blast("self_blast.out")
os.system("cp tmp_blast.out ref.scores")
subprocess.check_call("rm tmp_blast.out self_blast.out", shell=True)
if blast == "tblastn" or blast == "blastn" or blast == "blastp":
logging.logPrint("starting BLAST")
elif blast == "diamond":
logging.logPrint("starting Diamond")
else:
logging.logPrint("starting BLAT")
if "tblastn" == blast:
blast_against_each_genome_tblastn_dev(processors, "consensus.pep", filter)
elif "blastn" == blast:
blast_against_each_genome_blastn_dev(processors, filter, "consensus.fasta")
elif "blat" == blast:
blat_against_each_genome_dev("consensus.fasta",processors)
elif "blastp" == blast:
blastp_against_each_annotation("consensus.pep",processors,filter)
elif "diamond" == blast:
diamond_against_each_annotation("consensus.pep",processors)
else:
pass
else:
#########This section focuses on providing your own genes with -g############
logging.logPrint("Using pre-compiled set of predicted genes")
files = glob.glob(os.path.join(dir_path, "*.fasta"))
genbank_files = glob.glob(os.path.join(dir_path, "*.gbk"))
if len(genbank_files)>0:
for hit in genbank_files:
base = os.path.basename(hit)
reduced_hit = base.replace(".gbk","")
"""This is to ensure that genes are aligned back against the genome"""
os.chdir(fastadir)
SeqIO.convert("%s/%s" % (dir_path, base), "genbank", "%s.fasta.new" % reduced_hit, "fasta")
os.chdir(start_dir)
if len(files)==0 and len(genbank_files)==0:
print("no usable reference genomes found!")
sys.exit()
else:
pass
gene_path=os.path.abspath("%s" % genes)
"""new method: aa,nt,unknown"""
data_type = find_data_type(gene_path)
dup_ids = test_duplicate_header_ids(gene_path)
if dup_ids == "True":
pass
elif dup_ids == "False":
print("duplicate headers identified, exiting..")
sys.exit()
clusters = get_cluster_ids(gene_path)
os.chdir("%s" % fastadir)
if gene_path.endswith(".pep"):
if data_type == "aa":
pass
else:
print("File is supposed to contain proteins, but doesn't look correct..exiting")
sys.exit()
os.system("cp %s %s/genes.pep" % (gene_path,fastadir))
if blast=="tblastn" or blast=="blastp":
logging.logPrint("using %s on peptides" % blast)
try:
subprocess.check_call("makeblastdb -in genes.pep -dbtype prot > /dev/null 2>&1", shell=True)
except:
logging.logPrint("problem encountered formatting BLAST database")
sys.exit()
blast_against_self_tblastn("blastp", "genes.pep", "genes.pep", "tmp_blast.out", processors, filter)
elif blast=="diamond":
logging.logPrint("using %s on peptides" % blast)
try:
subprocess.check_call("diamond makedb --in %s -d self > /dev/null 2>&1" % gene_path, shell=True)
except:
logging.logPrint("problem encountered formatting DIAMOND database")
subprocess.check_call("diamond blastp -p 4 -d self -f 6 -q %s -o tmp_blast.out > /dev/null 2>&1" % gene_path, shell=True)
elif blast=="blat" or blast=="blastn":
print("Nucleotide aligner not compatible with protein sequences...exiting")
sys.exit()
#Aligning back against each genome
if blast == "tblastn":
logging.logPrint("starting TBLASTN")
blast_against_each_genome_tblastn_dev(processors,gene_path,filter)
elif blast == "blastp":
"""I will need to first do gene prediction for each genome"""
for infile in glob.glob(os.path.join(dir_path, '*.fasta')):
name=get_seq_name(infile)
try:
os.symlink("%s" % infile, os.path.join(dir_path, os.path.dirname(dir_path)))
except:
copyfile("%s" % infile, "%s/%s.new" % (fastadir,name))
logging.logPrint("Predicting genes with Prodigal")
predict_genes(fastadir, processors, intergenics)
logging.logPrint("BlastP starting")
blastp_against_each_annotation("genes.pep",processors,filter)
elif blast == "diamond":
for infile in glob.glob(os.path.join(dir_path, '*.fasta')):
name=get_seq_name(infile)
try:
os.symlink("%s" % infile, os.path.join(dir_path, os.path.dirname(dir_path)))
except:
copyfile("%s" % infile, "%s/%s.new" % (fastadir,name))
logging.logPrint("Predicting genes with Prodigal")
predict_genes(fastadir, processors, intergenics)
logging.logPrint("Diamond starting")
diamond_against_each_annotation(gene_path,processors)
elif gene_path.endswith(".fasta"):
if data_type == "nt":
pass
else:
print("File is supposed to contain nucleotides, but doesn't look correct..exiting ")
sys.exit()
os.system("cp %s %s" % (gene_path,fastadir))
if blast == "diamond" or blast == "blastp":
print("protein alignment not compatible with nucleotide input..exiting")
sys.exit()
if "tblastn" == blast:
logging.logPrint("using tblastn")
translate_genes(gene_path,"genes.pep",min_pep_length)
try:
subprocess.check_call("makeblastdb -in %s -dbtype nucl > /dev/null 2>&1" % gene_path, shell=True)
except:
logging.logPrint("problem encountered with BLAST database")
sys.exit()
blast_against_self_tblastn("tblastn", gene_path, "genes.pep", "tmp_blast.out", processors, filter)
logging.logPrint("starting BLAST")
blast_against_each_genome_tblastn_dev(processors, "genes.pep", filter)
os.system("cp genes.pep %s" % start_dir)
elif "blastn" == blast:
logging.logPrint("using blastn")
try:
subprocess.check_call("makeblastdb -in %s -dbtype nucl > /dev/null 2>&1" % gene_path, shell=True)
except:
logging.logPrint("Database not formatted correctly...exiting")
sys.exit()
try:
blast_against_self_blastn("blastn", gene_path, gene_path, "tmp_blast.out", filter, processors)
except:
print("problem with blastn, exiting")
sys.exit()
logging.logPrint("starting BLAST")
try:
blast_against_each_genome_blastn_dev(processors, filter, gene_path)
except:
print("problem with blastn, exiting")
sys.exit()
elif "blat" == blast:
logging.logPrint("using blat")
blat_against_self(gene_path, gene_path, "tmp_blast.out", processors)
logging.logPrint("starting BLAT")
blat_against_each_genome_dev(gene_path,processors)
else:
pass
else:
print("input file format not supported")
sys.exit()
subprocess.check_call("sort -u -k 1,1 tmp_blast.out > self_blast.out", shell=True)
os.system("cp self_blast.out ref.scores")
ref_scores=parse_self_blast("self_blast.out")
subprocess.check_call("rm tmp_blast.out self_blast.out", shell=True)
"""testing block complete"""
if blast=="blat":
logging.logPrint("BLAT complete")
elif blast=="diamond":
logging.logPrint("Diamond complete")
else:
logging.logPrint("BLAST done")
if dup_toggle == "T":
logging.logPrint("Finding duplicates")
find_dups_dev(ref_scores, length, max_plog, min_hlog, clusters, processors)
logging.logPrint("Finding duplicates complete")
else:
logging.logPrint("Duplicate searching turned off")
parse_blast_report_dev("false",4)
curr_dir=os.getcwd()
table_files = glob.glob(os.path.join(curr_dir, "*.filtered.unique"))
files_and_temp_names = [(str(idx), os.path.join(curr_dir, f))
for idx, f in enumerate(table_files)]
names=[]
table_list = []
nr_sorted=sorted(clusters)
centroid_list = []
centroid_list.append(" ")
for x in nr_sorted:
centroid_list.append(x)
table_list.append(centroid_list)
logging.logPrint("starting matrix building")
new_names,new_table = new_loop_dev(files_and_temp_names, processors, clusters)
new_table_list = table_list+new_table
open("ref.list", "a").write("\n")
for x in nr_sorted:
open("ref.list", "a").write("%s\n" % x)
names_out = open("names.txt", "w")
names_redux = [val for subl in new_names for val in subl]
for x in names_redux: names_out.write("".join(x)+"\n")
names_out.close()
create_bsr_matrix_dev(new_table_list)
divide_values("bsr_matrix", ref_scores)
subprocess.check_call("paste ref.list BSR_matrix_values.txt > %s/bsr_matrix_values.txt" % start_dir, shell=True)
try:
if dup_toggle == "T":
subprocess.check_call("cp dup_matrix.txt names.txt consensus.pep duplicate_ids.txt consensus.fasta %s" % ap, shell=True, stderr=open(os.devnull, 'w'))
else:
subprocess.check_call("cp names.txt consensus.pep consensus.fasta %s" % ap, shell=True, stderr=open(os.devnull, 'w'))
except:
pass
if "T" in f_plog:
logging.logPrint("filtering duplicates")
num_filtered = filter_paralogs("%s/bsr_matrix_values.txt" % start_dir, "duplicate_ids.txt")
logging.logPrint("%s duplicates filtered" % str(num_filtered))
if "NULL" in prefix:
os.system("cp bsr_matrix_values_filtered.txt %s/%s_paralogs_filtered_bsr_matrix_values.txt" % (start_dir,"".join(rename)))
else:
os.system("cp bsr_matrix_values_filtered.txt %s/%s_paralogs_filtered_bsr_matrix_values.txt" % (start_dir,prefix))
os.chdir("%s" % ap)
logging.logPrint("matrix built")
if "NULL" in prefix:
if dup_toggle == "T":
os.system("mv dup_matrix.txt %s_dup_matrix.txt" % "".join(rename))
os.system("mv duplicate_ids.txt %s_duplicate_ids.txt" % "".join(rename))
else:
pass
os.system("mv names.txt %s_names.txt" % "".join(rename))
os.system("mv bsr_matrix_values.txt %s_bsr_matrix.txt" % "".join(rename))
if os.path.isfile("consensus.fasta"):
os.system("mv consensus.fasta %s_consensus.fasta" % "".join(rename))
if os.path.isfile("consensus.pep"):
os.system("mv consensus.pep %s_consensus.pep" % "".join(rename))
else:
if dup_toggle == "T":
os.system("mv dup_matrix.txt %s_dup_matrix.txt" % prefix)
os.system("mv duplicate_ids.txt %s_duplicate_ids.txt" % prefix)
else:
pass
os.system("mv names.txt %s_names.txt" % prefix)
os.system("mv bsr_matrix_values.txt %s_bsr_matrix.txt" % prefix)
if os.path.isfile("consensus.fasta"):
os.system("mv consensus.fasta %s_consensus.fasta" % prefix)
if os.path.isfile("consensus.pep"):
os.system("mv consensus.pep %s_consensus.pep" % prefix)
if "NULL" in prefix:
outfile = open("%s_run_parameters.txt" % "".join(rename), "w")
else:
outfile = open("%s_run_parameters.txt" % prefix, "w")
outfile.write("-d %s \\\n" % directory)
outfile.write("-i %s \\\n" % id)
outfile.write("-f %s \\\n" % filter)
outfile.write("-p %s \\\n" % processors)
outfile.write("-g %s \\\n" % genes)
outfile.write("-c %s \\\n" % cluster_method)
outfile.write("-b %s \\\n" % blast)
outfile.write("-l %s \\\n" % length)
outfile.write("-m %s \\\n" % max_plog)
outfile.write("-n %s \\\n" % min_hlog)
outfile.write("-t %s \\\n" % f_plog)
outfile.write("-k %s \\\n" % keep)
outfile.write("-s %s \\\n" % filter_peps)
outfile.write("-e %s \\\n" % filter_scaffolds)
outfile.write("-x %s \\\n" % prefix)
outfile.write("-y %s \\\n" % intergenics)
outfile.write("-ml %s \\\n" % min_len)
outfile.write("-z %s\n" % dup_toggle)
outfile.write("temp data stored here if kept: %s" % fastadir)
outfile.close()
logging.logPrint("all Done")
if "T" == keep:
pass
else:
os.system("rm -rf %s" % fastadir)
os.chdir("%s" % ap)