def setUp(self):
self.converter = Converter()
self.example = Example()
self.converter.gff3parser = Mock_gff3_parser
self.converter._print_rntptt_title = Mock_func().print_rntptt_title
self.converter.tsspredator = Mock_TSSPredatorReader()
self.converter._read_file = Mock_func().mock_read_file
self.gff_file = self.example.gff_file
self.ptt_out = self.example.ptt_out
self.rnt_out = self.example.rnt_out
self.srna_out = self.example.srna_out
self.embl_file = self.example.embl_file
self.embl_out = self.example.embl_out
self.multi_embl = self.example.multi_embl
self.gff_out = self.example.gff_out
self.mastertable = self.example.mastertable
self.tss_file = self.example.tss_file
self.fasta_file = self.example.fasta_file
self.transterm = self.example.transterm
self.term_file = self.example.term_file
self.circ_file = self.example.circrna_table
self.circ_all = self.example.circrna_all
self.circ_best = self.example.circrna_best
self.test_folder = "test_folder"
self.mock_args = MockClass()
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fasta = os.path.join(self.test_folder, "fasta")
self.snp_folder = os.path.join(self.test_folder, "snp")
self.table = os.path.join(self.test_folder, "table")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.snp_folder)
os.mkdir(self.table)
os.mkdir(os.path.join(self.test_folder, "compare_reference"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs"))
os.mkdir(
os.path.join(self.test_folder,
"compare_reference/seqs/with_BAQ"))
os.mkdir(
os.path.join(self.test_folder, "compare_reference/statistics"))
args = self.mock_args.mock()
args.types = "reference"
args.out_folder = self.test_folder
args.fastas = self.fasta
self.snp = SNPCalling(args)
self.mock = Mock_func()
def setUp(self):
self.mock = Mock_func()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.tsss = "test_folder/tsss"
self.srnas = "test_folder/sRNA"
self.out = "test_folder/output"
self.trans = "test_folder/trans"
self.fastas = "test_folder/fastas"
self.tex = "test_folder/tex"
self.frag = "test_folder/frag"
self.gffs = "test_folder/gffs"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(self.out)
os.mkdir(self.trans)
os.mkdir(self.fastas)
os.mkdir(self.tex)
os.mkdir(self.frag)
os.mkdir(self.srnas)
os.mkdir(self.gffs)
args = self.mock_args.mock()
args.tsss = self.tsss
args.srnas = self.srnas
args.out_folder = self.out
args.trans = self.trans
args.fastas = self.fastas
self.sorf = sORFDetection(args)
def setUp(self):
self.test_folder = "test_folder"
self.mock_args = MockClass()
self.mock = Mock_func()
self.tsss = os.path.join(self.test_folder, "tsss")
self.trans = os.path.join(self.test_folder, "trans")
self.utr5s = os.path.join(self.test_folder, "utr5s")
self.utr3s = os.path.join(self.test_folder, "utr3s")
self.output = os.path.join(self.test_folder, "output")
self.gffs = os.path.join(self.test_folder, "gffs")
self.out_gff = os.path.join(self.output, "gffs")
self.stat = os.path.join(self.test_folder, "stat")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.gffs)
os.mkdir(self.tsss)
os.mkdir(self.stat)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.utr5s)
os.mkdir(os.path.join(self.utr5s, "tmp"))
os.mkdir(self.utr3s)
os.mkdir(os.path.join(self.utr3s, "tmp"))
os.mkdir(self.output)
os.mkdir(self.out_gff)
os.mkdir(os.path.join(self.output, "tables"))
args = self.mock_args.mock()
args.tsss = self.tsss
args.trans = self.trans
args.utr5s = self.utr5s
args.utr3s = self.utr3s
args.output_folder = self.output
args.terms = None
self.operon = OperonDetection(args)
def setUp(self):
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.example = Example()
self.test_folder = "test_folder"
self.trans = "test_folder/trans"
self.out = "test_folder/output"
self.wigs = "test_folder/wigs"
self.gffs = "test_folder/gffs"
self.tsss = "test_folder/tsss"
self.fastas = "test_folder/fastas"
self.manual = "test_folder/manuals"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.trans)
os.mkdir(self.out)
os.mkdir(self.wigs)
os.mkdir(self.gffs)
os.mkdir(self.tsss)
os.mkdir(self.fastas)
os.mkdir(self.manual)
args = self.mock_args.mock()
args.out_folder = self.out
args.ta_files = self.trans
args.gffs = self.gffs
args.wig_folder = self.wigs
args.fastas = self.fastas
args.manual = self.manual
self.tss = TSSpredator(args)
def setUp(self):
self.test_folder = "test_project"
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
os.mkdir(self.test_folder)
self.example = Example()
self.mock_args = MockClass()
def setUp(self):
self.mock_args = MockClass()
self.example = Example()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = "test_folder/gffs"
self.srnas = "test_folder/srnas"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.seq = "test_folder/output/sRNA_seqs"
self.rnaup = "test_folder/output/RNAup"
self.rnaplex = "test_folder/output/RNAplex"
self.merge = "test_folder/output/merge"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.gffs)
os.mkdir(self.out)
os.mkdir(self.srnas)
os.mkdir(self.fastas)
os.mkdir(self.rnaup)
os.mkdir(self.rnaplex)
os.mkdir(self.seq)
os.mkdir(self.merge)
os.mkdir(os.path.join(self.rnaup, "test"))
args = self.mock_args.mock()
args.out_folder = self.out
args.srnas = self.srnas
args.fastas = self.fastas
args.gffs = self.gffs
self.star = sRNATargetPrediction(args)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.gffs = "test_folder/gffs"
self.stat = "test_folder/stat"
self.trans = "test_folder/tran"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out)
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.stat)
os.mkdir(self.trans)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.out_folder = self.out
args.trans = self.trans
self.sub = SubLocal(args)
def setUp(self):
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.example = Example()
self.test_folder = "test_folder"
self.trans = "test_folder/trans"
self.out = "test_folder/output"
self.gffs = "test_folder/gffs"
self.tsss = "test_folder/tsss"
self.terms = "test_folder/terms"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.out)
os.mkdir(self.gffs)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.terms)
args = self.mock_args.mock()
args.tsss = self.tsss
args.trans = self.trans
args.out_folder = self.out
self.utr = UTRDetection(args)
def setUp(self):
self.segemehl = Mock_segemehl()
self.samtools = Mock_samtools()
self.mock_args = MockClass()
self.example = Example()
self.test_folder = "test_folder"
self.fasta_folder = os.path.join(self.test_folder, "fasta")
self.gff_folder = os.path.join(self.test_folder, "gff")
self.out_folder = os.path.join(self.test_folder, "output")
self.read_folder = os.path.join(self.test_folder, "read")
self.splice_folder = os.path.join(self.test_folder, "splice")
self.alignment_path = os.path.join(self.out_folder, "segemehl_align")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
if (not os.path.exists(self.fasta_folder)):
os.mkdir(self.fasta_folder)
os.mkdir(os.path.join(self.fasta_folder, "tmp"))
if (not os.path.exists(self.gff_folder)):
os.mkdir(self.gff_folder)
if (not os.path.exists(self.out_folder)):
os.mkdir(self.out_folder)
if (not os.path.exists(self.read_folder)):
os.mkdir(self.read_folder)
if (not os.path.exists(self.splice_folder)):
os.mkdir(self.splice_folder)
args = self.mock_args.mock()
args.output_folder = self.out_folder
args.gffs = self.gff_folder
args.align = True
args.fastas = self.fasta_folder
self.circ = CircRNADetection(args)
def setUp(self):
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.example = Example()
self.test_folder = "test_folder"
self.trans = "test_folder/trans"
self.out = "test_folder/output"
self.tex = "test_folder/tex"
self.frag = "test_folder/frag"
self.gffs = "test_folder/gffs"
self.tsss = "test_folder/tsss"
self.terms = "test_folder/terms"
self.stat = "test_folder/output/statistics"
self.out_gff = "test_folder/output/gffs"
self.out_table = "test_folder/output/tables"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.trans)
os.mkdir(self.out)
os.mkdir(self.tex)
os.mkdir(self.frag)
os.mkdir(os.path.join(self.frag, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.tsss)
os.mkdir(self.terms)
os.mkdir(self.stat)
os.mkdir(self.out_gff)
os.mkdir(self.out_table)
args = self.mock_args.mock()
args.out_folder = self.out
self.tran = TranscriptDetection(args)
def setUp(self):
self.example = Example()
self.mock = Mock_func()
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.ref_embls = "test_folder/embls"
self.output_path = "test_folder/output"
self.tar_fastas = "test_folder/tar_fasta"
self.ref_fastas = "test_folder/ref_fasta"
self.gff_outfolder = "test_folder/gffs"
self.ref_gbk = "test_folder/gbk"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.ref_embls)
os.mkdir(self.ref_gbk)
os.mkdir(self.output_path)
os.mkdir(self.tar_fastas)
os.mkdir(self.ref_fastas)
os.mkdir(self.gff_outfolder)
args = self.mock_args.mock()
args.output_path = self.output_path
args.ref_embls = self.ref_embls
args.ref_gbk = self.ref_gbk
args.tar_fastas = self.tar_fastas
args.ref_fastas = self.ref_fastas
args.gff_outfolder = self.gff_outfolder
self.ratt = RATT(args)
self.example = Example()
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.test_folder = "test_folder"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.gffs = "test_folder/gffs"
self.srnas = "test_folder/srnas"
self.trans = "test_folder/trans"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out)
os.mkdir(self.fastas)
os.mkdir(self.gffs)
os.mkdir(self.srnas)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.out, "tables"))
os.mkdir(os.path.join(self.out, "gffs"))
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(os.path.join(self.fastas, "tmp"))
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.trans = self.trans
args.out_folder = self.out
args.srnas = self.srnas
self.term = Terminator(args)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.fasta = "test_folder/fasta"
self.wigs = "test_folder/wig"
self.gff = "test_folder/gff"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.wigs)
os.mkdir(self.gff)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fastas = os.path.join(self.test_folder, "fasta")
self.wigs = os.path.join(self.test_folder, "wigs")
self.gffs = os.path.join(self.test_folder, "gffs")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.wigs)
os.mkdir(os.path.join(self.wigs, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
def setUp(self):
self.test_folder = "test_folder"
self.mock_args = MockClass()
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(os.path.join(self.test_folder, "tmp_id_list"))
# os.mkdir(os.path.join(self.test_folder, "tmp_nospecific"))
os.mkdir(os.path.join(self.test_folder, "with_strain"))
os.mkdir(os.path.join(self.test_folder, "with_strain/test_ptt"))
os.mkdir(os.path.join(self.test_folder, "without_strain"))
os.mkdir(os.path.join(self.test_folder, "without_strain/test_ptt"))
os.mkdir(os.path.join(self.test_folder, "all_results"))
os.mkdir(os.path.join(self.test_folder, "best_results"))
os.mkdir(os.path.join(self.test_folder, "figures"))
self.ppi = PPINetwork(self.test_folder)
self.mock = Mock_func()
self.example = Example()
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = os.path.join(self.test_folder, "gffs")
self.fastas = os.path.join(self.test_folder, "fastas")
self.out_folder = os.path.join(self.test_folder, "output")
self.database = os.path.join(self.test_folder, "database")
self.seq_path = os.path.join(self.test_folder, "seqs")
self.tables = os.path.join(self.out_folder, "tables")
self.stat = os.path.join(self.out_folder, "statistics")
self.scan = os.path.join(self.test_folder, "scan")
self.tsss = os.path.join(self.test_folder, "tsss")
self.trans = os.path.join(self.test_folder, "trans")
self.out_gff = os.path.join(self.out_folder, "gffs")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.out_folder)
os.mkdir(self.database)
os.mkdir(self.seq_path)
os.mkdir(os.path.join(self.out_folder, "tmp_table"))
os.mkdir(os.path.join(self.out_folder, "tmp_scan"))
os.mkdir(os.path.join(self.out_folder, "tmp_fasta"))
os.mkdir(os.path.join(self.out_folder, "scan_Rfam"))
os.mkdir(self.tables)
os.mkdir(self.scan)
os.mkdir(self.stat)
os.mkdir(self.out_gff)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.ribos_out_folder = self.out_folder
args.database = self.database
args.tsss = self.tsss
args.trans = self.trans
args.program = 'riboswtich'
self.ribo = Ribos(args)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.output = os.path.join(self.test_folder, "output")
self.tex_wig = os.path.join(self.test_folder, "tex")
self.frag_wig = os.path.join(self.test_folder, "frag")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tex_wig)
os.mkdir(self.frag_wig)
os.mkdir(self.output)
self.fasta = os.path.join(self.test_folder, "aaa.fa")
gen_file(self.fasta, self.example.fasta)
args = self.mock_args.mock()
args.output_folder = self.output
args.fasta = self.fasta
self.screen = Screen(args, self.output)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gffs = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gffs)):
os.mkdir(self.gffs)
self.go_folder = os.path.join(self.test_folder, "go_folder")
if (not os.path.exists(self.go_folder)):
os.mkdir(self.go_folder)
self.all_strain = "all_genomes_uniprot.csv"
self.trans = os.path.join(self.test_folder, "tran_folder")
if (not os.path.exists(self.trans)):
os.mkdir(self.trans)
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.gffs = self.gffs
args.trans = self.trans
self.go = GoTermFinding(args)
def setUp(self):
self.mock_args = MockClass()
self.example = Example()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = "test_folder/gffs"
self.tsss = "test_folder/tsss"
self.sorf = "test_folder/sORF"
self.out = "test_folder/output"
self.trans = "test_folder/trans"
self.fastas = "test_folder/fastas"
self.tex = "test_folder/tex"
self.frag = "test_folder/frag"
self.pros = "test_folder/pros"
self.terms = "test_folder/terms"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.gffs)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.out)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.tex)
os.mkdir(self.frag)
os.mkdir(self.pros)
os.mkdir(os.path.join(self.pros, "tmp"))
os.mkdir(self.sorf)
os.mkdir(os.path.join(self.sorf, "tmp"))
os.mkdir(self.terms)
args = self.mock_args.mock()
args.tss_folder = self.tsss
args.pro_folder = self.pros
args.out_folder = self.out
args.sorf_file = self.sorf
args.fastas = self.fastas
args.trans = self.trans
args.terms = self.terms
self.srna = sRNADetection(args)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.out_folder = "test_folder/output"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out_folder)
os.mkdir(os.path.join(self.out_folder, "fasta_output"))
self.tss_folder = os.path.join(self.test_folder, "tss_folder")
if (not os.path.exists(self.tss_folder)):
os.mkdir(self.tss_folder)
self.gff_folder = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gff_folder)):
os.mkdir(self.gff_folder)
self.fa_folder = os.path.join(self.test_folder, "fa_folder")
if (not os.path.exists(self.fa_folder)):
os.mkdir(self.fa_folder)
args = self.mock_args.mock()
args.tsss = self.tss_folder
args.fastas = self.fa_folder
args.gffs = self.gff_folder
args.output_folder = self.out_folder
self.meme = MEME(args)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()