class TestSeqFixer(unittest.TestCase):
def setUp(self):
self.fixer = SeqFixer()
def test_initialize(self):
self.assertFalse(self.fixer.terminal_ns)
self.assertFalse(self.fixer.start_stop_codons)
def test_fix_terminal_ns(self):
self.assertFalse(self.fixer.terminal_ns)
self.fixer.fix_terminal_ns()
self.assertTrue(self.fixer.terminal_ns)
def test_fix_start_stop_codons(self):
self.assertFalse(self.fixer.start_stop_codons)
self.fixer.fix_start_stop_codons()
self.assertTrue(self.fixer.start_stop_codons)
def test_dirty(self):
self.assertFalse(self.fixer.dirty)
class TestSeqFixer(unittest.TestCase):
def setUp(self):
self.fixer = SeqFixer()
def test_initialize(self):
self.assertFalse(self.fixer.terminal_ns)
self.assertFalse(self.fixer.start_stop_codons)
def test_fix_terminal_ns(self):
self.assertFalse(self.fixer.terminal_ns)
self.fixer.fix_terminal_ns()
self.assertTrue(self.fixer.terminal_ns)
def test_fix_start_stop_codons(self):
self.assertFalse(self.fixer.start_stop_codons)
self.fixer.fix_start_stop_codons()
self.assertTrue(self.fixer.start_stop_codons)
def test_dirty(self):
self.assertFalse(self.fixer.dirty)
def __init__(self):
self.seqs = []
self.annot = Annotator()
self.filter_mgr = FilterManager()
self.stats_mgr = StatsManager()
self.seq_fixer = SeqFixer()
class ConsoleController:
no_genome_message = "It looks like no genome is currently loaded. Try the 'load' command.\n"+\
"Type 'help load' to learn how to use it, or just 'help' for general advice.\n"
## Setup, loading and saving sessions
def __init__(self):
self.seqs = []
self.annot = Annotator()
self.filter_mgr = FilterManager()
self.stats_mgr = StatsManager()
self.seq_fixer = SeqFixer()
def genome_is_loaded(self):
for seq in self.seqs:
if seq.genes:
return True
return False
def barf_folder(self, line):
if not self.seqs:
return self.no_genome_message
elif len(line) == 0:
sys.stderr.write("Usage: barffolder <directory>\n")
return
else:
# Create directory, open files
os.system('mkdir '+line)
gff = open(line+'/genome.gff', 'w')
removed_gff = open(line+'/genome.removed.gff', 'w')
tbl = open(line+'/genome.tbl', 'w')
fasta = open(line+'/genome.fasta', 'w')
mrna_fasta = open(line+'/genome.mrna.fasta', 'w')
cds_fasta = open(line+'/genome.cds.fasta', 'w')
protein_fasta = open(line+'/genome.proteins.fasta', 'w')
# Deep copy each seq, apply fixes and filters, write
sys.stderr.write("Writing gff, tbl and fasta...\n")
for seq in self.seqs:
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
gff.write(cseq.to_gff())
removed_gff.write(cseq.removed_to_gff())
tbl.write(cseq.to_tbl())
mrna_fasta.write(cseq.to_mrna_fasta())
cds_fasta.write(cseq.to_cds_fasta())
protein_fasta.write(cseq.to_protein_fasta())
fasta.write(cseq.to_fasta())
# Close files
gff.close()
tbl.close()
fasta.close()
mrna_fasta.close()
cds_fasta.close()
protein_fasta.close()
return "Genome written to " + line
def load_folder(self, line):
if not line:
line = "."
fastapath = line + '/genome.fasta'
gffpath = line + '/genome.gff'
# Verify files
if not os.path.isfile(fastapath):
sys.stderr.write("Failed to find " + fastapath + ". No genome was loaded.")
return
if not os.path.isfile(gffpath):
sys.stderr.write("Failed to find " + gffpath + ". No genome was loaded.")
return
# Read the fasta
sys.stderr.write("Reading fasta...\n")
self.read_fasta(fastapath)
sys.stderr.write("Done.\n")
# Read the gff
sys.stderr.write("Reading gff...\n")
self.read_gff(gffpath)
sys.stderr.write("Done.\n")
# Clear stats; read in new stats
self.stats_mgr.clear_all()
for seq in self.seqs:
self.stats_mgr.update_ref(seq.stats())
def set_filter_arg(self, filter_name, val):
self.filter_mgr.set_filter_arg(filter_name, val)
def get_filter_arg(self, filter_name):
return self.filter_mgr.get_filter_arg(filter_name)
def set_filter_remove(self, filter_name, remove):
self.filter_mgr.set_filter_remove(filter_name, remove)
def apply_filters(self):
for seq in self.seqs:
self.filter_mgr.apply_filters(seq)
def fix_terminal_ns(self):
self.seq_fixer.fix_terminal_ns()
return "Terminal Ns will now be fixed."
def fix_start_stop_codons(self):
self.seq_fixer.fix_start_stop_codons()
return "Will verify and create start/stop codons."
## Assorted utilities
def get_n_seq_ids(self, number):
"""Returns a message indicating the first n seq_ids in the genome.
If no seqs loaded, returns a message to that effect. If fewer than n
seqs loaded, returns the seq_ids of those seqs."""
if not self.seqs:
return "No sequences currently in memory.\n"
else:
if len(self.seqs) < number:
number = len(self.seqs)
seq_list = []
for seq in self.seqs:
seq_list.append(seq.header)
if len(seq_list) == number:
break
result = "First " + str(len(seq_list)) + " seq ids are: "
result += format_list_with_strings(seq_list)
return result
def get_n_gene_ids(self, number):
"""Returns a message indicating the first n gene_ids in the genome.
If no genes are present, returns a message to that effect. If fewer than n
genes are loaded, returns the gene_ids of those genes."""
genes_list = []
while len(genes_list) < number:
for seq in self.seqs:
genes_list.extend(seq.get_gene_ids())
# List may now contain more than 'number' ids, or it may contain zero
if not genes_list:
return "No genes currently in memory.\n"
if len(genes_list) > number:
genes_list = genes_list[:number]
result = "First " + str(len(genes_list)) + " gene ids are: "
result += format_list_with_strings(genes_list)
return result
def get_n_mrna_ids(self, number):
"""Returns a message indicating the first n mrna_ids in the genome.
If no mrnas are present, returns a message to that effect. If fewer than n
mrnas are loaded, returns the mrna_ids of those mrnas."""
mrnas_list = []
while len(mrnas_list) < number:
for seq in self.seqs:
mrnas_list.extend(seq.get_mrna_ids())
# List may now contain more than 'number' ids, or it may contain zero
if not mrnas_list:
return "No mrnas currently in memory.\n"
if len(mrnas_list) > number:
mrnas_list = mrnas_list[:number]
result = "First " + str(len(mrnas_list)) + " mrna ids are: "
result += format_list_with_strings(mrnas_list)
return result
## Reading in files
def read_fasta(self, line):
reader = FastaReader()
self.seqs = reader.read(open(line, 'r'))
def read_gff(self, line):
gffreader = GFFReader()
reader = open(line, 'rb')
genes = gffreader.read_file(reader)
for gene in genes:
self.add_gene(gene)
## Output info to console
def barf_gene_gff(self, line):
if not self.seqs:
return self.no_genome_message
else:
for seq in self.seqs:
if seq.contains_gene(line):
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
return cseq.gene_to_gff(line)
def barf_seq(self, line):
if not self.seqs:
return self.no_genome_message
else:
args = line.split(' ')
if len(args) == 1:
seq_id = args[0]
for seq in self.seqs:
if seq.header == seq_id:
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
return cseq.get_subseq()
elif len(args) == 3:
seq_id = args[0]
start = int(args[1])
stop = int(args[2])
for seq in self.seqs:
if seq.header == seq_id:
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
return cseq.get_subseq(start, stop)
else:
return "Usage: barfseq <seq_id> <start_index> <end_index>\n"
def barf_cds_seq(self, line):
if not self.seqs:
return self.no_genome_message
else:
name = line
for seq in self.seqs:
if seq.contains_mrna(name):
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
return cseq.extract_cds_seq(name)
return "Error: Couldn't find mRNA.\n"
def cds_to_gff(self, line):
if not self.seqs:
return self.no_genome_message
else:
name = line
for seq in self.seqs:
if seq.contains_mrna(name):
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
return cseq.cds_to_gff(name)
return "Error: Couldn't find mRNA.\n"
def cds_to_tbl(self, line):
if not self.seqs:
return self.no_genome_message
else:
name = line
for seq in self.seqs:
if seq.contains_mrna(name):
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
return cseq.cds_to_tbl(name)
return "Error: Couldn't find mRNA.\n"
def barf_gene_tbl(self, line):
if not self.seqs:
return self.no_genome_message
else:
output = ">Feature SeqId\n"
for seq in self.seqs:
if seq.contains_gene(line):
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
output += cseq.gene_to_tbl(line)
return output
def stats(self):
if not self.seqs:
return self.no_genome_message
else:
number_of_gagflags = 0
first_line = "Number of sequences: " + str(len(self.seqs)) + "\n"
if self.filter_mgr.dirty or self.seq_fixer.dirty:
self.stats_mgr.clear_alt()
sys.stderr.write("Calculating statistics on genome...\n")
for seq in self.seqs:
# Deep copy seq, apply fixes and filters, then update stats
cseq = copy.deepcopy(seq)
self.seq_fixer.fix(cseq)
self.filter_mgr.apply_filters(cseq)
self.stats_mgr.update_alt(cseq.stats())
number_of_gagflags += cseq.number_of_gagflags()
self.filter_mgr.dirty = False
self.seq_fixer.dirty = False
last_line = "(" + str(number_of_gagflags) + " features flagged)\n"
return first_line + self.stats_mgr.summary() + last_line
## Utility methods
def add_gene(self, gene):
for seq in self.seqs:
if seq.header == gene.seq_name:
seq.add_gene(gene)
def get_locus_tag(self):
locus_tag = ""
for seq in self.seqs:
if locus_tag:
break
else:
locus_tag = seq.get_locus_tag()
return locus_tag
def clear_seqs(self):
self.seqs[:] = []
def contains_mrna(self, mrna_id):
for seq in self.seqs:
if seq.contains_mrna(mrna_id):
return True
return False
def contains_gene(self, gene_id):
for seq in self.seqs:
if seq.contains_gene(gene_id):
return True
return False
def contains_seq(self, seq_id):
for seq in self.seqs:
if seq.header == seq_id:
return True
return False
def can_write_to_path(self, path):
if len(path.split()) > 1:
return False
else:
return not os.path.exists(path)
def setUp(self):
self.fixer = SeqFixer()
def setUp(self):
self.fixer = SeqFixer()