class TestFilterManager(unittest.TestCase):
def setUp(self):
self.filter_mgr = FilterManager()
def test_modify_filter_arg(self):
fake_seq = Mock()
self.filter_mgr.filters['cds_shorter_than'] = Mock()
self.filter_mgr.filters['cds_shorter_than'].arg = 0
self.filter_mgr.filters['cds_shorter_than'].remove = True
self.filter_mgr.apply_filter('cds_shorter_than', '30', False, fake_seq)
self.assertEqual(self.filter_mgr.get_filter_arg('cds_shorter_than'), 30)
self.filter_mgr.filters['cds_shorter_than'].apply.assert_called_with(fake_seq)
class TestFilterManager(unittest.TestCase):
def setUp(self):
self.filter_mgr = FilterManager()
def test_modify_filter_arg(self):
fake_seq = Mock()
self.filter_mgr.filters['cds_shorter_than'] = Mock()
self.filter_mgr.filters['cds_shorter_than'].arg = 0
self.filter_mgr.filters['cds_shorter_than'].remove = True
self.filter_mgr.apply_filter('cds_shorter_than', '30', False, fake_seq)
self.assertEqual(self.filter_mgr.get_filter_arg('cds_shorter_than'), 30)
self.filter_mgr.filters['cds_shorter_than'].apply.assert_called_with(fake_seq)
class TestFilterManager(unittest.TestCase):
def setUp(self):
self.filter_mgr = FilterManager()
def test_modify_filter_arg(self):
self.filter_mgr.dirty = False
self.filter_mgr.set_filter_arg('cds_shorter_than', '30')
self.assertTrue(self.filter_mgr.dirty)
self.assertEqual(self.filter_mgr.get_filter_arg('cds_shorter_than'),
30)
self.filter_mgr.dirty = False
self.filter_mgr.set_filter_arg('cds_shorter_than', '30')
self.assertFalse(self.filter_mgr.dirty)
def __init__(self):
self.seqs = []
self.removed_features = []
self.filter_mgr = FilterManager()
self.stats_mgr = StatsManager()
class Controller:
def __init__(self):
self.seqs = []
self.removed_features = []
self.filter_mgr = FilterManager()
self.stats_mgr = StatsManager()
def execute(self, args):
"""At a minimum, write a fasta, gff and tbl to output directory. Optionally do more."""
# Verify and read fasta file
fastapath = args.fasta
if not os.path.isfile(fastapath):
sys.stderr.write("Failed to find " + fastapath + ". No genome was loaded.\n")
sys.exit()
sys.stderr.write("Reading fasta...\n")
self.read_fasta(fastapath)
sys.stderr.write("Done.\n")
# Create output directory
out_dir = "gag_output"
if args.out:
out_dir = args.out
os.system('mkdir ' + out_dir)
# Verify and read gff file
# This step also writes genome.ignored.gff,
# genome.invalid.gff and genome.comments.gff
gffpath = args.gff
if not os.path.isfile(gffpath):
sys.stderr.write("Failed to find " + gffpath + ". No genome was loaded.")
return
sys.stderr.write("Reading gff...\n")
self.read_gff(gffpath, out_dir)
sys.stderr.write("Done.\n")
# Calculate stats before genome is modified
sys.stderr.write("Calculating stats on original genome\n")
for seq in self.seqs:
self.stats_mgr.update_ref(seq.stats())
# Optional annotation step
if args.anno:
anno_filename = args.anno
self.annotate_from_file(anno_filename)
# Optional step to trim sequences, subsequences or features
if args.trim:
trim_filename = args.trim
self.trim_from_file(trim_filename)
# Optional step to create start and stop codons
if args.fix_start_stop:
sys.stderr.write("Creating start and stop codons...\n")
self.fix_start_stop_codons()
# Optional step to fix terminal Ns
if args.fix_terminal_ns:
sys.stderr.write("Fixing terminal Ns...\n")
self.fix_terminal_ns()
# Optional filtering steps
# Remove
if args.remove_cds_shorter_than:
min_length = args.remove_cds_shorter_than
sys.stderr.write("Removing CDS shorter than %s...\n" % min_length)
self.apply_filter("cds_shorter_than", min_length, "REMOVE")
if args.remove_cds_longer_than:
max_length = args.remove_cds_longer_than
sys.stderr.write("Removing CDS longer than %s...\n" % max_length)
self.apply_filter("cds_longer_than", max_length, "REMOVE")
if args.remove_exons_shorter_than:
min_length = args.remove_exons_shorter_than
sys.stderr.write("Removing exons shorter than %s...\n" % min_length)
self.apply_filter("exon_shorter_than", min_length, "REMOVE")
if args.remove_exons_longer_than:
max_length = args.remove_exons_longer_than
sys.stderr.write("Removing exons longer than %s...\n" % max_length)
self.apply_filter("exon_longer_than", max_length, "REMOVE")
if args.remove_introns_shorter_than:
min_length = args.remove_introns_shorter_than
sys.stderr.write("Removing exons shorter than %s...\n" % min_length)
self.apply_filter("intron_shorter_than", min_length, "REMOVE")
if args.remove_introns_longer_than:
max_length = args.remove_introns_longer_than
sys.stderr.write("Removing exons longer than %s...\n" % max_length)
self.apply_filter("intron_longer_than", max_length, "REMOVE")
if args.remove_genes_shorter_than:
min_length = args.remove_genes_shorter_than
sys.stderr.write("Removing genes shorter than %s...\n" % min_length)
self.apply_filter("gene_shorter_than", min_length, "REMOVE")
if args.remove_genes_longer_than:
max_length = args.remove_genes_longer_than
sys.stderr.write("Removing genes longer than %s...\n" % max_length)
self.apply_filter("gene_longer_than", max_length, "REMOVE")
# Flag
if args.flag_cds_shorter_than:
min_length = args.flag_cds_shorter_than
sys.stderr.write("Flagging CDS shorter than %s...\n" % min_length)
self.apply_filter("cds_shorter_than", min_length, "FLAG")
if args.flag_cds_longer_than:
max_length = args.flag_cds_longer_than
sys.stderr.write("Flagging CDS longer than %s...\n" % max_length)
self.apply_filter("cds_longer_than", max_length, "FLAG")
if args.flag_exons_shorter_than:
min_length = args.flag_exons_shorter_than
sys.stderr.write("Flagging exons shorter than %s...\n" % min_length)
self.apply_filter("exon_shorter_than", min_length, "FLAG")
if args.flag_exons_longer_than:
max_length = args.flag_exons_longer_than
sys.stderr.write("Flagging exons longer than %s...\n" % max_length)
self.apply_filter("exon_longer_than", max_length, "FLAG")
if args.flag_introns_shorter_than:
min_length = args.flag_introns_shorter_than
sys.stderr.write("Flagging exons shorter than %s...\n" % min_length)
self.apply_filter("intron_shorter_than", min_length, "FLAG")
if args.flag_introns_longer_than:
max_length = args.flag_introns_longer_than
sys.stderr.write("Flagging exons longer than %s...\n" % max_length)
self.apply_filter("intron_longer_than", max_length, "FLAG")
if args.flag_genes_shorter_than:
min_length = args.flag_genes_shorter_than
sys.stderr.write("Flagging genes shorter than %s...\n" % min_length)
self.apply_filter("gene_shorter_than", min_length, "FLAG")
if args.flag_genes_longer_than:
max_length = args.flag_genes_longer_than
sys.stderr.write("Flagging genes longer than %s...\n" % max_length)
self.apply_filter("gene_longer_than", max_length, "FLAG")
# Write fasta, gff and tbl file to output folder
# Open files
fasta = open(out_dir + '/genome.fasta', 'w')
gff = open(out_dir + '/genome.gff', 'w')
tbl = open(out_dir + '/genome.tbl', 'w')
proteins = open(out_dir + '/genome.proteins.fasta', 'w')
removed = open(out_dir + '/genome.removed.gff', 'w')
stats_file = open(out_dir + '/genome.stats', 'w')
# Calculate stats on modified genome
sys.stderr.write("Calculating stats on modified genome\n")
for seq in self.seqs:
self.stats_mgr.update_alt(seq.stats())
# Write stats file
sys.stderr.write("Writing stats file to " + out_dir + "/ ...\n")
for line in self.stats_mgr.summary():
stats_file.write(line)
# Write fasta, gff, tbl, protein fasta
sys.stderr.write("Writing gff, tbl and fasta to " + out_dir + "/ ...\n")
gff.write("##gff-version 3\n")
for seq in self.seqs:
fasta.write(seq.to_fasta())
gff.write(seq.to_gff())
tbl.write(seq.to_tbl())
proteins.write(seq.to_protein_fasta())
# Write removed.gff
for feature in self.removed_features:
removed.write(feature.to_gff())
# Close files
gff.close()
tbl.close()
fasta.close()
proteins.close()
removed.close()
stats_file.close()
def add_annotations_from_list(self, anno_list):
for seq in self.seqs:
seq.add_annotations_from_list(anno_list)
def trim_from_file(self, filename):
if not os.path.isfile(filename):
sys.stderr.write("Error: " + filename + " is not a file. Nothing trimmed.\n")
return
trimlist = self.read_bed_file(open(filename, 'rb'))
if not trimlist:
sys.stderr.write("Failed to read .bed file; nothing trimmed.\n")
return
else:
self.trim_from_list(trimlist)
def annotate_from_file(self, filename):
if not os.path.isfile(filename):
sys.stderr.write("Error: " + filename + " is not a file. Nothing annotated.\n")
return
annos = self.read_annotation_file(open(filename, 'rb'))
if not annos:
sys.stderr.write("Failed to read annotations from " + filename + "; no annotations added.\n")
return
else:
sys.stderr.write("Adding annotations to genome ...\n")
self.add_annotations_from_list(annos)
sys.stderr.write("...done\n")
def trim_from_list(self, trimlist):
for seq in self.seqs:
# In the case that there are multiple regions to trim in a single
# sequence, trim from the end so indices don't get messed up
to_trim_this_seq = [x for x in trimlist if x[0] == seq.header]
to_trim_this_seq = sorted(to_trim_this_seq, key=lambda entry: entry[2], reverse=True)
for entry in to_trim_this_seq:
removed_genes = seq.trim_region(entry[1], entry[2])
self.removed_features.extend(removed_genes)
sys.stderr.write("Trimmed " + entry[0] + " from ")
sys.stderr.write(str(entry[1]) + " to " + str(entry[2]) + "\n")
self.remove_empty_features(seq)
def get_filter_arg(self, filter_name):
return self.filter_mgr.get_filter_arg(filter_name)
def apply_filter(self, filter_name, val, filter_mode):
for seq in self.seqs:
self.filter_mgr.apply_filter(filter_name, val, filter_mode, seq)
self.remove_empty_features(seq)
def fix_terminal_ns(self):
for seq in self.seqs:
seq.remove_terminal_ns()
self.remove_empty_features(seq)
def fix_start_stop_codons(self):
for seq in self.seqs:
seq.create_starts_and_stops()
## Reading in files
def read_fasta(self, line):
reader = FastaReader()
self.seqs = reader.read(open(line, 'r'))
def read_gff(self, line, prefix):
# Takes prefix b/c reader returns comments, invalids, ignored
# and this method writes them to output files
# That's kind of messy
gffreader = GFFReader()
reader = open(line, 'rb')
genes, comments, invalids, ignored = gffreader.read_file(reader)
for gene in genes:
self.add_gene(gene)
# Write comments, invalid lines and ignored features
with open(prefix + "/genome.comments.gff", 'w') as comments_file:
for comment in comments:
comments_file.write(comment)
with open(prefix + "/genome.invalid.gff", 'w') as invalid_file:
for invalid in invalids:
invalid_file.write(invalid)
with open(prefix + "/genome.ignored.gff", 'w') as ignored_file:
for item in ignored:
ignored_file.write(item)
def read_bed_file(self, io_buffer):
trimlist = []
for line in io_buffer:
splitline = line.strip().split('\t')
if len(splitline) != 3:
return []
else:
try:
entry = [splitline[0], int(splitline[1]), int(splitline[2])]
except ValueError:
sys.stderr.write("Error reading .bed file. Non-integer value ")
sys.sdterr.write("in column 2 or 3. Here is the line:\n")
sys.stderr.write(line)
return []
trimlist.append(entry)
return trimlist
def read_annotation_file(self, io_buffer):
annos = []
for line in io_buffer:
splitline = line.strip().split('\t')
if len(splitline) != 3:
return []
else:
annos.append(splitline)
return annos
## Clean up
def remove_empty_features(self, seq):
"""Removes any empty mRNAs or genes from a seq and adds them to self.removed_features."""
self.removed_features.extend(seq.remove_empty_mrnas())
self.removed_features.extend(seq.remove_empty_genes())
def stats(self):
if not self.seqs:
return self.no_genome_message
else:
number_of_gagflags = 0
# TODO have stats mgr handle "number of sequences"
first_line = "Number of sequences: " + str(len(self.seqs)) + "\n"
sys.stderr.write("Calculating statistics on genome...\n")
self.stats_mgr.clear_alt()
for seq in self.seqs:
self.stats_mgr.update_alt(seq.stats())
number_of_gagflags += seq.number_of_gagflags()
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 remove_from_list(self, bad_list):
# First remove any seqs on the list
to_remove = []
for seq in self.seqs:
if seq.header in bad_list:
to_remove.append(seq)
if to_remove:
for seq in to_remove:
self.seqs.remove(seq)
sys.stderr.write("Warning: removing seq " + seq.header + ".\n")
sys.stderr.write("You must reload genome to get this sequence back.\n")
self.removed_features.extend(to_remove)
# Now pass the list down to each seq
for seq in self.seqs:
removed_from_seq = seq.remove_from_list(bad_list)
self.removed_features.extend(removed_from_seq)
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 __init__(self):
self.seqs = []
self.removed_features = []
self.filter_mgr = FilterManager()
self.stats_mgr = StatsManager()
class Controller(object):
def __init__(self):
self.seqs = []
self.removed_features = []
self.filter_mgr = FilterManager()
self.stats_mgr = StatsManager()
def execute(self, args):
"""At a minimum, write a fasta, gff and tbl to output directory. Optionally do more."""
# Verify and read fasta file
fastapath = args.fasta
if not os.path.isfile(fastapath):
sys.stderr.write("Failed to find " + fastapath + ". No genome was loaded.\n")
sys.exit()
sys.stderr.write("Reading fasta...\n")
self.read_fasta(fastapath)
sys.stderr.write("Done.\n")
# Create output directory
out_dir = "gag_output"
if args.out:
out_dir = args.out
os.system('mkdir ' + out_dir)
# Verify and read gff file
# This step also writes genome.ignored.gff,
# genome.invalid.gff and genome.comments.gff
gffpath = args.gff
if not os.path.isfile(gffpath):
sys.stderr.write("Failed to find " + gffpath + ". No genome was loaded.")
return
sys.stderr.write("Reading gff...\n")
self.read_gff(gffpath, out_dir)
sys.stderr.write("Done.\n")
# Calculate stats before genome is modified
sys.stderr.write("Calculating stats on original genome\n")
for seq in self.seqs:
self.stats_mgr.update_ref(seq.stats())
# Optional annotation step
if args.anno:
anno_filename = args.anno
self.annotate_from_file(anno_filename)
# Optional step to trim sequences, subsequences or features
if args.trim:
trim_filename = args.trim
self.trim_from_file(trim_filename)
# Optional step to create start and stop codons
if args.fix_start_stop:
sys.stderr.write("Creating start and stop codons...\n")
self.fix_start_stop_codons()
# Optional step to fix terminal Ns
if args.fix_terminal_ns:
sys.stderr.write("Fixing terminal Ns...\n")
self.fix_terminal_ns()
# Optional filtering steps
# Remove
if args.remove_cds_shorter_than:
min_length = args.remove_cds_shorter_than
sys.stderr.write("Removing CDS shorter than %s...\n" % min_length)
self.apply_filter("cds_shorter_than", min_length, "REMOVE")
if args.remove_cds_longer_than:
max_length = args.remove_cds_longer_than
sys.stderr.write("Removing CDS longer than %s...\n" % max_length)
self.apply_filter("cds_longer_than", max_length, "REMOVE")
if args.remove_exons_shorter_than:
min_length = args.remove_exons_shorter_than
sys.stderr.write("Removing exons shorter than %s...\n" % min_length)
self.apply_filter("exon_shorter_than", min_length, "REMOVE")
if args.remove_exons_longer_than:
max_length = args.remove_exons_longer_than
sys.stderr.write("Removing exons longer than %s...\n" % max_length)
self.apply_filter("exon_longer_than", max_length, "REMOVE")
if args.remove_introns_shorter_than:
min_length = args.remove_introns_shorter_than
sys.stderr.write("Removing exons shorter than %s...\n" % min_length)
self.apply_filter("intron_shorter_than", min_length, "REMOVE")
if args.remove_introns_longer_than:
max_length = args.remove_introns_longer_than
sys.stderr.write("Removing exons longer than %s...\n" % max_length)
self.apply_filter("intron_longer_than", max_length, "REMOVE")
if args.remove_genes_shorter_than:
min_length = args.remove_genes_shorter_than
sys.stderr.write("Removing genes shorter than %s...\n" % min_length)
self.apply_filter("gene_shorter_than", min_length, "REMOVE")
if args.remove_genes_longer_than:
max_length = args.remove_genes_longer_than
sys.stderr.write("Removing genes longer than %s...\n" % max_length)
self.apply_filter("gene_longer_than", max_length, "REMOVE")
# Flag
if args.flag_cds_shorter_than:
min_length = args.flag_cds_shorter_than
sys.stderr.write("Flagging CDS shorter than %s...\n" % min_length)
self.apply_filter("cds_shorter_than", min_length, "FLAG")
if args.flag_cds_longer_than:
max_length = args.flag_cds_longer_than
sys.stderr.write("Flagging CDS longer than %s...\n" % max_length)
self.apply_filter("cds_longer_than", max_length, "FLAG")
if args.flag_exons_shorter_than:
min_length = args.flag_exons_shorter_than
sys.stderr.write("Flagging exons shorter than %s...\n" % min_length)
self.apply_filter("exon_shorter_than", min_length, "FLAG")
if args.flag_exons_longer_than:
max_length = args.flag_exons_longer_than
sys.stderr.write("Flagging exons longer than %s...\n" % max_length)
self.apply_filter("exon_longer_than", max_length, "FLAG")
if args.flag_introns_shorter_than:
min_length = args.flag_introns_shorter_than
sys.stderr.write("Flagging exons shorter than %s...\n" % min_length)
self.apply_filter("intron_shorter_than", min_length, "FLAG")
if args.flag_introns_longer_than:
max_length = args.flag_introns_longer_than
sys.stderr.write("Flagging exons longer than %s...\n" % max_length)
self.apply_filter("intron_longer_than", max_length, "FLAG")
if args.flag_genes_shorter_than:
min_length = args.flag_genes_shorter_than
sys.stderr.write("Flagging genes shorter than %s...\n" % min_length)
self.apply_filter("gene_shorter_than", min_length, "FLAG")
if args.flag_genes_longer_than:
max_length = args.flag_genes_longer_than
sys.stderr.write("Flagging genes longer than %s...\n" % max_length)
self.apply_filter("gene_longer_than", max_length, "FLAG")
# Write fasta, gff and tbl file to output folder
# Open files
fasta = open(out_dir + '/genome.fasta', 'w')
gff = open(out_dir + '/genome.gff', 'w')
tbl = open(out_dir + '/genome.tbl', 'w')
proteins = open(out_dir + '/genome.proteins.fasta', 'w')
mrna = open(out_dir + '/genome.mrna.fasta', 'w')
removed = open(out_dir + '/genome.removed.gff', 'w')
stats_file = open(out_dir + '/genome.stats', 'w')
# Calculate stats on modified genome
sys.stderr.write("Calculating stats on modified genome\n")
for seq in self.seqs:
self.stats_mgr.update_alt(seq.stats())
# Write stats file
sys.stderr.write("Writing stats file to " + out_dir + "/ ...\n")
for line in self.stats_mgr.summary():
stats_file.write(line)
# Write fasta, gff, tbl, protein fasta
sys.stderr.write("Writing gff, tbl and fasta to " + out_dir + "/ ...\n")
gff.write("##gff-version 3\n")
for seq in self.seqs:
if seq.is_empty():
continue
fasta.write(seq.to_fasta())
gff.write(seq.to_gff())
if not args.skip_empty_scaffolds or len(seq.genes) > 0:
# Possibly skip empty sequences
tbl.write(seq.to_tbl())
proteins.write(seq.to_protein_fasta())
mrna.write(seq.to_mrna_fasta())
# Write removed.gff
for feature in self.removed_features:
removed.write(feature.to_gff())
# Close files
gff.close()
tbl.close()
fasta.close()
proteins.close()
removed.close()
stats_file.close()
def add_annotations_from_list(self, anno_list):
for seq in self.seqs:
seq.add_annotations_from_list(anno_list)
def trim_from_file(self, filename):
if not os.path.isfile(filename):
sys.stderr.write("Error: " + filename + " is not a file. Nothing trimmed.\n")
return
trimlist = read_bed_file(open(filename, 'rb'))
if not trimlist:
sys.stderr.write("Failed to read .bed file; nothing trimmed.\n")
return
else:
self.trim_from_list(trimlist)
def annotate_from_file(self, filename):
if not os.path.isfile(filename):
sys.stderr.write("Error: " + filename + " is not a file. Nothing annotated.\n")
return
annos = read_annotation_file(open(filename, 'rb'))
if not annos:
sys.stderr.write("Failed to read annotations from " + filename + "; no annotations added.\n")
return
else:
sys.stderr.write("Adding annotations to genome ...\n")
self.add_annotations_from_list(annos)
sys.stderr.write("...done\n")
def trim_from_list(self, trimlist):
for seq in self.seqs:
# In the case that there are multiple regions to trim in a single
# sequence, trim from the end so indices don't get messed up
to_trim_this_seq = [x for x in trimlist if x[0] == seq.header]
to_trim_this_seq = sorted(to_trim_this_seq, key=lambda _entry: _entry[2], reverse=True)
for entry in to_trim_this_seq:
removed_genes = seq.trim_region(entry[1], entry[2])
self.removed_features.extend(removed_genes)
sys.stderr.write("Trimmed " + entry[0] + " from ")
sys.stderr.write(str(entry[1]) + " to " + str(entry[2]) + "\n")
self.remove_empty_features(seq)
def get_filter_arg(self, filter_name):
return self.filter_mgr.get_filter_arg(filter_name)
def apply_filter(self, filter_name, val, filter_mode):
for seq in self.seqs:
self.filter_mgr.apply_filter(filter_name, val, filter_mode, seq)
self.remove_empty_features(seq)
def fix_terminal_ns(self):
for seq in self.seqs:
seq.remove_terminal_ns()
self.remove_empty_features(seq)
def fix_start_stop_codons(self):
for seq in self.seqs:
seq.create_starts_and_stops()
# Reading in files
def read_fasta(self, line):
reader = FastaReader()
self.seqs = reader.read(open(line, 'r'))
def read_gff(self, line, prefix):
# Takes prefix b/c reader returns comments, invalids, ignored
# and this method writes them to output files
# That's kind of messy
gffreader = GFFReader()
reader = open(line, 'rb')
genes, comments, invalids, ignored = gffreader.read_file(reader)
for gene in genes:
self.add_gene(gene)
# Write comments, invalid lines and ignored features
with open(prefix + "/genome.comments.gff", 'w') as comments_file:
for comment in comments:
comments_file.write(comment)
with open(prefix + "/genome.invalid.gff", 'w') as invalid_file:
for invalid in invalids:
invalid_file.write(invalid)
with open(prefix + "/genome.ignored.gff", 'w') as ignored_file:
for item in ignored:
ignored_file.write(item)
# Clean up
def remove_empty_features(self, seq):
"""Removes any empty mRNAs or genes from a seq and adds them to self.removed_features."""
self.removed_features.extend(seq.remove_empty_mrnas())
self.removed_features.extend(seq.remove_empty_genes())
def stats(self):
if not self.seqs:
return "error: no sequences"
else:
number_of_gagflags = 0
# TODO have stats mgr handle "number of sequences"
first_line = "Number of sequences: " + str(len(self.seqs)) + "\n"
sys.stderr.write("Calculating statistics on genome...\n")
self.stats_mgr.clear_alt()
for seq in self.seqs:
self.stats_mgr.update_alt(seq.stats())
number_of_gagflags += seq.number_of_gagflags()
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 remove_from_list(self, bad_list):
# First remove any seqs on the list
to_remove = []
for seq in self.seqs:
if seq.header in bad_list:
to_remove.append(seq)
if to_remove:
for seq in to_remove:
self.seqs.remove(seq)
sys.stderr.write("Warning: removing seq " + seq.header + ".\n")
sys.stderr.write("You must reload genome to get this sequence back.\n")
self.removed_features.extend(to_remove)
# Now pass the list down to each seq
for seq in self.seqs:
removed_from_seq = seq.remove_from_list(bad_list)
self.removed_features.extend(removed_from_seq)
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 __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.filter_mgr = FilterManager()
def setUp(self):
self.filter_mgr = FilterManager()
