def test_indexstar_and_mapstar(self):
genome = make_fasta_file(num_sequences=2, seq_len=1000, rnd_seed=0)
fastq = make_fastq_file(genome=genome, rnd_seed=0)
command_basic = [
'iCount',
'indexstar',
genome,
self.dir,
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_basic), 0)
command_basic = [
'iCount',
'mapstar',
fastq,
self.dir,
self.dir2,
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_basic), 0)
def setUp(self):
self.dir = get_temp_dir()
self.index_dir = get_temp_dir()
self.genome = make_fasta_file(num_sequences=2, seq_len=1000)
self.reads = make_fastq_file(genome=self.genome)
self.annotation = make_file_from_list([
['1', '.', 'gene', '10', '20', '.', '+', '.', 'gene_id "A";'],
[
'1', '.', 'transcript', '10', '20', '.', '+', '.',
'gene_id "A"; transcript_id "AA";'
],
[
'1', '.', 'exon', '10', '20', '.', '+', '.',
'gene_id "A"; transcript_id "AA"; exon_number "1";'
],
])
warnings.simplefilter("ignore", ResourceWarning)
def test_indexstar_and_mapstar_full(self):
genome = make_fasta_file(num_sequences=2, seq_len=1000, rnd_seed=0)
fastq = make_fastq_file(genome=genome, rnd_seed=0)
command_full = [
'iCount',
'indexstar',
genome,
self.dir,
'--annotation',
self.gtf,
'--overhang',
'100',
'--overhang_min',
'8',
'--threads',
'1',
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_full), 0)
command_full = [
'iCount',
'mapstar',
fastq,
self.dir,
self.dir2,
'--annotation',
self.gtf,
'--multimax',
'50',
'--mismatches',
'2',
'--threads',
'1',
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_full), 0)
def setUp(self):
warnings.simplefilter("ignore", (ResourceWarning, ImportWarning))
# Make fai and fasta file:
self.fai_data = {'1': 1000}
self.fai = make_file_from_list(list(self.fai_data.items()), bedtool=False, extension='fai')
random.seed(0) # pylint:disable=no-member
random_seeds = random.randint(10**5, size=len(self.fai)) # pylint:disable=no-member
self.seqs = {name: make_sequence(size, rnd_seed=rseed) for (name, size), rseed in
zip(self.fai_data.items(), random_seeds)}
self.fasta = make_fasta_file(sequences=self.seqs.values(), headers=self.seqs.keys())
# Make annotation:
self.gtf = make_file_from_list(extension='gtf', data=[
# Gene #1, positive strand:
['1', '.', 'gene', '100', '499', '.', '+', '.', attrs(gid='G1')],
# Transcript #1
['1', '.', 'transcript', '100', '249', '.', '+', '.', attrs(gid='G1', tid='T1')],
['1', '.', 'exon', '100', '149', '.', '+', '.', attrs(gid='G1', tid='T1', exn=1)],
['1', '.', 'exon', '200', '229', '.', '+', '.', attrs(gid='G1', tid='T1', exn=2)],
['1', '.', 'CDS', '200', '229', '.', '+', '.', attrs(gid='G1', tid='T1', exn=2)],
['1', '.', 'exon', '240', '249', '.', '+', '.', attrs(gid='G1', tid='T1', exn=3)],
# Transcript #2
['1', '.', 'transcript', '240', '499', '.', '+', '.', attrs(gid='G1', tid='T2')],
['1', '.', 'exon', '240', '299', '.', '+', '.', attrs(gid='G1', tid='T2', exn=1)],
['1', '.', 'CDS', '240', '299', '.', '+', '.', attrs(gid='G1', tid='T2', exn=1)],
['1', '.', 'exon', '400', '499', '.', '+', '.', attrs(gid='G1', tid='T2', exn=2)],
['1', '.', 'CDS', '400', '499', '.', '+', '.', attrs(gid='G1', tid='T2', exn=2)],
# Gene #2, positive strand:
['1', '.', 'gene', '600', '799', '.', '+', '.', attrs(gid='G2')],
# Transcript #3
['1', '.', 'transcript', '600', '799', '.', '+', '.', attrs(gid='G2', tid='T3')],
['1', '.', 'exon', '600', '649', '.', '+', '.', attrs(gid='G2', tid='T3', exn=1)],
['1', '.', 'CDS', '600', '649', '.', '+', '.', attrs(gid='G2', tid='T3', exn=1)],
['1', '.', 'exon', '750', '799', '.', '+', '.', attrs(gid='G2', tid='T3', exn=2)],
['1', '.', 'CDS', '750', '799', '.', '+', '.', attrs(gid='G2', tid='T3', exn=2)],
# Gene #3, negative strand:
['1', '.', 'gene', '800', '899', '.', '-', '.', 'gene_id "G3";'],
# Transcript #4
['1', '.', 'transcript', '800', '899', '.', '-', '.', attrs(gid='G3', tid='T4')],
['1', '.', 'exon', '800', '899', '.', '-', '.', attrs(gid='G3', tid='T4', exn=1)],
['1', '.', 'CDS', '800', '899', '.', '-', '.', attrs(gid='G3', tid='T4', exn=1)],
])
# Define positions of cross-links:
self.read_data = [
# [name, chromosome, sequence_len, read_start, strand]
('name01:rbc:CCCC', '1', 50, 80, '+'),
('name02:rbc:CCCC', '1', 50, 140, '+'),
('name03:rbc:AAAA', '1', 50, 142, '+'),
('name04:rbc:CCCC', '1', 50, 142, '+'),
('name05:rbc:CCCC', '1', 30, 160, '+'),
('name06:rbc:CCCC', '1', 30, 163, '+'),
('name07:rbc:GGGG', '1', 30, 163, '+'),
('name08:rbc:CCCC', '1', 20, 205, '+'),
('name09:rbc:CCCC', '1', 50, 235, '+'),
('name10:rbc:CCCC', '1', 50, 480, '+'),
('name11:rbc:CCCC', '1', 30, 530, '+'),
('name12:rbc:CCCC', '1', 30, 610, '+'),
('name13:rbc:CCCC', '1', 30, 549, '-'),
]
# Make reads from genome, pointing to specific pre-detemrined cross-link positions:
random_seeds = random.randint(10**5, size=len(self.read_data)) # pylint:disable=no-member
self.reads = get_temp_file_name(extension='fastq')
with open(self.reads, 'wt') as ofile:
for (name, chrom, length, xlink, strand), rseed in zip(self.read_data, random_seeds):
seq = self.seqs[chrom][xlink: xlink + length]
if strand == '-':
seq = self.seqs[chrom][xlink - length: xlink]
compl_bases = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
seq = ''.join([compl_bases[nuc] for nuc in seq[::-1]])
ofile.write('@' + name + '\n')
ofile.write(seq + '\n')
ofile.write('+' + '\n')
ofile.write(
make_quality_scores(len(seq), min_chr=65, max_chr=73, rnd_seed=rseed) + '\n')
# Make a "strange" read:
# pylint: disable=undefined-loop-variable
seq = self.seqs[chrom][250: 295] + self.seqs[chrom][310: 380]
ofile.write('@' + 'name_strange:rbc:GGGG' + '\n')
ofile.write(seq + '\n')
ofile.write('+' + '\n')
ofile.write(
make_quality_scores(len(seq), min_chr=70, max_chr=73, rnd_seed=rseed) + '\n')