def check_dir_download(self):
found = worldbase.dir(download=True)
found.sort()
found2 = worldbase.dir('', download=True)
found2.sort()
assert len(found) == 0
assert found == found2
def check_dir_download(self):
found = worldbase.dir(download=True)
found.sort()
found2 = worldbase.dir('', download=True)
found2.sort()
assert len(found) == 0
assert found == found2
def check_dir_re(self):
expected=['Bio.Annotation.annoDB', 'Bio.Annotation.map',
'Bio.Seq.Swissprot.sp42', 'Bio.Seq.frag', 'Bio.Seq.spmap']
expected.sort()
found = worldbase.dir('^Bio', 'r')
found.sort()
assert found == expected
expected = ['Bio.Seq.Swissprot.sp42', 'Bio.Seq.spmap']
expected.sort()
found = worldbase.dir('^Bio\..+\.sp', 'r')
found.sort()
assert found == expected
def check_dir_re(self):
expected = [
'Bio.Annotation.annoDB', 'Bio.Annotation.map',
'Bio.Seq.Swissprot.sp42', 'Bio.Seq.frag', 'Bio.Seq.spmap'
]
expected.sort()
found = worldbase.dir('^Bio', 'r')
found.sort()
assert found == expected
expected = ['Bio.Seq.Swissprot.sp42', 'Bio.Seq.spmap']
expected.sort()
found = worldbase.dir('^Bio\..+\.sp', 'r')
found.sort()
assert found == expected
def check_dir_noargs(self):
found = worldbase.dir()
found.sort()
found2 = worldbase.dir('')
found2.sort()
assert found == found2
def check_dir_noargs(self):
found = worldbase.dir()
found.sort()
found2 = worldbase.dir('')
found2.sort()
assert found == found2
def main():
usage = 'usage: %prog [options] <transcript id>'
parser = OptionParser(usage)
parser.add_option(
'-a',
dest='align_t',
type='float',
default=0.01,
help='Minimum % of the transcript that must align [Default: %default]')
parser.add_option(
'-l',
dest='lncrna_gtf',
default='/Users/dk/research/common/data/lncrna/lnc_catalog.gtf',
help='lncRNA gtf file [Default: %default]')
parser.add_option(
'-m',
dest='merge_t',
type='int',
default=40,
help=
'Minimum distance between alignment blocks to merge into a single exon [Default: %default]'
)
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide transcript id and genome')
else:
transcript_id = args[0]
# get human genome
hg19 = worldbase.Bio.Seq.Genome.HUMAN.hg19()
# get gene exon intervals
gene_ivals = []
transcript_length = 0
for line in open(options.lncrna_gtf):
a = line.split('\t')
kv = gff.gtf_kv(a[8])
if kv['transcript_id'] == transcript_id:
chrom = a[0]
start = int(a[3])
end = int(a[4])
strand = 1 * (a[6] == '+') - 1 * (
a[6] == '-') # assuming all orientations are the same
gene_id = kv['gene_id']
gene_ivals.append(hg19[chrom][start:end])
transcript_length += end - start
# get hg19 msa
msa = worldbase.Bio.MSA.UCSC.hg19_multiz46way()
# map returned sequences back to genome name
idDict = ~(msa.seqDict)
# hash alignments by genome
genome_blocks = {}
for gi in gene_ivals:
for src, dest, edg in msa[gi].edges():
genome_blocks.setdefault(idDict[dest], []).append(dest)
#print repr(gi), repr(src), repr(dest), idDict[dest], edg.length()
# check for enough alignment
for gen_chr in genome_blocks.keys():
aligned_nt = sum([b.stop - b.start for b in genome_blocks[gen_chr]])
print gen_chr, aligned_nt, float(aligned_nt) / transcript_length
if aligned_nt < options.align_t * transcript_length:
del genome_blocks[gen_chr]
# for each genome
worldbase_genomes = worldbase.dir('Bio.Seq.Genome')
for gen_chr in genome_blocks:
genome_blocks[gen_chr].sort(block_cmp)
# make gtf lines / merge alignments
b = genome_blocks[gen_chr][0]
gff_strand = '+' * (b.orientation
== strand) + '-' * (b.orientation != strand)
gff_cols = [[
b.id, 'PygrTransMap', 'exon', b._abs_interval[0] + 1,
b._abs_interval[1], '.', gff_strand, '.',
'gene_id "%s"; transcript_id "%s"; exon_number "1";' % (
gene_id,
transcript_id,
)
]]
exon_num = 2
for i in range(1, len(genome_blocks[gen_chr])):
if gff_cols[-1][4] + options.merge_t >= genome_blocks[gen_chr][
i]._abs_interval[0]:
# merge with prior
gff_cols[-1][4] = genome_blocks[gen_chr][i]._abs_interval[1]
else:
# add new exon
b = genome_blocks[gen_chr][i]
gff_cols.append([
b.id, 'PygrTransMap', 'exon', b._abs_interval[0] + 1,
b._abs_interval[1], '.', gff_strand, '.',
'gene_id "%s"; transcript_id "%s"; exon_number "%d";' %
(gene_id, transcript_id, exon_num)
])
exon_num += 1
# print gtf
gtf_out = open('%s_%s.gtf' % (transcript_id, gen_chr), 'w')
for gc in gff_cols:
print >> gtf_out, '\t'.join([str(c) for c in gc])
gtf_out.close()
# get genomic sequence
gen = gen_chr[:gen_chr.find('.')]
chrom = gen_chr[gen_chr.find('.') + 1:]
wb_gen = [wgen for wgen in worldbase_genomes if wgen.find(gen) != -1]
if len(wb_gen) > 1:
print >> sys.stderr, 'Detected >1 worldbase genome matching %s' % gen
print >> sys.stderr, ' '.join(wb_gen)
gen_seq = worldbase.__call__(wb_gen[0])
# get transcript sequence
seq = ''
for gc in gff_cols:
seq += str(gen_seq[gc[0]][gc[3] - 1:gc[4]])
if gff_cols[0][6] == '-':
seq = dna.rc(seq)
# print fasta
fasta_out = open('%s_%s.fa' % (transcript_id, gen_chr), 'w')
print >> fasta_out, '>%s_gene=%s_%s\n%s' % (transcript_id, gene_id,
gen_chr, seq)
fasta_out.close()
def main():
usage = 'usage: %prog [options] <transcript id>'
parser = OptionParser(usage)
parser.add_option('-a', dest='align_t', type='float', default=0.01, help='Minimum % of the transcript that must align [Default: %default]')
parser.add_option('-l', dest='lncrna_gtf', default='/Users/dk/research/common/data/lncrna_mm9/lnc_catalog.gtf', help='lncRNA gtf file [Default: %default]')
parser.add_option('-m', dest='merge_t', type='int', default=40, help='Minimum distance between alignment blocks to merge into a single exon [Default: %default]')
(options,args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide transcript id')
else:
transcript_id = args[0]
# get human genome
mm9 = worldbase.Bio.Seq.Genome.MOUSE.mm9()
# get gene exon intervals
gene_ivals = []
transcript_length = 0
for line in open(options.lncrna_gtf):
a = line.split('\t')
kv = gff.gtf_kv(a[8])
if kv['transcript_id'] == transcript_id:
chrom = a[0]
start = int(a[3])
end = int(a[4])
strand = 1*(a[6]=='+') - 1*(a[6]=='-') # assuming all orientations are the same
gene_id = kv['gene_id']
gene_ivals.append(mm9[chrom][start:end])
transcript_length += end-start
# get mm9 msa
msa = worldbase.Bio.MSA.UCSC.mm9_multiz30way()
# map returned sequences back to genome name
idDict = ~(msa.seqDict)
# hash alignments by genome
genome_blocks = {}
for gi in gene_ivals:
for src, dest, edg in msa[gi].edges():
genome_blocks.setdefault(idDict[dest],[]).append(dest)
#print repr(gi), repr(src), repr(dest), idDict[dest], edg.length()
# check for enough alignment
for gen_chr in genome_blocks.keys():
aligned_nt = sum([b.stop-b.start for b in genome_blocks[gen_chr]])
print gen_chr, aligned_nt, float(aligned_nt)/transcript_length
if aligned_nt < options.align_t*transcript_length:
del genome_blocks[gen_chr]
# for each genome
worldbase_genomes = worldbase.dir('Bio.Seq.Genome')
for gen_chr in genome_blocks:
genome_blocks[gen_chr].sort(block_cmp)
# make gtf lines / merge alignments
b = genome_blocks[gen_chr][0]
gff_strand = '+'*(b.orientation==strand) + '-'*(b.orientation!=strand)
gff_cols = [[b.id, 'PygrTransMap', 'exon', b._abs_interval[0]+1, b._abs_interval[1], '.', gff_strand, '.', 'gene_id "%s"; transcript_id "%s"; exon_number "1";' % (gene_id, transcript_id,)]]
exon_num = 2
for i in range(1,len(genome_blocks[gen_chr])):
if gff_cols[-1][4] + options.merge_t >= genome_blocks[gen_chr][i]._abs_interval[0]:
# merge with prior
gff_cols[-1][4] = genome_blocks[gen_chr][i]._abs_interval[1]
else:
# add new exon
b = genome_blocks[gen_chr][i]
gff_cols.append([b.id, 'PygrTransMap', 'exon', b._abs_interval[0]+1, b._abs_interval[1], '.', gff_strand, '.', 'gene_id "%s"; transcript_id "%s"; exon_number "%d";' % (gene_id, transcript_id, exon_num)])
exon_num += 1
# print gtf
gtf_out = open('%s_%s.gtf' % (transcript_id, gen_chr), 'w')
for gc in gff_cols:
print >> gtf_out, '\t'.join([str(c) for c in gc])
gtf_out.close()
# get genomic sequence
gen = gen_chr[:gen_chr.find('.')]
chrom = gen_chr[gen_chr.find('.')+1:]
wb_gen = [wgen for wgen in worldbase_genomes if wgen.find(gen) != -1]
if len(wb_gen) > 1:
print >> sys.stderr, 'Detected >1 worldbase genome matching %s' % gen
print >> sys.stderr, ' '.join(wb_gen)
gen_seq = worldbase.__call__(wb_gen[0])
# get transcript sequence
seq = ''
for gc in gff_cols:
seq += str(gen_seq[gc[0]][gc[3]-1:gc[4]])
if gff_cols[0][6] == '-':
seq = dna.rc(seq)
# print fasta
fasta_out = open('%s_%s.fa' % (transcript_id, gen_chr), 'w')
print >> fasta_out, '>%s_gene=%s_%s\n%s' % (transcript_id,gene_id,gen_chr,seq)
fasta_out.close()