def getGTFcontent(gtf_file):
"""
Extract GTF features
"""
GFH = _open_file(gtf_file)
gtf_content, recall = dict(), None
for rec in GFH:
rec = rec.strip('\n\r')
#skip empty line fasta identifier and commented line
if not rec or rec[0] in ['#', '>']:
continue
#skip the genome sequence
if not re.search('\t', rec):
continue
parts = rec.split('\t')
assert len(parts) >= 8, rec
if re.search(r'^(start_codon|start-codon|startcodon)$', parts[2], re.IGNORECASE):
continue
gid= tid= gname= tname= ttype = None
for attb in parts[-1].split(';'):
if re.search(r'^\s?$', attb):
continue
attb = re.sub('"', '', attb).strip()
attb = attb.split()
if re.search(r'^(gene_id|geneid|name)$', attb[0], re.IGNORECASE):
gid = attb[1]
elif re.search(r'^(transcript_id|transcriptId)$', attb[0], re.IGNORECASE):
tid = attb[1]
elif re.search(r'^(gene_name|genename)$', attb[0], re.IGNORECASE):
gname = attb[1]
elif re.search(r'^(transcript_name|transcriptname)$', attb[0], re.IGNORECASE):
tname = attb[1]
elif re.search(r'^(transcript_type)$', attb[0], re.IGNORECASE):
ttype = attb[1]
if gid == tid: #UCSC GTF files, gene & transcript have same identifier
gid = 'Gene:'+str(gid)
tid = 'Transcript:'+str(tid)
if tid == None: #JGI GTF file dont have transcript ID for CDS line
tid = recall
exon= cds= sp_cod= st_cod = []
if re.search(r'^exon$', parts[2], re.IGNORECASE):
exon = [(int(parts[3]), int(parts[4]))]
elif re.search(r'^CDS$', parts[2], re.IGNORECASE):
cds = [(int(parts[3]), int(parts[4]))]
elif re.search(r'^(stop_codon|stop-codon|stopcodon)$', parts[2], re.IGNORECASE):
sp_cod = [(int(parts[3]), int(parts[4]))]
else: #other lines are not required to GFF line
continue
#creating feature connections
if parts[0] in gtf_content: # adding to existing chromosome
if (gid, parts[1]) in gtf_content[parts[0]].keys(): # adding to existing gene
if tid in gtf_content[parts[0]][(gid, parts[1])].keys(): # adding to existing transcript
if exon:
gtf_content[parts[0]][(gid, parts[1])][tid]['exon'].append(exon[0])
elif cds:
gtf_content[parts[0]][(gid, parts[1])][tid]['CDS'].append(cds[0])
elif sp_cod:
gtf_content[parts[0]][(gid, parts[1])][tid]['sp_cod'].append(sp_cod[0])
else: # inserting new transcript
gtf_content[parts[0]][(gid, parts[1])][tid] = dict(exon = exon,
CDS = cds,
sp_cod = sp_cod,
info = [parts[6], parts[5], gname, tname, ttype])
else: # inserting new gene
gtf_content[parts[0]][(gid, parts[1])] = {tid : dict(exon = exon,
CDS = cds,
sp_cod = sp_cod,
info = [parts[6], parts[5], gname, tname, ttype])}
else: # inserting new chromosome identifier
gtf_content[parts[0]] = {(gid, parts[1]) : {tid : dict(exon = exon,
CDS = cds,
sp_cod = sp_cod,
info = [parts[6], parts[5], gname, tname, ttype])}}
recall = tid #set previous id for CDS line
GFH.close()
return gtf_content
def getGTFcontent(gtf_file):
"""
Extract GTF features
"""
GFH = _open_file(gtf_file)
gtf_content, recall = dict(), None
for rec in GFH:
rec = rec.strip('\n\r')
#skip empty line fasta identifier and commented line
if not rec or rec[0] in ['#', '>']:
continue
#skip the genome sequence
if not re.search('\t', rec):
continue
parts = rec.split('\t')
assert len(parts) >= 8, rec
if re.search(r'^(start_codon|start-codon|startcodon)$', parts[2],
re.IGNORECASE):
continue
gid = tid = gname = tname = ttype = None
for attb in parts[-1].split(';'):
if re.search(r'^\s?$', attb):
continue
attb = re.sub('"', '', attb).strip()
attb = attb.split()
if re.search(r'^(gene_id|geneid|name)$', attb[0], re.IGNORECASE):
gid = attb[1]
elif re.search(r'^(transcript_id|transcriptId)$', attb[0],
re.IGNORECASE):
tid = attb[1]
elif re.search(r'^(gene_name|genename)$', attb[0], re.IGNORECASE):
gname = attb[1]
elif re.search(r'^(transcript_name|transcriptname)$', attb[0],
re.IGNORECASE):
tname = attb[1]
elif re.search(r'^(transcript_type)$', attb[0], re.IGNORECASE):
ttype = attb[1]
if gid == tid: #UCSC GTF files, gene & transcript have same identifier
gid = 'Gene:' + str(gid)
tid = 'Transcript:' + str(tid)
if tid == None: #JGI GTF file dont have transcript ID for CDS line
tid = recall
exon = cds = sp_cod = st_cod = []
if re.search(r'^exon$', parts[2], re.IGNORECASE):
exon = [(int(parts[3]), int(parts[4]))]
elif re.search(r'^CDS$', parts[2], re.IGNORECASE):
cds = [(int(parts[3]), int(parts[4]))]
elif re.search(r'^(stop_codon|stop-codon|stopcodon)$', parts[2],
re.IGNORECASE):
sp_cod = [(int(parts[3]), int(parts[4]))]
else: #other lines are not required to GFF line
continue
#creating feature connections
if parts[0] in gtf_content: # adding to existing chromosome
if (gid, parts[1]
) in gtf_content[parts[0]].keys(): # adding to existing gene
if tid in gtf_content[parts[0]][(
gid,
parts[1])].keys(): # adding to existing transcript
if exon:
gtf_content[parts[0]][(gid,
parts[1])][tid]['exon'].append(
exon[0])
elif cds:
gtf_content[parts[0]][(gid,
parts[1])][tid]['CDS'].append(
cds[0])
elif sp_cod:
gtf_content[parts[0]][(
gid, parts[1])][tid]['sp_cod'].append(sp_cod[0])
else: # inserting new transcript
gtf_content[parts[0]][(gid, parts[1])][tid] = dict(
exon=exon,
CDS=cds,
sp_cod=sp_cod,
info=[parts[6], parts[5], gname, tname, ttype])
else: # inserting new gene
gtf_content[parts[0]][(gid, parts[1])] = {
tid:
dict(exon=exon,
CDS=cds,
sp_cod=sp_cod,
info=[parts[6], parts[5], gname, tname, ttype])
}
else: # inserting new chromosome identifier
gtf_content[parts[0]] = {
(gid, parts[1]): {
tid:
dict(exon=exon,
CDS=cds,
sp_cod=sp_cod,
info=[parts[6], parts[5], gname, tname, ttype])
}
}
recall = tid #set previous id for CDS line
GFH.close()
return gtf_content
pc_final_map = dict()
for ptype, ctypes in pc_map.items():
unique_ctypes = list(set(ctypes))
unique_ctypes.sort()
pc_final_map[ptype] = unique_ctypes
# some cases the GFF file represents a single feature type
if not pc_final_map:
for fid, stypes in parent_sts.items():
pc_final_map[stypes] = dict()
# generate a report on feature id mapping in the file
print '------------------------------------------------------'
print 'Parent feature type | Associated child feature type(s)'
print '------------------------------------------------------'
for key, value in pc_final_map.items():
print key[0], key[1]
for child_to in value:
print '\t\t|',child_to[0], child_to[1]
print
print '------------------------------------------------------'
if __name__=='__main__':
try:
gff_file = sys.argv[1]
except:
print "Incorrect arguments supplied"
print __doc__
sys.exit(-1)
gff_handle = _open_file(gff_file)
parent_child_id_map(gff_handle)
def gbk_parse(fname):
"""
Extract genome annotation recods from genbank format
"""
fhand = _open_file(gbkfname)
unk = 1
for record in SeqIO.parse(fhand, "genbank"):
gene_tags = dict()
tx_tags = collections.defaultdict(list)
exon = collections.defaultdict(list)
cds = collections.defaultdict(list)
mol_type, chr_id = None, None
for rec in record.features:
if rec.type == 'source':
mol_type = rec.qualifiers['mol_type'][0]
try:
chr_id = rec.qualifiers['chromosome'][0]
except:
chr_id = record.name
continue
strand='-'
strand='+' if rec.strand>0 else strand
fid = None
try:
fid = rec.qualifiers['gene'][0]
except:
pass
transcript_id = None
try:
transcript_id = rec.qualifiers['transcript_id'][0]
except:
pass
if re.search(r'gene', rec.type):
gene_tags[fid] = (rec.location._start.position+1,
rec.location._end.position,
strand,
rec.type,
rec.qualifiers['note'][0])
elif rec.type == 'exon':
exon[fid].append((rec.location._start.position+1,
rec.location._end.position))
elif rec.type=='CDS':
cds[fid].append((rec.location._start.position+1,
rec.location._end.position))
else:
# get all transcripts
if transcript_id:
tx_tags[fid].append((rec.location._start.position+1,
rec.location._end.position,
transcript_id,
rec.type))
# record extracted, generate feature table
unk = feature_table(chr_id, mol_type, strand, gene_tags, tx_tags, cds, exon, unk)
#break
fhand.close()
for ptype, ctypes in pc_map.items():
unique_ctypes = list(set(ctypes))
unique_ctypes.sort()
pc_final_map[ptype] = unique_ctypes
# some cases the GFF file represents a single feature type
if not pc_final_map:
for fid, stypes in parent_sts.items():
pc_final_map[stypes] = dict()
# generate a report on feature id mapping in the file
print '------------------------------------------------------'
print 'Parent feature type | Associated child feature type(s)'
print '------------------------------------------------------'
for key, value in pc_final_map.items():
print key[0], key[1]
for child_to in value:
print '\t\t|', child_to[0], child_to[1]
print
print '------------------------------------------------------'
if __name__ == '__main__':
try:
gff_file = sys.argv[1]
except:
print "Incorrect arguments supplied"
print __doc__
sys.exit(-1)
gff_handle = _open_file(gff_file)
parent_child_id_map(gff_handle)
def bed_parse(qfile, source_name):
"""
Process BED file
"""
BEDfh = _open_file(qfile)
print "##gff-version 3"
for rec in BEDfh:
rec = rec.strip("\n\r")
if not rec or rec[0] in ["#"]:
continue
if not re.search("\t", rec):
continue
line = rec.split("\t")
assert len(line) >= 12, rec
# checking the consistency b/w start of exon and number of exons
if len(line[-1].split(",")) != len(line[-2].split(",")):
continue
rstart = line[-1].split(",")
if rstart[-1] == "":
rstart.pop()
exon_len = line[-2].split(",")
if exon_len[-1] == "":
exon_len.pop()
if line[5] != "+" and line[5] != "-":
line[5] = "." # replace the unknown strand with '.'
pline = [
str(line[0]),
source_name,
"gene",
str(int(line[1]) + 1),
line[2],
line[4],
line[5],
".",
"ID=Gene:" + line[3] + ";Name=Gene:" + line[3],
]
print "\t".join(pline)
pline = [
str(line[0]),
source_name,
"transcript",
str(int(line[1]) + 1),
line[2],
line[4],
line[5],
".",
"ID=" + line[3] + ";Name=" + line[3] + ";Parent=Gene:" + line[3],
]
print "\t".join(pline)
st = int(line[1])
for ex_cnt in range(int(line[-3])):
start = st + int(rstart[ex_cnt]) + 1
stop = start + int(exon_len[ex_cnt]) - 1
if ex_cnt > 0:
pline = [
str(line[0]),
source_name,
"intron",
str(intron_start),
str(start - 1),
line[4],
line[5],
".",
"Parent=" + line[3],
]
print "\t".join(pline)
pline = [
str(line[0]),
source_name,
"exon",
str(start),
str(stop),
line[4],
line[5],
".",
"Parent=" + line[3],
]
print "\t".join(pline)
intron_start = stop + 1
BEDfh.close()
def gbk_parse(fname):
"""
Extract genome annotation recods from genbank format
"""
fhand = _open_file(gbkfname)
unk = 1
for record in SeqIO.parse(fhand, "genbank"):
gene_tags = dict()
tx_tags = collections.defaultdict(list)
exon = collections.defaultdict(list)
cds = collections.defaultdict(list)
mol_type, chr_id = None, None
for rec in record.features:
if rec.type == 'source':
mol_type = rec.qualifiers['mol_type'][0]
try:
chr_id = rec.qualifiers['chromosome'][0]
except:
chr_id = record.name
continue
strand = '-'
strand = '+' if rec.strand > 0 else strand
fid = None
try:
fid = rec.qualifiers['gene'][0]
except:
pass
transcript_id = None
try:
transcript_id = rec.qualifiers['transcript_id'][0]
except:
pass
if re.search(r'gene', rec.type):
gene_tags[fid] = (rec.location._start.position + 1,
rec.location._end.position, strand, rec.type,
rec.qualifiers['note'][0])
elif rec.type == 'exon':
exon[fid].append((rec.location._start.position + 1,
rec.location._end.position))
elif rec.type == 'CDS':
cds[fid].append((rec.location._start.position + 1,
rec.location._end.position))
else:
# get all transcripts
if transcript_id:
tx_tags[fid].append(
(rec.location._start.position + 1,
rec.location._end.position, transcript_id, rec.type))
# record extracted, generate feature table
unk = feature_table(chr_id, mol_type, strand, gene_tags, tx_tags, cds,
exon, unk)
#break
fhand.close()