def parseLine(self,line):
line = line.rstrip('\n')
ff = line.split('\t')
#chr1 unknown CDS 3054734 3054733 . + -1 gene_id "ENSMUSG00000090025"; gene_name "ENSMUSG00000090025"; transcript_id "ENSMUST00000160944";
f = Feature()
f.qid = ff[0]
f.type1 = ff[1]
f.type2 = ff[2]
f.qstart = int(ff[3])
f.qend = int(ff[4])
if ff[5] != ".":
f.score = double(ff[5])
if ff[6] != ".":
if ff[6] == "+":
f.strand = 1
elif ff[6] == 1:
f.strand = 1
elif ff[6] == "-":
f.strand = -1
elif ff[6] == -1:
f.strand = -1
if ff[7] != ".":
f.phase = int(ff[7])
featf = ff[8].split(';')
for feat in featf:
feat = feat.strip()
tmp = feat.split(' ')
if len(tmp) == 2:
key = tmp[0].strip()
val = tmp[1].strip()
val = val.strip('"')
f.hitattr[key] = val
if key == "transcript_id":
f.hid = val
return f
def nextGFF(self):
for line in self.fh:
if line is None:
return
if re.search('^##FASTA', line):
return None
if re.search('^#', line):
continue
line = line.rstrip('\n')
ff = line.split('\t')
##gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
#!genome-build ASM72083v1
#!genome-build-accession NCBI_Assembly:GCF_000720835.1
##sequence-region NZ_JODT01000001.1 1 388890
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=67256
#NZ_JODT01000001.1 RefSeq region 1 388890 . + . ID=id0;Dbxref=taxon:67256;collection-date=2010;country=Japan: Suginami%2C Tokyo;culture-collection=NRRL:B-2120;gbkey=Src;isolation-source=garden soil;mol_type=genomic DNA;strain=NRRL B-2120;sub-species=achromogenes
#NZ_JODT01000001.1 RefSeq gene 283 1188 . - . ID=gene0;Name=IH25_RS0100010;gbkey=Gene;locus_tag=IH25_RS0100010
#NZ_JODT01000001.1 Protein Homology CDS 283 1188 . - 0 ID=cds0;Parent=gene0;Dbxref=Genbank:WP_030600633.1;Name=WP_030600633.1;gbkey=CDS;product=DeoR faimly transcriptional regulator;protein_id=WP_030600633.1;transl_table=11
#NZ_JODT01000001.1 RefSeq gene 1391 2839 . - . ID=gene1;Name=IH25_RS0100015;gbkey=Gene;locus_tag=IH25_RS0100015
#NZ_JODT01000001.1 Protein Homology CDS 1391 2839 . - 0 ID=cds1;Parent=gene1;Dbxref=Genbank:WP_030600636.1;Name=WP_030600636.1;Note=catalyzes the reduction of nonspecific electron acceptors such as 2%2C6-dimethyl-1%2C4-benzoquinone and 5-hydroxy-1%2C4-naphthaquinone%3B does not have lipoamide dehydrogenase activity;gbkey=CDS;product=flavoprotein disulfide reductase;protein_id=WP_030600636.1;transl_table=11
#NZ_JODT01000001.1 RefSeq gene 2936 3373 . + . ID=gene2;Name=IH25_RS0100020;gbkey=Gene;locus_tag=IH25_RS0100020
#NZ_JODT01000001.1 Protein Homology CDS 2936 3373 . + 0 ID=cds2;Parent=gene2;Dbxref=Genbank:WP_030600640.1;Name=WP_030600640.1;gbkey=CDS;product=gamma-glutamyl cyclotransferase;protein_id=WP_030600640.1;transl_table=11
#NZ_JODT01000001.1 RefSeq gene 3499 4323 . + . ID=gene3;Name=IH25_RS0100025;gbkey=Gene;locus_tag=IH25_RS0100025
#NZ_JODT01000001.1 Protein Homology CDS 3499 4323 . + 0 ID=cds3;Parent=gene3;Dbxref=Genbank:WP_03060
if len(ff) < 8:
raise Exception(
"GFF line needs 8 or more fields to parse [%s]" % line)
f = Feature()
f.qid = ff[0]
f.type1 = ff[1]
f.type2 = ff[2]
f.qstart = int(ff[3])
f.qend = int(ff[4])
f.score = ff[5]
f.strand = ff[6]
f.phase = ff[7]
if f.score == ".":
f.score = 0
else:
f.score = int(f.score)
if f.strand == "+":
f.strand = 1
if f.strand == "-":
f.strand = -1
if f.strand == ".":
f.strand = 0
if len(ff) > 8:
hidstr = ff[8]
hitattr = {}
hffarr = hidstr.split(';')
for hff in hffarr:
tmparr = hff.split('=')
hitattr[tmparr[0]] = tmparr[1]
f.hitattr = hitattr
return f