validate_genelocustatsoptions
)
from abgpgenelocusdirectory import AbgpGeneLocusDirectory
from lib_sequencerepetitiveness import annotatedproteinsequencerepetitivenesscheck
# construct the command line option parser
parser = abgpoptparser()
genelocustatsoptions(parser)
parser.remove_option('--explain')
# parse the command line & validate
(OPTIONS, args) = parser.parse_args()
validate_genelocustatsoptions(parser,OPTIONS)
# change directory to the one specified by optparse option
os.chdir(OPTIONS.DIRECTORY)
locus = AbgpGeneLocusDirectory(OPTIONS.DIRECTORY)
input = locus.toinputdict()
# do geneconfirmation
input,gene_status = geneconfirmation(input,verbose=True)
# do a protein sequence repetitiveness check
IS_REPETITIVE = annotatedproteinsequencerepetitivenesscheck(input)
# do a check on tiny/small exons
HAS_SMALL_OR_TINY_EXONS = annotatedgeneexonsizeevaluation(input)
# do check on noncannocical splice sites
for org in input.keys():
status, warnings = confirmcanonicalsplicesites(input[org]['genomeseq'],
input[org]['gff-gene'],exon_fmethod=GFF_CDS_FMETHOD,verbose=False)
thisoption = parser.get_option('--dirwithloci')
thisoption.help = 'give statistics for all the AbfgpGeneLocusDirectories in this --dirwithloci'
thisoption = parser.get_option('--filewithloci')
thisoption.help = 'give statistics for all the AbfgpGeneLocusDirectories listed in this --filewithloci'
(OPTIONS, args) = parser.parse_args()
OPTIONS.target = None # dummy option
validate_abgpinputoptions(parser,OPTIONS)
validate_abgpoptions(parser,OPTIONS)
################################################################################
################################################################################
if OPTIONS.loci:
input = {} # input data structure, empty
for locusdir in OPTIONS.loci:
locus = AbgpGeneLocusDirectory(locusdir)
locuskey = locus._create_auto_key(
identifier2organism=ABGP_LOCUS_IDENTIFIER2ORGANISM_MAPPING
)
if input.has_key(locuskey):
for suffix in list('abcdefghijklmnopqrstuvwxyz'):
if not input.has_key(locuskey+suffix):
input.update( locus.toinputdict(key=locuskey+suffix) )
break
else:
input.update( locus.toinputdict(key=locuskey) )
else:
print "Exception.NoAbgpGeneLocusDirectoriesProvided"
print ""
parser.print_help()
sysexit()