def main():
req_args = ['virus annotation file',
'% MSA cutoff']
examples = ['../../Data/ProfileScan/hiv.prosite',
'90']
utils_scripting.checkStart(sys.argv, req_args, examples, len(req_args), True)
annotation_file = sys.argv[1]
conserved_cutoff = float(sys.argv[2])
[virus2annotation, virus2proteinCount] = getCounts(annotation_file)
for vp in virus2annotation.keys():
for pattern in virus2annotation[vp]:
percent = (float(100) * float(len(virus2annotation[vp][pattern])) /
float(len(virus2proteinCount[vp])))
if percent >= conserved_cutoff:
print vp + '\t0\t0\t' + pattern + '\tseq\tELM'
sys.stderr.write(vp + '\t' + pattern + '\t' + str(percent) + '\n')
def main():
req_args = ['virus annotation file',
'annotation tool',
'% MSA cutoff']
examples = ['../../Data/ProfileScan/hiv.prosite',
'ProfileScan',
'90']
utils_scripting.checkStart(sys.argv, req_args, examples, len(req_args), True)
annotation_file = sys.argv[1]
tool = sys.argv[2]
conserved_cutoff = float(sys.argv[3])
protein2annotation = utils_motif.protein2annotation(annotation_file,
{tool:True})
[virus2annotation, virus2proteinCount] = getCounts(protein2annotation)
for vp in virus2annotation.keys():
for motif in virus2annotation[vp].keys():
percent = (float(100) * float(virus2annotation[vp][motif]) /
float(virus2proteinCount[vp]))
if percent >= conserved_cutoff:
print vp + '\t0\t0\t' + motif + '\tseq\t' + tool
sys.stderr.write(vp + '\t' + motif + '\t' + str(percent) + '\n')
for s in seq:
tempSeq = tempSeq + s
offset = 0
while match:
for elm in pattern2elm[elm_pattern]:
printResult(protein, elm,
match, tempSeq, offset)
tempSeq = tempSeq[int(match.start())+1:]
offset += int( match.start() ) + 1
match = p.search(tempSeq)
req_args = ['pattern file',
'fasta file']
examples = ['../../Data/ELM/elm2pattern',
'../../Data/FASTA/Human/hprd.intr.fasta']
utils_scripting.checkStart(sys.argv, req_args, examples, len(req_args), True)
input_pattern_file = sys.argv[1]
fasta_file = sys.argv[2]
pattern2regex = {}
pattern2elm = defaultdict(dict)
with open(input_pattern_file) as f:
for line in f:
elm, pattern = line.strip().split('\t')
pattern2elm[pattern][elm] = True
for pattern in pattern2elm:
pattern2regex[pattern] = re.compile(pattern)
for protein, seq in utils.fasta_iter(fasta_file):
matchSeq(protein, seq, pattern2elm, pattern2regex)
