def reportSlicesTXT(slices, sequence, maskFlag):
if maskFlag == 'DOM':
- coordstr = '|GlobDoms:'
+ coordstr = 'GlobDoms '
elif maskFlag == 'DIS':
- coordstr = '|Disorder:'
+ coordstr = 'Disorder '
else:
raise SystemExit
if slices == []:
def runGlobPlot():
try:
- smoothFrame = int(sys.argv[1])
- DOM_joinFrame = int(sys.argv[2])
- DOM_peakFrame = int(sys.argv[3])
- DIS_joinFrame = int(sys.argv[4])
- DIS_peakFrame = int(sys.argv[5])
- file = str(sys.argv[6])
+ smoothFrame = 10
+ DOM_joinFrame = 15
+ DOM_peakFrame = 74
+ DIS_joinFrame = 4
+ DIS_peakFrame = 5
+ file = str(sys.argv[1])
db = open(file,'r')
except:
print 'Usage:'
- print ' ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame FASTAfile'
- print ' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
- print ' Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
+ print ' ./GlobPipe.py FASTAfile'
raise SystemExit
parser = Fasta.RecordParser()
iterator = Fasta.Iterator(db,parser)
globdoms, globdis = getSlices(dydx_vector, DOM_joinFrame, DOM_peakFrame, DIS_joinFrame, DIS_peakFrame)
s_domMask, coordstrDOM = reportSlicesTXT(globdoms, seq, 'DOM')
s_final, coordstrDIS = reportSlicesTXT(globdis, s_domMask, 'DIS')
- sys.stdout.write('>'+cur_record.title+coordstrDOM+coordstrDIS+'\n')
+ sys.stdout.write('>'+cur_record.title+'\n')
+ sys.stdout.write('# '+coordstrDOM+'\n')
+ sys.stdout.write('# '+coordstrDIS+'\n')
# UNCOMMENT THIS IF NEED TO PRODUCE PER RESEDUE VALUES
+ sys.stdout.write('# RESIDUE' + '\t' + 'DYDX' + '\t' + 'RAW' + '\t' +'SMOOTHED\n')
for i in range(len(dydx_vector)):
# dydx (positive values seems to indicate disorder in rows more than ~6 chars) raw smoothed
sys.stdout.write(seq[i]+'\t'+fpformat.fix(dydx_vector[i],4)+ '\t'+fpformat.fix(smooth[i],4)+'\t'+fpformat.fix(sum_vector[i],4)+ '\n')