def write_output_file(outDir, res, name, e_di, sum, exMat):
'''
Write the output of edits and bowtie files.
'''
fname = '{}/{}/{}_{}.txt'.format(outDir, name, res, name)
with open(fname, 'a+') as f:
for k, v in e_di.iteritems():
f.write('{}\tCount:{}\tEM:{}'.format(k, ftoi(sum[k]), ftoi(exMat[k])))
for edit in sorted(v):
item = '{}:{}'.format(edit, ftoi(v[edit]))
f.write('\t{}'.format(item))
f.write('\n')
with open(fname, 'r') as f:
logging.info(fname)
logging.info(f.read())
def write_output_file(outDir, res, name, e_di, sum, exMat):
'''
Write the output of edits and bowtie files.
'''
fname = '{}/{}/{}_{}.txt'.format(outDir, name, res, name)
with open(fname, 'a+') as f:
for k, v in e_di.iteritems():
f.write('{}\tCount:{}\tEM:{}'.format(k, ftoi(sum[k]),
ftoi(exMat[k])))
for edit in sorted(v):
item = '{}:{}'.format(edit, ftoi(v[edit]))
f.write('\t{}'.format(item))
f.write('\n')
with open(fname, 'r') as f:
logging.info(fname)
logging.info(f.read())
def write_processed_shrimp_output(hits, tags, mirLi, mirStr, shrimp_dir):
'''
Write the processed shrimp output to chromosomal directory in g1Results.
'''
dname = '{}/g1Results'.format(os.path.dirname(shrimp_dir))
read_size = os.path.basename(shrimp_dir)
for win, tag in hits.iteritems():
chr, st, sp, str = alter_window_name(win)
dirName = '{}/{}'.format(dname, chr)
if not os.path.exists(dirName):
os.makedirs(dirName)
fname = '{}/{}.results_{}'.format(dirName, win, read_size)
if len(tag) > 0:
with open(fname, 'w') as fo:
for h in hits[win]:
readTag, window, strand, cSt, cEn, rSt, rEn, rLen, score, estr, null = hits[win][h].split('\t')
if 'M' in str:
pos = int(sp) - int(cEn)
winStr = '-'
else:
pos = int(st) + int(cSt)
winStr = '+'
mir = check_if_mir(chr, pos, winStr, mirLi, mirStr)
fo.write('{}{}\t{}\n'.format(hits[win][h], mir, ftoi(tags[h][win])))
def write_processed_shrimp_output(hits, tags, mirLi, mirStr, shrimp_dir):
'''
Write the processed shrimp output to chromosomal directory in g1Results.
'''
dname = '{}/g1Results'.format(os.path.dirname(shrimp_dir))
read_size = os.path.basename(shrimp_dir)
for win, tag in hits.iteritems():
chr, st, sp, str = alter_window_name(win)
dirName = '{}/{}'.format(dname, chr)
if not os.path.exists(dirName):
try:
os.makedirs(dirName)
except:
pass
fname = '{}/{}.results_{}'.format(dirName, win, read_size)
if len(tag) > 0:
with open(fname, 'w') as fo:
for h in hits[win]:
readTag, window, strand, cSt, cEn, rSt, rEn, rLen, score, estr, null = hits[win][h].split('\t')
if 'M' in str:
pos = int(sp) - int(cEn)
winStr = '-'
else:
pos = int(st) + int(cSt)
winStr = '+'
mir = check_if_mir(chr, pos, winStr, mirLi, mirStr)
fo.write('{}{}\t{}\n'.format(hits[win][h], mir, ftoi(tags[h][win])))
