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])))