You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Traceback (most recent call last):
File "reditools2.0-master/src/cineca/parallel_reditools.py", line 576, in
little_files = sorted(little_files, key = lambda x: (keys.index(x[1]) if x[1] in keys else keys.index("chr"+x[1]), int(x[2])))
File "reditools2.0-master/src/cineca/parallel_reditools.py", line 576, in
little_files = sorted(little_files, key = lambda x: (keys.index(x[1]) if x[1] in keys else keys.index("chr"+x[1]), int(x[2])))
ValueError: 'chrKI270748' is not in list
solution:
line 568 : print(little_file)
line 569 : pieces = re.sub("..", "", os.path.basename(little_file)).split("#")
line 570 : pieces.insert(0, little_file)
line 571 : little_files.append(pieces)
......
line 574 : keys = chromosomes.keys()
the keys is ['chr1', 'chr10', 'chr11','KI270712.1', 'KI270706.1','GL000221.1']
but the little_files is [['test_results/temp/chr1#72347729#75371875.gz', 'chr1', '72347729', '75371875'],['test_results/temp/KI270711.1#4615#37277.gz', 'KI270711'],['test_results/temp/KI270330.1#1306#1455.gz', 'KI270330']]
So it is possible that something went wrong during the name conversion.
I check the line 569 : pieces = re.sub("..", "", os.path.basename(little_file)).split("#")
The identification character "..*" can remove the '.gz' character, while it also remove the decimal point of a chromosome sequence(KI270711.1--KI270711).
Correct it : pieces = re.sub(r".gz", "", os.path.basename(little_file)).split("#")
The text was updated successfully, but these errors were encountered:
Traceback (most recent call last):
File "reditools2.0-master/src/cineca/parallel_reditools.py", line 576, in
little_files = sorted(little_files, key = lambda x: (keys.index(x[1]) if x[1] in keys else keys.index("chr"+x[1]), int(x[2])))
File "reditools2.0-master/src/cineca/parallel_reditools.py", line 576, in
little_files = sorted(little_files, key = lambda x: (keys.index(x[1]) if x[1] in keys else keys.index("chr"+x[1]), int(x[2])))
ValueError: 'chrKI270748' is not in list
solution:
line 568 : print(little_file)
line 569 : pieces = re.sub("..", "", os.path.basename(little_file)).split("#")
line 570 : pieces.insert(0, little_file)
line 571 : little_files.append(pieces)
......
line 574 : keys = chromosomes.keys()
the keys is ['chr1', 'chr10', 'chr11','KI270712.1', 'KI270706.1','GL000221.1']
but the little_files is [['test_results/temp/chr1#72347729#75371875.gz', 'chr1', '72347729', '75371875'],['test_results/temp/KI270711.1#4615#37277.gz', 'KI270711'],['test_results/temp/KI270330.1#1306#1455.gz', 'KI270330']]
So it is possible that something went wrong during the name conversion.
I check the line 569 : pieces = re.sub("..", "", os.path.basename(little_file)).split("#")
The identification character "..*" can remove the '.gz' character, while it also remove the decimal point of a chromosome sequence(KI270711.1--KI270711).
Correct it : pieces = re.sub(r".gz", "", os.path.basename(little_file)).split("#")
The text was updated successfully, but these errors were encountered: