I have the below file names and would like to group them:
Group1:
C7_S6_L001.sorted.bam
C7_S6_L002.sorted.bam
C7_S6_L003.sorted.bam
C7_S6_L004.sorted.bam
Group2:
CL3_S8_L001.sorted.bam
CL3_S8_L002.sorted.bam
CL3_S8_L003.sorted.bam
CL3_S8_L004.sorted.bam
Group3:
CL5-B1_S4_L001.sorted.bam
CL5-B1_S4_L002.sorted.bam
CL5-B1_S4_L003.sorted.bam
CL5-B1_S4_L004.sorted.bam
How would the regular expression looks for it?
Thank you in advance.
Assuming the grouping key is everything before the _L and digits at the beginning of file names, you can use the following regular expression to capture the group keys using saving groups:
([A-Z0-9-_]+)_L\d{3}\.sorted\.bam
Working example using defaultdict collection:
from collections import defaultdict
from pprint import pprint
import re
filenames = [
"C7_S6_L001.sorted.bam",
"C7_S6_L002.sorted.bam",
"C7_S6_L003.sorted.bam",
"C7_S6_L004.sorted.bam",
"CL3_S8_L001.sorted.bam",
"CL3_S8_L002.sorted.bam",
"CL3_S8_L003.sorted.bam",
"CL3_S8_L004.sorted.bam",
"CL5-B1_S4_L001.sorted.bam",
"CL5-B1_S4_L002.sorted.bam",
"CL5-B1_S4_L003.sorted.bam",
"CL5-B1_S4_L004.sorted.bam"
]
pattern = re.compile(r"([A-Z0-9-_]+)_L\d{3}\.sorted\.bam")
grouped = defaultdict(list)
for filename in filenames:
match = pattern.search(filename)
if match:
key = match.group(1)
grouped[key].append(filename)
pprint(grouped)
Prints:
defaultdict(<class 'list'>,
{'C7_S6': ['C7_S6_L001.sorted.bam',
'C7_S6_L002.sorted.bam',
'C7_S6_L003.sorted.bam',
'C7_S6_L004.sorted.bam'],
'CL3_S8': ['CL3_S8_L001.sorted.bam',
'CL3_S8_L002.sorted.bam',
'CL3_S8_L003.sorted.bam',
'CL3_S8_L004.sorted.bam'],
'CL5-B1_S4': ['CL5-B1_S4_L001.sorted.bam',
'CL5-B1_S4_L002.sorted.bam',
'CL5-B1_S4_L003.sorted.bam',
'CL5-B1_S4_L004.sorted.bam']})
