Parse unique filenames better in python/Snakemake

Question

I have a series of samples that will be names unique header. For instance the sample could be labeled (SC892138_CTGAAGCT-ACTCTGAG or SC892138_unisample)_L001_001.star_rg_added.sorted.dmark.bam. Or(SC892155_CTGAAGCT-ACTCTGAG or SC892155_unisample)_L001_001.star_rg_added.sorted.dmark.bam. Or some other number after SC. I can parse out SC###### value for each sample, but I want to get to this:SC892155_CTGAAGCT-ACTCTGAG. How do I parse this out?

import os
import glob
import itertools
import pandas
from collections import defaultdict

workdir: os.environ['PWD']

## ---- The parser may have to be customized for each run ---- ##
def parse_sampleID(filename):
    return filename.split('/')[-1].split('_')[0]


fastqs = glob.glob('/P/A/T/H/S/*star_rg_added.sorted.dmark.bam')

d = defaultdict(list)
for key, value in itertools.groupby(fastqs, parse_sampleID):
    d[key] += list(value)

# Need to modify sampleIDs to bams not R1/R2 files
sampleIDs = d.keys()

Asked By: Genetics

||

Source

Answer 1

Maybe you aren’t sharing enough examples to illustrate the problem adequately?

Option #1 based on provided information:

paths_n_fns = [
    "/P/A/T/H/S/SC892138_CTGAAGCT-ACTCTGAG_L001_001.star_rg_added.sorted.dmark.bam",
    "/P/A/T/H/S/SC892138_unisample_L001_001.star_rg_added.sorted.dmark.bam",
    "/P/A/T/H/S/SC892155_CTGAAGCT-ACTCTGAG_L001_001.star_rg_added.sorted.dmark.bam",
    "/P/A/T/H/S/SC892155_unisample_L001_001.star_rg_added.sorted.dmark.bam"
]

def parse_sampleID(path_n_filename):
    if "unisample" in path_n_filename:
        return path_n_filename.split('/')[-1].split('_')[0]
    return path_n_filename.split('/')[-1].split('_L')[0]

sample_ids = []
for paths_n_fn in paths_n_fns:
    sample_ids.append(parse_sampleID(paths_n_fn))
sample_ids

Output from option #1

['SC892138_CTGAAGCT-ACTCTGAG',
 'SC892138',
 'SC892155_CTGAAGCT-ACTCTGAG',
 'SC892155']

Option #2 based on provided information:

paths_n_fns = [
    "/P/A/T/H/S/SC892138_CTGAAGCT-ACTCTGAG_L001_001.star_rg_added.sorted.dmark.bam",
    "/P/A/T/H/S/SC892138_unisample_L001_001.star_rg_added.sorted.dmark.bam",
    "/P/A/T/H/S/SC892155_CTGAAGCT-ACTCTGAG_L001_001.star_rg_added.sorted.dmark.bam",
    "/P/A/T/H/S/SC892155_unisample_L001_001.star_rg_added.sorted.dmark.bam"
]

def parse_sampleID(path_n_filename):
    if "unisample" in path_n_filename:
        return path_n_filename.split('/')[-1].split('_')[0]
    parts = path_n_filename.split('/')[-1].split('_',2)
    return "_".join([parts[0],parts[1]])

sample_ids = []
for paths_n_fn in paths_n_fns:
    sample_ids.append(parse_sampleID(paths_n_fn))
sample_ids

Output from option #2

['SC892138_CTGAAGCT-ACTCTGAG',
 'SC892138',
 'SC892155_CTGAAGCT-ACTCTGAG',
 'SC892155']

Answered By: Wayne

Parse unique filenames better in python/Snakemake

Question:

Answers:

Option #1 based on provided information:

Output from option #1

Option #2 based on provided information:

Output from option #2