A single genomic locus

The Mclumi dedup_basic module allows users to work out a deduplicated molecules at a given genomic locus. This module can be seen as the most basic unit of deduplicating other RNA-seq reads and it simply gives a line of summarized statistics.

1. CLI

mclumi dedup_basic -m mcl -ed 1 -infv 1.6 -expv 2 -ibam ./example_bundle.bam -obam ./dedup.bam

2. Python inline

from mclumi.deduplicate.monomer.DedupBasic import dedupBasic

umikit = dedupBasic(
        mode='internal',

        # method='unique',
        # method='cluster',
        # method='adjacency',
        # method='directional',
        method='mcl',
        # method='mcl_val',
        # method='mcl_ed',

        bam_fpn='example/data/example_bundle.bam',
        mcl_fold_thres=1.5,
        inflat_val=1.6,
        exp_val=2,
        iter_num=100,
        verbose=True,
        ed_thres=1,
        is_sv=False,
        sv_fpn='example/data/basic/assigned_sorted_dedup.bam',
    )

run Mclumi internally.
22/10/2021 20:09:44 logger: ===>reading the bam file... /home/students/j.sun/store/software/us/mcl/mclumi/example/data/example_bundle.bam
[E::idx_find_and_load] Could not retrieve index file for '/home/students/j.sun/store/software/us/mcl/mclumi/example/data/example_bundle.bam'
22/10/2021 20:09:44 logger: ===>reading BAM time: 0.00s
22/10/2021 20:09:44 logger: =========>start converting bam to df...
22/10/2021 20:09:53 logger: =========>time to df: 8.247s
22/10/2021 20:09:53 logger: ======># of raw reads: 1175027
22/10/2021 20:09:53 logger: ======># of reads with qualified chrs: 1175027
22/10/2021 20:09:53 logger: ======># of unique umis: 1949
22/10/2021 20:09:53 logger: ======># of redundant umis: 1175027
22/10/2021 20:09:53 logger: ======>edit distance thres: 1
22/10/2021 20:09:53 logger: ===>start building umi graphs...
22/10/2021 20:10:35 logger: ===>time for building umi graphs: 41.11s
22/10/2021 20:10:35 logger: ===>start deduplication by the mcl method...
22/10/2021 20:10:41 logger: ======>finish finding deduplicated umis in 6.17s
22/10/2021 20:10:41 logger: ======># of umis deduplicated to be 44
22/10/2021 20:10:41 logger: ======>calculate average edit distances between umis...
22/10/2021 20:10:41 logger: ======>finish calculating ave eds in 0.00s
22/10/2021 20:10:41 logger: ======># of deduplicated unique umis 1905 on the basis of the unique method
22/10/2021 20:10:41 logger: ======># of deduplicated reads 1116981 on the basis of the unique method
5.0    1
Name: ave_eds, dtype: int64
22/10/2021 20:10:41 logger: ======>start writing deduplicated reads to BAM...
22/10/2021 20:10:41 logger: ======># of the total reads left after deduplication: 44
22/10/2021 20:10:41 logger: ======>finish writing in 0.00s