gut-demo.ngl

ngless "1.1"
import "parallel" version "1.0"
import "mocat" version "1.0"
import "motus" version "0.1"
import "igc" version "1.0"

samples = readlines('igc.demo.short')
sample = lock1(samples)

input = load_mocat_sample(sample)

input = preprocess(input, keep_singles=False) using |read|:
    read = substrim(read, min_quality=25)
    if len(read) < 45:
        discard

mapped = map(input, reference='hg19')

mapped = select(mapped) using |mr|:
    mr = mr.filter(min_match_size=45, min_identity_pc=90, action={unmatch})
    if mr.flag({mapped}):
        discard

input = as_reads(mapped)


mapped = map(input, reference='igc', mode_all=True)

counts = count(mapped,
            features=['OGs'],
            normalization={scaled})

collect(counts,
        current=sample,
        allneeded=samples,
        ofile='igc.profiles.txt')

mapped = map(input, reference='motus', mode_all=True)

counted = count(mapped, features=['gene'], multiple={dist1})

motus_table = motus(counted)
collect(motus_table,
        current=sample,
        allneeded=samples,
        ofile='motus-counts.txt')