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IMP: make reverse primer (adapter) optional for denoise-ccs (#168)
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@colinvwood
colinvwood authored Aug 21, 2024
1 parent ae3a2df commit 7d89c3b
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Showing 9 changed files with 549 additions and 285 deletions.
12 changes: 8 additions & 4 deletions q2_dada2/_denoise.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

import os
import tempfile
from typing import Optional
import hashlib
import subprocess

Expand Down Expand Up @@ -411,9 +412,9 @@ def denoise_pyro(demultiplexed_seqs: SingleLanePerSampleSingleEndFastqDirFmt,


def denoise_ccs(demultiplexed_seqs: SingleLanePerSampleSingleEndFastqDirFmt,
front: str, adapter: str, max_mismatch: int = 2,
indels: bool = False, trunc_len: int = 0,
trim_left: int = 0, max_ee: float = 2.0,
front: str, adapter: Optional[str] = None,
max_mismatch: int = 2, indels: bool = False,
trunc_len: int = 0, trim_left: int = 0, max_ee: float = 2.0,
trunc_q: int = 2, min_len: int = 20, max_len: int = 0,
pooling_method: str = 'independent',
chimera_method: str = 'consensus',
Expand Down Expand Up @@ -448,7 +449,6 @@ def denoise_ccs(demultiplexed_seqs: SingleLanePerSampleSingleEndFastqDirFmt,
'--removed_primer_directory', nop_fp,
'--filtered_directory', filt_fp,
'--forward_primer', str(front),
'--reverse_primer', str(adapter),
'--max_mismatch', str(max_mismatch),
'--indels', str(indels),
'--truncation_length', str(trunc_len),
Expand All @@ -465,6 +465,10 @@ def denoise_ccs(demultiplexed_seqs: SingleLanePerSampleSingleEndFastqDirFmt,
'--learn_min_reads', str(n_reads_learn),
'--homopolymer_gap_penalty', 'NULL',
'--band_size', '32']

if adapter is not None:
cmd += ['--reverse_primer', str(adapter)]

try:
run_commands([cmd])
except subprocess.CalledProcessError as e:
Expand Down
9 changes: 8 additions & 1 deletion q2_dada2/assets/run_dada.R
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Original file line number Diff line number Diff line change
Expand Up @@ -303,7 +303,14 @@ cat("DADA2:", as.character(packageVersion("dada2")), "/",
if(primer.removed.dir!='NULL'){ #for CCS read analysis
cat("1) Removing Primers\n")
nop <- file.path(primer.removed.dir, basename(unfilts))
prim <- suppressWarnings(removePrimers(unfilts, nop, primer, dada2:::rc(primerR),

# reverse complement reverse primer only if provided
if (primerR != 'NULL') {
primerR <- dada2::rc(primerR)
} else {
primerR <- NULL
}
prim <- suppressWarnings(removePrimers(unfilts, nop, primer, primerR,
max.mismatch = maxMismatch, allow.indels = indels,
orient = TRUE, verbose = TRUE))
cat(ifelse(file.exists(nop), ".", "x"), sep="")
Expand Down
21 changes: 10 additions & 11 deletions q2_dada2/tests/data/expected/ccs-default-stats.tsv
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@@ -1,11 +1,10 @@
sample-id input primer-removed percentage of input primer-removed filtered percentage of input passed filter denoised non-chimeric percentage of input non-chimeric
#q2:types numeric numeric numeric numeric numeric numeric numeric numeric
R11_1_P2C2 200 158 79 137 68.5 89 89 44.5
R3_1_P2C2 200 152 76 119 59.5 90 90 45
R3_2_P2C2 200 160 80 124 62 89 89 44.5
R3_3_P2C2 200 164 82 127 63.5 99 99 49.5
R9_1_P2C2 200 152 76 118 59 96 96 48
R9_1B_P2C2 200 164 82 138 69 90 90 45
R9_2_P2C2 200 152 76 124 62 68 68 34
R9_3_P2C2 200 151 75.5 124 62 49 49 24.5
R9_4_P2C2 200 160 80 132 66 51 51 25.5
sample-id input primer-removed percentage of input primer-removed filtered percentage of input passed filter denoised non-chimeric percentage of input non-chimeric
R11_1_P2C2 200.0 176.0 88.0 145.0 72.5 41.0 41.0 20.5
R3_1_P2C2 200.0 173.0 86.5 134.0 67.0 69.0 64.0 32.0
R3_2_P2C2 200.0 176.0 88.0 130.0 65.0 48.0 48.0 24.0
R3_3_P2C2 200.0 180.0 90.0 136.0 68.0 65.0 65.0 32.5
R9_1_P2C2 200.0 168.0 84.0 127.0 63.5 33.0 33.0 16.5
R9_1B_P2C2 200.0 178.0 89.0 144.0 72.0 47.0 47.0 23.5
R9_2_P2C2 200.0 171.0 85.5 139.0 69.5 23.0 23.0 11.5
R9_3_P2C2 200.0 169.0 84.5 135.0 67.5 17.0 17.0 8.5
R9_4_P2C2 200.0 177.0 88.5 140.0 70.0 29.0 29.0 14.5
302 changes: 132 additions & 170 deletions q2_dada2/tests/data/expected/ccs-default.fasta
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154 changes: 67 additions & 87 deletions q2_dada2/tests/data/expected/ccs-default.tsv
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Original file line number Diff line number Diff line change
@@ -1,87 +1,67 @@
# Constructed from biom file
#OTU ID R11_1_P2C2 R3_1_P2C2 R3_2_P2C2 R3_3_P2C2 R9_1_P2C2 R9_1B_P2C2 R9_2_P2C2 R9_3_P2C2 R9_4_P2C2
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11 changes: 11 additions & 0 deletions q2_dada2/tests/data/expected/ccs-reverse-primer-stats.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
sample-id input primer-removed percentage of input primer-removed filtered percentage of input passed filter denoised non-chimeric percentage of input non-chimeric
#q2:types numeric numeric numeric numeric numeric numeric numeric numeric
R11_1_P2C2 200 158 79 137 68.5 89 89 44.5
R3_1_P2C2 200 152 76 119 59.5 90 90 45
R3_2_P2C2 200 160 80 124 62 89 89 44.5
R3_3_P2C2 200 164 82 127 63.5 99 99 49.5
R9_1_P2C2 200 152 76 118 59 96 96 48
R9_1B_P2C2 200 164 82 138 69 90 90 45
R9_2_P2C2 200 152 76 124 62 68 68 34
R9_3_P2C2 200 151 75.5 124 62 49 49 24.5
R9_4_P2C2 200 160 80 132 66 51 51 25.5
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