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IMP: make reverse primer (adapter) optional for denoise-ccs #168

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merged 1 commit into from
Aug 21, 2024
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IMP: make reverse primer (adapter) optional for denoise-ccs #168

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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 @@ -409,9 +410,9 @@ 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 @@ -446,7 +447,6 @@ 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 @@ -463,6 +463,10 @@ 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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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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Original file line number Diff line number Diff line change
@@ -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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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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02daea313e5f82389bb6c51aec98b542 0.0 0.0 7.0 0.0 0.0 0.0 0.0 0.0 0.0
9361eb755b5011691e8ffb895a5200f9 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0
905c6cbc09c29cfc58fed9c96de271df 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 0.0
5711efb796f39f652ec27f7c2bf1407a 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0
6ac99d275dda4b5dfdf268196c76da34 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0
824b4940befd7e30c204b35005d30587 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 5.0
448c25ffc8c351587b6c074609b32d7a 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0
fcfb66badc962ce3572799f5c30d0471 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 12.0
21dee8cd03a575e10f1cced377e8d81f 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
bccdb2d89a4c43c9153c21a8ce8e67b5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
a941311fdd87ae1ce300513505f06c04 0.0 0.0 0.0 0.0 0.0 0.0 7.0 0.0 0.0
f3f0b542b49617d6b33ef32e557d579d 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.0
0cb2b87ebf129b9f2f03c2d02745e712 0.0 0.0 0.0 0.0 0.0 13.0 0.0 0.0 0.0
e7875dced86a0dc454aeaf1c3f0e338a 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
d96d02515f3b3c8d732adae26348fea1 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0
dadd7342bb41e2211e1e0f0482c97d8c 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0
4fb750193f77cc802cd12bd2d755d34b 6.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
3f96beb35c34019d6ba6be3afa995ec5 9.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
39d6403c00d97caca1515c93cbab9b14 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0
b3c76d626021d8fe9ef85ba79e91493c 0.0 0.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0
190720eec1c619ee87948d5e2b0c87a8 0.0 0.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0
0977ffe109a7af0d2211916e403afbc2 4.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
13d404d5f78b3e4e5b07b30724e880fd 5.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
ac843449032fb15f2e36d61ea0e3c4f9 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
a1feb45433841be18f0264ef7599b648 7.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
83897d3c123983f50c00952790a30225 5.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
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
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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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