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test.jinja
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test.jinja
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# @copyright 2016-2021 Clarity Genomics BVBA
# @copyright 2012-2016 Bonsai Bioinformatics Research Group
# @copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
#
# SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
# This is a free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# SortMeRNA is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
#
# contributors: Jenya Kopylova jenya.kopylov@gmail.com
# Laurent Noé laurent.noe@lifl.fr
# Pierre Pericard pierre.pericard@lifl.fr
# Daniel McDonald wasade@gmail.com
# Mikaël Salson mikael.salson@lifl.fr
# Hélène Touzet helene.touzet@lifl.fr
# Rob Knight robknight@ucsd.edu
#
# file: test.jinja
# created: Oct 27, 2019 Sun
#
# Tests configuration
# Rendered using Jinja
#
exclude.list: ['t42','t43', 't52'] # tests to skip in bulk runs
tests:
# output type | alignment type
# refs reads zip pair pair_in pair_out out2 sout zout other | best N min_lis seeds
t0: [ 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 2 ]
t0_1: [ 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 2 ]
t1: test_blast_format_1 - single reference + single read
t2: test_cigar_lcs_1
t3: test_environmental_output
t4: test_indexing_split_databases. No alignment, just a multi-part index build
t5: test_mate_pairs - part 1
t6: []
t7: []
t8: []
t9: test_output_all_alignments_f_rc
t10: []
t11: []
t12: [ 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 5, 2, 2 ]
t13: []
t14: []
t15: []
# output type | alignment type
# refs reads zip pair pair_in pair_out out2 sout zout other | best N min_lis seeds
t16: [ 2, 2, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 2, 2 ]
t16_2: [ 2, 2, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 2, 2 ]
t16_3: [ 2, 2, 1, 1, 0, 0, 0, 0, 1, 0, 1, 2, 2, 2 ]
t16_4: [ 2, 2, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 2, 2 ]
t16_5: [ 2, 2, 1, 1, 0, 0, 0, 0, 1, 0, 0, 2, 2, 2 ]
t16_6: [ 2, 2, 1, 1, 0, 0, 1, 0, 1, 0, 1, 1, 2, 2 ]
t16_7: [ 2, 2, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 2, 2 ]
t16_8: [ 2, 2, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 2, 2 ]
t16_9: [ 2, 2, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 2, 2 ]
#
t17: []
t18: []
# output type | alignment type
# refs reads zip pair pair_in pair_out out2 sout zout other | best N min_lis seeds
t19: [ 2, 2, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 2, 2 ]
t19_1: [ 2, 2, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 2, 2 ]
t19_2: [ 2, 2, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 2, 2 ]
t19_3: [ 2, 2, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 2, 2 ]
t19_4: [ 2, 2, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 2, 2 ]
t19_5: [ 2, 2, 0, 1, 0, 0, 1, 0, 1, 0, 1, 1, 2, 2 ]
#
t20: [ 2, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 2, 2 ]
t20_1: [ 2, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 2, 2 ]
t20_2: [ 2, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 2, 2 ]
t20_3: [ 2, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 2, 2 ]
t20_4: [ 2, 1, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 2, 2 ]
#
t21: []
t22: []
t23: []
t24: []
t25: []
t26: []
t27: []
t28: []
t29: []
t30: []
# output type | alignment type
# refs reads zip pair pair_in pair_out out2 sout zout other | best N min_lis seeds
t31: []
t32: []
t33: []
t34: []
t35: []
t36: []
t37: []
t38: []
t39: []
# output type | alignment type
# refs reads zip pair pair_in pair_out out2 sout zout other | best N min_lis seeds
t40: [ 2, 2, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 2, 2 ]
# stress test: 8 refs + 1M reads
t41: [ 2, 2, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 2, 2 ]
# stress test: 8 refs + 10M reads
t42: [ 2, 2, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 2, 2 ]
# stress test: 8 refs + 50M reads
t43: [ 2, 2, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 2, 2 ]
# test catenated gzip - issue 221,263,272,283: 1 ref + 2 files (224) reads
t44: [ 2, 2, 1, 1, 0, 0, 1, 0, 1, 0, 1, 1, 2, 2 ]
# test catenated gzip - issue 221,263,272,283: 8 refs + 2 files (1M) reads
t44_2: [ 2, 2, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 2, 2 ]
# issue 288 8 refs + 1 files (1M) reads
t45: [ 2, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 2, 2 ]
# issue 288-2 segfault: 1 refs, 1 files (10K) reads,
t46: [ 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 2 ]
# 2 refs, 1 files (1M) reads, no zip
t47: [ 2, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 2, 2 ]
t48: []
t49: []
t50: []
t0:
name: blast + single ref + single read
inf: |
single reference + single read
Compares expected alignment (see 't0.validate.files[0]' below) to the newly produced one
refs reads paired paired_in paired_out out2 sout zout other
------------------------------------------------------------------- output type
1 1 - - - - - - -
best N min_lis seeds
---------------------- alignment type
1 1 2 2
cmd:
- -ref
- {{ SMR_SRC }}/data/test_ref.fasta
- -reads
- {{ SMR_SRC }}/data/test_read.fasta
- -sam
- -blast
- '0'
- -v
- -threads
- '1'
- -workdir
- {{WRK_DIR}}
validate:
func: t0 # name of the validation function
num_reads: 1
num_hits: 1
num_fail: 0
min_len: 1487
max_len: 1487
blast_score: 2430
blast_bitscore: 2069
files:
- {{ SMR_SRC }}/data/t0_expected_alignment.blast
t0_1:
name: test_blast_format_0_other
info: |
refs reads paired paired_in paired_out out2 sout zout other
------------------------------------------------------------------ output type
1 1 - - - - - - -
best N min_lis seeds
---------------------- alignment type
1 1 2 2
cmd:
- -ref
- {{ SMR_SRC }}/data/test_ref.fasta
- -reads
- {{ SMR_SRC }}/data/test_read.fasta
- -sam
- -blast
- '1 qstrand qcov'
- -v
- -threads
- '1'
- -workdir
- {{WRK_DIR}}
validate:
func:
files:
aligned.log:
num_reads: 1
num_hits: 1
num_fail: 0
min_len: 1487
max_len: 1487
aligned.blast:
num_recs: 1
n_yid_ycov: 0
aligned.sam:
blast_score: 2430
blast_bitscore: 2069
ref:
- {{ SMR_SRC }}/data/t0_expected_alignment.blast
t1:
name: test_blast_format_1
inf: |
same input as t0
using default number of threads (2)
blast format is different than tests 0, 0_other
cmd:
- -ref
- {{ SMR_SRC }}/data/test_ref.fasta
- -reads
- {{ SMR_SRC }}/data/test_read.fasta
- -sam
- -blast
- '1'
- -v
- -threads
- '1'
- -workdir
- {{WRK_DIR}}
validate:
func:
files:
aligned.log:
num_reads: 1
num_hits: 1
num_fail: 0
min_len: 1487
max_len: 1487
aligned.blast:
num_recs: 1
n_yid_ycov: 0
aligned.sam:
pid_pcov.blast:
ref:
- {{ SMR_SRC }}/data/t0_expected_alignment.blast
t2:
name: test_cigar_lcs_1
cmd:
- -ref
- {{ SMR_SRC }}/data/test_ref.fasta
- -reads
- {{ SMR_SRC }}/data/test_read.fasta
- -sam
- -blast
- '1 qstrand cigar'
- -v
- -threads
- '1'
- -workdir
- {{WRK_DIR}}
validate:
func: t2
# expected alignment
expected: [ "AB271211", "Unc49508", "93.5", "1430", "64", "30", "58", "1487", "1", "1446", "0",
"2069", "+", "57S57M2I12M2D4M2I29M1D11M2I3M2D11M1I7M1D13M5D4M3D9M2D3M7D1260M" ]
t3:
name: test_environmental_output
info: |
search for a single best alignment per read i.e.
refs reads paired paired_in paired_out out2 sout zout other
------------------------------------------------------------------- output type
1 1 - - - - - - -
best N min_lis seeds
---------------------- alignment type
true 1 2 2
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set2_environmental_study_550_amplicon.fasta
- -max_pos
- '250'
- -otu_map
- -de_novo_otu
- -id
- '0.97'
- -coverage
- '0.97'
- -fastx
- -other
- -blast
- '1 cigar qcov'
- -v
#- -no-best
#- -num_alignments
#- '2'
- -threads
- {{THREADS or '\'4\''}}
- -dbg-level
- {{DBG_LEVEL or '\'0\''}}
- -task
- {{TASK or '\'4\''}}
- -workdir
- {{WRK_DIR}}
validate:
func:
non_aligned_id: L1S23.273699_272664 # 0_64412 the only non-aligned read of this test
files:
aligned.log:
num_reads: 100000
num_hits: 99999
num_fail: 1
n_yid_ycov: 47981 # lin:43678 pass SW + %Cov + %ID
n_denovo: 4441 # lin:11080 (52018 420) pass SW & fail (%Cov & %ID) num_denovo + num_pass_id_cov = num_hits
num_groups: 265 # LIN:257, WIN:4441
aligned.fa: 99999
other.fa: 1
aligned_denovo.fa: 4441
otu_map.txt: 265
aligned.blast:
num_recs: 99999 # num_pass_id_cov + num_denovo + num_y_id_n_cov + num_n_id_y_cov = 19995 = num_hits
n_yid_ycov: 47981 # lin:43678 num_pass_id ⋂ num_pass_cov
n_yid_ncov: 1513 # lin:6571 ID + !COV
n_nid_ycov: 46064 # lin:38670 !ID + COV
n_denovo: 4441 # lin:11080 !ID + !COV
runtime:
win:
- threads: 8
sec: [13, 0.7, 4] # align, log, reports
t4:
name: test_indexing_split_databases
info: |
No alignment is performed, just building a multi-part index
cmd:
- -ref
- {{ SMR_SRC }}/data/gg_13_8_ref_set.fasta # 27,424 bytes (27KB) file
- -reads
- {{ SMR_SRC }}/data/test_read.fasta # single read
- -m
- '0.05'
- -v
- -index
- '1'
- -workdir
- {{WRK_DIR}}
validate:
func: t4
files:
aligned.log:
num_reads: 1
num_hits: 1
num_fail: 0
min_len: 1487
max_len: 1487
idx_sfx_win: 7828442710921335713
idx_sfx_lin: 12011197668640222139
num_idx: 7 # 7 index files of each kind is generated
t5:
name: test_mate_pairs - part 1
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set4_mate_pairs_metatranscriptomics_1.fastq.gz # 5,000 reads
- -reads
- {{ SMR_SRC }}/data/set4_mate_pairs_metatranscriptomics_2.fastq.gz # 5,000 reads
- -max_pos
- '250'
- -fastx
- -other
- -v
- -threads
- '5'
- -workdir
- {{WRK_DIR}}
#- -pid
validate:
func:
files:
aligned.log:
num_reads: 10000
num_hits: 6000
num_fail: 4000
aligned.fq.gz: 6000
other.fq.gz: 4000
variant: sanger # fastq quality variant
t6:
name: test_mate_pairs - part 2 - paired_in
info: |
-e min_sw hits
1 49 6000
0.001 59 6000
1e-7 74 6000
1e-12 93 6000
1e-15 105 6000
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set4_mate_pairs_metatranscriptomics_1.fastq # 5,000 reads
- -reads
- {{ SMR_SRC }}/data/set4_mate_pairs_metatranscriptomics_2.fastq # 5,000 reads
- -max_pos
- '250'
- -fastx
- -other
- -paired_in
- -blast
- '1 cigar qcov'
- -v
- -e
- '0.01'
- -threads
- '4'
- -workdir
- {{WRK_DIR}}
validate:
func:
files:
aligned.log:
num_reads: 10000
num_hits: 6000
num_fail: 4000
aligned.blast:
num_recs: 6000
n_yid_ycov: 5623
n_yid_ncov:
n_nid_ycov:
n_denovo: # num_pass_id ⋂ num_pass_cov
aligned.fq: 10000 # paired_in
other.fq: 0
pid_pcov.blast: # n_yid_ycov 5623 debug file
variant: sanger # fastq quality variant
t7:
name: test_mate_pairs - part 3 - paired_out
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set4_mate_pairs_metatranscriptomics_1.fastq # 5,000 reads
- -reads
- {{ SMR_SRC }}/data/set4_mate_pairs_metatranscriptomics_2.fastq # 5,000 reads
- -max_pos
- '250'
- -fastx
- -other
- -paired_out
- -v
- -workdir
- {{WRK_DIR}}
validate:
func:
files:
aligned.log:
num_reads: 10000
num_hits: 6000
num_fail: 4000
aligned.fq: 2000 # paired_out
other.fq: 8000
variant: sanger # fastq quality variant
t8:
name: test_multiple_databases_search
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -ref
- {{ SMR_SRC }}/data/silva-arc-16s-database-id95.fasta
- -reads
- {{ SMR_SRC }}/data/set7_arc_bac_16S_database_match.fasta # 6 reads
- -fastx
- -v
- -workdir
- {{WRK_DIR}}
validate:
func:
files:
aligned.log:
num_reads: 6
num_hits: 4
num_fail: 2
aligned.fa: 4
t9:
name: test_output_all_alignments_f_rc
cmd:
- -ref
- {{ SMR_SRC }}/data/ref_GQ099317_forward_and_rc.fasta
- -reads
- {{ SMR_SRC }}/data/illumina_GQ099317.fasta # 1 read
- -num_alignments
- '0'
- -mismatch
- '-3'
- -sam
- -v
- -workdir
- {{ WRK_DIR }}
- -threads
- '1'
validate:
func: t9
num_reads: 1
num_hits: 1
num_fail: 0
sam_alignments_expected: [
[
'GQ099317.1.1325_157_453_0:0:0_0:0:0_99/1',
'0',
'GQ099317.1.1325_157_453_0:0:0_0:0:0_99/1',
'1',
'255',
'101M',
'*',
'0',
'0',
'GCTGGCACGGAGTTAGCCGGGGCTTATAAATGGTACCGTCATTGATTCTTCCCATTCTTTCGAAGTTTACATCCCGAGGGACTTCATCCTTCACGCGGCGT',
'*',
'AS:i:202',
'NM:i:0'
],
[
'GQ099317.1.1325_157_453_0:0:0_0:0:0_99/1',
'16',
'GQ099317.1.1325_157_453_0:0:0_0:0:0_99/1',
'102',
'255',
'101M',
'*',
'0',
'0',
'ACGCCGCGTGAAGGATGAAGTCCCTCGGGATGTAAACTTCGAAAGAATGGGAAGAATCAATGACGGTACCATTTATAAGCCCCGGCTAACTCCGTGCCAGC',
'*',
'AS:i:202',
'NM:i:0'
]
]
t10:
name: test_ref_shorter_than_seed
note: |
This captures the output of the command and verifies the error message.
No output files are produced
cmd:
- -ref
- {{ SMR_SRC }}/data/ref_short_seqs.fasta
- -reads
- {{ SMR_SRC }}/data/illumina_GQ099317.fasta # 1 read
- -v
- -workdir
- {{ WRK_DIR }}
cwd:
capture: True
failonerror: False # False (continue the tests as this error was expected) | True (default) stop further tests
validate:
func: t10
err_msg: 'one of your sequences is shorter than the seed length 19'
t11:
name: test_simulated_amplicon_1_part_map
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set5_simulated_amplicon_silva_bac_16s.fasta
- -id
- '0.97'
- -coverage
- '0.97'
- -otu_map
- -de_novo_otu
- -blast
- '1 cigar qcov'
- -fastx
- -other
- -v
- -workdir
- {{ WRK_DIR }}
- -threads
- '3'
validate:
func:
files:
aligned.log:
num_reads: 30000
num_hits: 19995
num_fail: 10005
n_denovo: 1691 # 9831
n_yid_ycov: 10164 # 10164 + 9831 = 19995 pass_SW + pass_ID, not necessarily pass_Cov
num_groups: 4401
aligned.blast:
num_recs: 19995
n_yid_ycov: 10164 # pass_SW + pass_ID + pass_Cov
n_nid_ycov: 8122
n_yid_ncov: 11
n_denovo: 1691
n_pass_id: 10175 # yid_ycov + yid_ncov
n_pass_cov: 15054
aligned.fa: 19995
other.fa: 10005
aligned_denovo.fa:
otu_map.txt: 4401
t12:
name: test_simulated_amplicon_1_part_map
note: same as t11 + 'best 5'
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set5_simulated_amplicon_silva_bac_16s.fasta
- -fastx
- -blast
- '1 cigar qcov'
- -otu_map
- -de_novo_otu
- -other
- -id
- '0.97'
- -coverage
- '0.97'
- -v
- -threads
- {{THREADS or '\'5\''}}
- -workdir
- {{ WRK_DIR }} # have to use on AWS SSM where HOME is not set
validate:
func:
files:
aligned.log:
num_reads: 30000
num_hits: 19995
num_fail: 10005
n_yid_ycov: 10164
n_denovo: 1691
num_groups : 4401
min_sw: 49
aligned.blast:
num_recs: 19995 # num_pass_id_cov + num_denovo + num_y_id_n_cov + num_n_id_y_cov = 19995 = num_hits
n_yid_ycov: 10164 # num_pass_id ⋂ num_pass_cov
n_yid_ncov: 11 # ID + !COV
n_nid_ycov: 8122 # !ID + COV
n_denovo: 1691 # !ID + !COV
aligned.fa: 19995
other.fa: 10005
otu_map.txt: 4401
aligned_denovo.fa: # debug
pid_pcov.blast: # debug
t13:
name: test_simulated_amplicon_6_part_map
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set5_simulated_amplicon_silva_bac_16s.fasta
- -fastx
- -blast
- '1 cigar qcov'
- -otu_map
- -de_novo_otu
- -other
- -id
- '0.97'
- -coverage
- '0.97'
# indexing options
- -m
- '20'
- -v
- -threads
- {{THREADS or '\'5\''}}
- -workdir
- {{WRK_DIR}}
validate:
func:
files:
aligned.log:
num_reads: 30000
num_hits: 19995
num_fail: 10005
n_denovo: 1691
n_yid_ycov: 10164
num_groups: 4401
aligned.blast:
num_recs: 19995
n_yid_ycov: 10164 # pass_SW + pass_ID + pass_Cov
n_yid_ncov: 11
n_nid_ycov: 8122
n_denovo: 1691
n_yid: 10175
n_ycov: 15054
aligned.fa: 19995
other.fa: 10005
aligned_denovo.fa: 1691
otu_map.txt: 4401
t14:
name: test_simulated_amplicon_12_part_map
note: identical to t13 except using 12-part index instead of 6-part
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ SMR_SRC }}/data/set5_simulated_amplicon_silva_bac_16s.fasta
- -id
- '0.97'
- -coverage
- '0.97'
- -otu_map
- -de_novo_otu
- -blast
- '1 cigar qcov'
- -fastx
- -other
# indexing options
- -m
- '10'
- -v
- -workdir
- {{ WRK_DIR }}
validate:
func:
files:
aligned.log:
num_reads: 30000
num_hits: 19995
num_fail: 10005
n_denovo: 1691
n_yid_ycov: 10164 # 10164 + 9831 = 19995, pass_ID + pass_Cov, not necessarily pass_SW
num_groups: 4401 # 4400 before bug 52
aligned.fa: 19995
other.fa: 10005
aligned_denovo.fa: 1691
otu_map.txt: 4401
aligned.blast:
num_recs: 19995
n_yid_ycov: 10164 # pass_SW + pass_ID + pass_Cov
n_pass_id: 10175
n_pass_cov: 15054
n_denovo: 1691
t15:
name: test_threads
info: |
ref reads best N min_lis zip
---------------------------------
1 2 true 1 2 true
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_1_5k.fastq.gz # 5,000 reads
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_2_5k.fastq.gz # 5,000 reads
- -threads
- '6:2:2' # can be any 6 | 6:2 | 6:2:2
- '-a' # deprecated. Redirects to 'threads'
- '5'
- -v
- -workdir
- {{ WRK_DIR }}
validate:
func:
files:
aligned.log:
num_reads: 10000
num_hits: 9833
num_fail: 167
aligned.blast.gz:
num_recs: 9833
t16:
name: 2 read + zip + 1 best
info: |
refs reads zip pair pair_in pair_out out2 sout zout other
------------------------------------------------------------------- output type
2 2 1 1 - - - - - -
best N min_lis seeds
---------------------- alignment type
1 1 2 2
note:
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -ref
- {{ SMR_SRC }}/data/silva-arc-16s-database-id95.fasta
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_1_5k.fastq.gz # 5,000 reads
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_2_5k.fastq.gz # 5,000 reads
- -fastx
- -blast
- '1 qcov qstrand'
- -v
- -threads
- {{THREADS or '\'4\''}}
- -workdir
- {{WRK_DIR}}
cwd: {{ SMR_SRC }}
validate:
func:
variant: sanger # fastq quality variant
files:
aligned.log:
num_reads: 10000
num_hits: 9833
num_fail: 167
aligned.blast.gz:
num_recs: 9833
n_yid_ycov: 0
n_yid_ncov: 0
n_nid_ycov: 0
n_denovo: 0
aligned.fq.gz: 9833
pid_pcov.blast: # debug
t16_2:
name: 2 read + zip + all + relative paths
info: |
refs reads zip pair pair_in pair_out out2 sout zout other
------------------------------------------------------------------- output type
2 2 1 1 - - - - - -
best N min_lis seeds
---------------------- alignment type
1 0 2 2
note:
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -ref
- {{ SMR_SRC }}/data/silva-arc-16s-database-id95.fasta
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_1_5k.fastq.gz # 5,000 reads
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_2_5k.fastq.gz # 5,000 reads
- -fastx
- -blast
- '1 cigar qcov'
- -num_alignments
- '0'
- -v
- -threads
- {{THREADS or '\'4\''}}
- -workdir
- {{WRK_DIR}}
cwd: {{ SMR_SRC }}
validate:
func:
variant: sanger
files:
aligned.log:
num_reads: 10000
num_hits: 9833
num_fail: 167
aligned.blast.gz:
num_recs: 370707 # ~37 alignments per read
n_yid_ycov: 905
n_yid_ncov: 26656
n_nid_ycov: 66130
n_denovo: 277016
aligned.fq.gz: 9833
t16_3:
name: 2 reads + zip + 2 best + relative paths
info: |
refs reads zip pair pair_in pair_out out2 sout zout other
------------------------------------------------------------------- output type
2 2 1 1 - - - - - -
best N min_lis seeds
---------------------- alignment type
1 2 2 2
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -ref
- {{ SMR_SRC }}/data/silva-arc-16s-database-id95.fasta
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_1_5k.fastq.gz # 5,000 reads
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_2_5k.fastq.gz # 5,000 reads
- -fastx
- -blast
- '1 cigar qcov'
- -num_alignments
- '2'
- -v
- -threads
- {{THREADS or '\'4\''}}
- -workdir
- {{WRK_DIR}}
cwd: {{ SMR_SRC }}
validate:
func:
variant: sanger
files:
aligned.log:
num_reads: 10000
num_hits: 9833
num_fail: 167
aligned.blast.gz:
num_recs: 19638
n_yid_ycov: 816
n_yid_ncov: 201
n_nid_ycov: 11555
n_denovo: 7066
aligned.fq.gz: 9833
pid_pcov.blast:
t16_4:
name: 2 reads + zip + 1 no best + relative paths
info: |
refs reads zip pair pair_in pair_out out2 sout zout other
------------------------------------------------------------------- output type
2 2 1 1 - - - - - -
best N min_lis seeds
---------------------- alignment type
0 1 2 2
note:
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -ref
- {{ SMR_SRC }}/data/silva-arc-16s-database-id95.fasta
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_1_5k.fastq.gz # 5,000 reads
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_2_5k.fastq.gz # 5,000 reads
- -fastx
- -blast
- '1 cigar qcov'
- -no-best
- -v
- -threads
- {{THREADS or '\'4\''}}
- -workdir
- {{WRK_DIR}}
cwd: {{ SMR_SRC }}
validate:
func:
variant: sanger
files:
aligned.log:
num_reads: 10000
num_hits: 9833
num_fail: 167
aligned.blast.gz:
num_recs: 9833 # 1 alignment per read
n_yid_ycov: 70
n_yid_ncov: 224
n_nid_ycov: 3518
n_denovo: 6021
aligned.fq.gz: 9833
t16_5:
name: 2 reads + zip + 2 no best + relative paths
info: |
refs reads zip pair pair_in pair_out out2 sout zout other
------------------------------------------------------------------- output type
2 2 1 1 - - - - - -
best N min_lis seeds
---------------------- alignment type
0 2 2 2
cmd:
- -ref
- {{ SMR_SRC }}/data/silva-bac-16s-database-id85.fasta
- -ref
- {{ SMR_SRC }}/data/silva-arc-16s-database-id95.fasta
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_1_5k.fastq.gz # 5,000 reads
- -reads
- {{ DATA_DIR if DATA_DIR }}/bio/reads/rna/DRR121111_2_5k.fastq.gz # 5,000 reads
- -fastx
- -blast
- '1 cigar qcov'
- -no-best
- -num_alignments
- '2'
- -v
- -threads
- {{THREADS or '\'4\''}}
- -workdir
- {{WRK_DIR}}
cwd: {{ SMR_SRC }}
validate:
func:
variant: sanger
files:
aligned.log:
num_reads: 10000