From b54a646a97c6d80ad82c276ce469bef3eaf4126a Mon Sep 17 00:00:00 2001 From: mitradarja Date: Mon, 14 Aug 2023 22:13:24 +0200 Subject: [PATCH 1/5] [FIX] Fix input pathways for inser and delete. --- src/estimate.cpp | 2 +- src/ibf.cpp | 13 ++++++++++--- utils/README.md | 19 +++++++++++++++++-- 3 files changed, 28 insertions(+), 6 deletions(-) diff --git a/src/estimate.cpp b/src/estimate.cpp index 81af73e..9896f12 100644 --- a/src/estimate.cpp +++ b/src/estimate.cpp @@ -32,7 +32,7 @@ template void check_ibf(min_arguments const & args, IBFType const & ibf, std::vector & estimations_i, seqan3::dna4_vector const seq, std::vector & prev_counts, - exp_t const & expressions, uint16_t const k, std::vector const fprs, std::vector deleted) + exp_t const & expressions, uint16_t const k, std::vector const fprs, std::vector & deleted) { // Check, if one expression threshold for all or individual thresholds static constexpr bool multiple_expressions = std::same_as>>; diff --git a/src/ibf.cpp b/src/ibf.cpp index 93b1a5d..07d9b4a 100644 --- a/src/ibf.cpp +++ b/src/ibf.cpp @@ -1340,6 +1340,7 @@ std::vector insert(std::vector const & sequence else insert_helper(sequence_files,ibf_args, path_in, cutoffs, expression_by_genome_file, minimiser_args); + store_args(ibf_args, std::string{ibf_args.path_out} + "IBF_Data"); return ibf_args.expression_thresholds; } @@ -1349,6 +1350,7 @@ std::vector insert(std::vector const & minimise std::filesystem::path const expression_by_genome_file, std::filesystem::path path_in, bool samplewise) { std::vector cutoffs{}; + load_args(ibf_args, std::string{path_in} + "IBF_Data"); if (samplewise) insert_helper(minimiser_files, ibf_args, path_in, cutoffs, expression_by_genome_file); else @@ -1379,15 +1381,20 @@ void delete_bin(std::vector const & delete_files, { std::filesystem::path filename; if (samplewise) - filename = ibf_args.path_out.string() + "IBF_Level_" + std::to_string(i); + filename = path_in.string() + "IBF_Level_" + std::to_string(i); else - filename = ibf_args.path_out.string() + "IBF_" + std::to_string(ibf_args.expression_thresholds[i]); + filename = path_in.string() + "IBF_" + std::to_string(ibf_args.expression_thresholds[i]); seqan3::interleaved_bloom_filter ibf; load_ibf(ibf, filename); ibf.clear(bins_to_delete); - if (ibf_args.compressed) + if (samplewise) + filename = ibf_args.path_out.string() + "IBF_Level_" + std::to_string(i); + else + filename = ibf_args.path_out.string() + "IBF_" + std::to_string(ibf_args.expression_thresholds[i]); + + if (ibf_args.compressed) { seqan3::interleaved_bloom_filter ibf{ibf}; store_ibf(ibf, filename); diff --git a/utils/README.md b/utils/README.md index c1e4574..0e64596 100644 --- a/utils/README.md +++ b/utils/README.md @@ -29,7 +29,7 @@ python3 unify_results.py deseq_in_23.csv 19_23_infiles.lst accession.lst python3 unify_results.py deseq_in_39.csv 19_39_infiles.lst accession.lst ``` -Now, you can run the RScript "breastcancer.R" to analyze the differential expressed genes and generate the heatmap for the 67 +Now, you can run the RScript "breastcancer.R" to analyze the differential expressed genes and generate the heatmap for the 67 differential expressed genes from https://doi.org/10.1016/j.dib.2018.03.079. @@ -44,6 +44,22 @@ needle minimiser -k 21 -w 25 -t X SRR1313229.fastq.gz SRR1313228.fastq.gz SRR13 ``` For the ram friendly version a `--ram` was added to the previous command. +## Insertion and Deletion + +If Needle indices were built according to the scripts [here](https://github.com/MitraDarja/analysis_needle/tree/main). Then insertion and deletion were tested in the following way: + +``` +# Testing insertion +/usr/bin/time -v ../needle/build_thesis/bin/needle insertmin -o w_21/Insert_ -i w_21/SRR_ w_21/SRR1313229.fastq.minimiser w_21/SRR1313228.fastq.minimiser w_21/SRR1313227.fastq.minimiser w_21/SRR1313226.fastq.minimiser +/usr/bin/time -v ../needle/build_thesis/bin/needle insertmin -o w_25/Insert_ -i w_25/SRR_ w_25/SRR1313229.fastq.minimiser w_25/SRR1313228.fastq.minimiser w_25/SRR1313227.fastq.minimiser w_25/SRR1313226.fastq.minimiser +/usr/bin/time -v ../needle/build_thesis/bin/needle insertmin -o w_41/Insert_ -i w_41/SRR_ w_41/SRR1313229.fastq.minimiser w_41/SRR1313228.fastq.minimiser w_41/SRR1313227.fastq.minimiser w_41/SRR1313226.fastq.minimiser + +# Testing Deletion +/usr/bin/time -v ../needle/build_thesis/bin/needle delete -i w_21/SRR_ -o w_21/DeletedIBF_ 614 615 616 617 +/usr/bin/time -v ../needle/build_thesis/bin/needle delete -i w_25/SRR_ -o w_25/DeletedIBF_ 614 615 616 617 +/usr/bin/time -v ../needle/build_thesis/bin/needle delete -i w_41/SRR_ -o w_41/DeletedIBF_ 614 615 616 617 +``` + ## Differential Expression Download the sequencing experiments of the GEO experiment with the accession number GSE58135 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58135). Then create a Needle index in the following way, assuming all sequencing files are stored in a folder named GSE58135: @@ -82,4 +98,3 @@ RScrip tissue_type.R ``` The differential expressed genes can then by obtained via ShinyGo using Ontology.Jensen.TISSUES as a database. - From fb320364859152db9ba169407b0c70ac6502d2a7 Mon Sep 17 00:00:00 2001 From: Mitra Darja Darvish Date: Thu, 17 Aug 2023 11:35:49 +0200 Subject: [PATCH 2/5] [TEST] Add cli test for delete. --- test/cli/CMakeLists.txt | 1 + test/cli/delete_options_test.cpp | 17 +++++++++++++++++ 2 files changed, 18 insertions(+) diff --git a/test/cli/CMakeLists.txt b/test/cli/CMakeLists.txt index 00fb3b7..eb6c29e 100644 --- a/test/cli/CMakeLists.txt +++ b/test/cli/CMakeLists.txt @@ -12,3 +12,4 @@ target_use_datasources (estimate_options_test FILES IBF_1 mini_gen.fasta) add_cli_test (count_options_test.cpp) target_use_datasources (count_options_test FILES mini_example.fasta mini_gen.fasta mini_gen.genome) add_cli_test (delete_options_test.cpp) +target_use_datasources (delete_options_test FILES exp_01.fasta) diff --git a/test/cli/delete_options_test.cpp b/test/cli/delete_options_test.cpp index 431def9..d26b11b 100644 --- a/test/cli/delete_options_test.cpp +++ b/test/cli/delete_options_test.cpp @@ -20,3 +20,20 @@ TEST_F(delete_options_test, delete_no_options) EXPECT_EQ(result.out, expected); EXPECT_EQ(result.err, std::string{}); } + +TEST_F(delete_options_test, with_argument) +{ + estimate_ibf_arguments ibf_args{}; + minimiser_arguments minimiser_args{}; + ibf_args.expression_thresholds = {1, 2}; + std::vector fpr = {0.05}; + std::vector sequence_files = {data("exp_01.fasta"),data("exp_01.fasta")}; + ibf_args.path_out = "Test_"; + std::vector cutoffs{}; + ibf(sequence_files, ibf_args, minimiser_args, fpr, cutoffs); + + cli_test_result result = execute_app("needle delete -i ", "Test_ ", "0"); + EXPECT_EQ(result.exit_code, 0); + EXPECT_EQ(result.out, ""); + EXPECT_EQ(result.err, std::string{}); +} From fc9cbbe14e2fa8e25c31b712feeefb1691b5563f Mon Sep 17 00:00:00 2001 From: Mitra Darja Darvish Date: Thu, 17 Aug 2023 11:55:44 +0200 Subject: [PATCH 3/5] [MISC] Require arguments for count. --- src/main.cpp | 2 +- test/cli/count_options_test.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main.cpp b/src/main.cpp index 2b376ff..acb1d03 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -104,7 +104,7 @@ int run_needle_count(seqan3::argument_parser & parser) "for all sequences in the genome file based on the exact minimiser occurrences of " "the given sequence files. Please run genome beforehand to create the genome file."; parser.add_positional_option(sequence_files, "Please provide at least one sequence file."); - parser.add_option(include_file, '\0', "include", "Please provide one sequence file with transcripts."); + parser.add_option(include_file, '\0', "include", "Please provide one sequence file with transcripts.",seqan3::option_spec::required); parser.add_option(genome_file, '\0', "genome", "Please provide one *.genome file created with the genome command."); parser.add_flag(paired, 'p', "paired", "If set, experiments are paired. Default: Not paired."); diff --git a/test/cli/count_options_test.cpp b/test/cli/count_options_test.cpp index 58be972..5621882 100644 --- a/test/cli/count_options_test.cpp +++ b/test/cli/count_options_test.cpp @@ -28,7 +28,7 @@ TEST_F(count_options_test, no_options) TEST_F(count_options_test, fail_no_argument) { - cli_test_result result = execute_app("needle count", "--seed 0"); + cli_test_result result = execute_app("needle count", "--seed 0 --genome", data("mini_gen.genome")," --include", data("mini_gen.fasta")); std::string expected { "Error. Incorrect command line input for count. Not enough positional arguments provided " From e2fdbab8181cfc2d92f4772f815ee1682e34ad02 Mon Sep 17 00:00:00 2001 From: Mitra Darja Darvish Date: Thu, 17 Aug 2023 14:27:13 +0200 Subject: [PATCH 4/5] [MISC] Reproduce comparison with metagrpah. --- utils/README.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/utils/README.md b/utils/README.md index 0e64596..da87f39 100644 --- a/utils/README.md +++ b/utils/README.md @@ -1,5 +1,9 @@ # Evaluation of Needle count +## Comparison with kallisto and salmon +All scripts for the comparison with kallisto and salmon can be found in this [repo](https://github.com/MitraDarja/analysis_needle/tree/main), please use the provided scripts `run_simulated.sh` and `run_seqc.sh`. + + ## Differential Expression Download the sequencing experiments listed in accession.lst and the human transcripts from gencode as a fasta file. Then create a Needle-genome file via: @@ -60,6 +64,26 @@ If Needle indices were built according to the scripts [here](https://github.com/ /usr/bin/time -v ../needle/build_thesis/bin/needle delete -i w_41/SRR_ -o w_41/DeletedIBF_ 614 615 616 617 ``` +## Comparison with Reindeer and MetaGraph in regards of space and speed +The scripts for the comparison with Reindeer can be found in this [repo](https://github.com/MitraDarja/analysis_needle/tree/main). +There you can find what data to download and how Reindeer and Needle are run, here the commands for MetaGraph are given. Please, check out +the scripts before using them, as the paths to the executable need to be added and sometimes an input file created first. + + +``` +# Preprocessing +bash run_kmc.sh +bash run_build.sh +# From here on each step was considered for the comparison +/usr/bin/time -v bash run_clean.sh +/usr/bin/time -v bash run_clean_smooth.sh +bash metagraph.sh +``` + +### Preprocessing +The comparison of the preprocessing steps was based on the same files as the parallelization analysis. Use the script `compare_preprocess.sh` to obtain the numbers. + + ## Differential Expression Download the sequencing experiments of the GEO experiment with the accession number GSE58135 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58135). Then create a Needle index in the following way, assuming all sequencing files are stored in a folder named GSE58135: From f244e64c58de508df914a87926bf7b3334281f8f Mon Sep 17 00:00:00 2001 From: Mitra Darja Darvish Date: Thu, 17 Aug 2023 14:27:28 +0200 Subject: [PATCH 5/5] [MISC] Reproduce comparison with metagrpah. --- utils/compare_preprocess.sh | 13 + utils/metagraph.sh | 53 ++ utils/run_bcalm4.sh | 9 + utils/run_build.sh | 11 + utils/run_clean.sh | 11 + utils/run_clean_smooth.sh | 11 + utils/run_kmc.sh | 11 + utils/run_kmc4.sh | 8 + utils/samples.in | 1662 +++++++++++++++++++++++++++++++++++ 9 files changed, 1789 insertions(+) create mode 100644 utils/compare_preprocess.sh create mode 100644 utils/metagraph.sh create mode 100644 utils/run_bcalm4.sh create mode 100644 utils/run_build.sh create mode 100644 utils/run_clean.sh create mode 100644 utils/run_clean_smooth.sh create mode 100644 utils/run_kmc.sh create mode 100644 utils/run_kmc4.sh create mode 100644 utils/samples.in diff --git a/utils/compare_preprocess.sh b/utils/compare_preprocess.sh new file mode 100644 index 0000000..fad0c84 --- /dev/null +++ b/utils/compare_preprocess.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +needle="Set path to needle executable" +input_dir="Set to directory that contains the sequence files" + +# Comparison for 4 Threads, change thread number in each step to obtain numbers for 4 threads +/usr/bin/time -v -o needle_21_21_preprocess4.time $needle minimiser -k 21 -w 21 -t 4 --cutoff 49 $input_dir/SRR1313229.fastq.gz $input_dir/SRR1313228.fastq.gz $input_dir/SRR1313227.fastq.gz $input_dir/SRR1313226.fastq.gz +/usr/bin/time -v -o needle_25_21_preprocess4.time $needle minimiser -k 21 -w 25 -t 4 --cutoff 49 $input_dir/SRR1313229.fastq.gz $input_dir/SRR1313228.fastq.gz $input_dir/SRR1313227.fastq.gz $input_dir/SRR1313226.fastq.gz +/usr/bin/time -v -o needle_21_41_preprocess4.time $needle minimiser -k 21 -w 41 -t 4 --cutoff 49 $input_dir/SRR1313229.fastq.gz $input_dir/SRR1313228.fastq.gz $input_dir/SRR1313227.fastq.gz $input_dir/SRR1313226.fastq.gz + +# For both bcalm and kmc a file named "files.lst" with the path to the four files needs to be created. +/usr/bin/time -v -o bcalm_preprocess4.time bash run_bcalm4.sh +/usr/bin/time -v -o kmc_preprocess4.time bash run_kmc4.sh diff --git a/utils/metagraph.sh b/utils/metagraph.sh new file mode 100644 index 0000000..5b53fb2 --- /dev/null +++ b/utils/metagraph.sh @@ -0,0 +1,53 @@ +metagraph="Set path to metagraph executable" +out_dir="Set out directory" + +mkdir $out_dir/clean_anno +/usr/bin/time -v -o jointbuild.time $metagraph build -p 4 -k 21 --count-kmers --count-width 32 --outfile-base $out_dir/graph single_dbgs/clean/SRR*.fasta.gz &> jointbuilt.log +/usr/bin/time -v -o annotate_joint.time $metagraph annotate --separately -p 4 -i $out_dir/graph.dbg --anno-filename --count-kmers --count-width 32 -o $out_dir/clean_anno single_dbgs/clean/SRR*.fasta.gz &> anno.log + +mkdir $out_dir/rd0 +mkdir $out_dir/rd1 +mkdir $out_dir/rd2 +/usr/bin/time -v -o rd0.time $metagraph transform_anno -v --anno-type row_diff --count-kmers --row-diff-stage 0 --mem-cap-gb 500 -o $out_dir/rd0/rd -i $out_dir/graph.dbg -p 4 --disk-swap "" $out_dir/clean_anno/*.column.annodbg &>rd0.log +/usr/bin/time -v -o rd1.time $metagraph transform_anno -v --anno-type row_diff --count-kmers --row-diff-stage 1 --mem-cap-gb 500 -o $out_dir/rd1/rd -i $out_dir/graph.dbg -p 4 --disk-swap "" $out_dir/clean_anno/*.column.annodbg &> rd1.log +/usr/bin/time -v -o rd2.time $metagraph transform_anno -v --anno-type row_diff --count-kmers --row-diff-stage 2 --mem-cap-gb 500 -o $out_dir/rd2/rd -i $out_dir/graph.dbg -p 4 --disk-swap "" $out_dir/clean_anno/*.column.annodbg &> rd2.log + +/usr/bin/time -v -o anno.time $metagraph transform_anno --anno-type row_diff_int_brwt --greedy --fast --subsample 1000000 -i $out_dir/graph.dbg -o $out_dir/annotation_final $out_dir/rd2/*.column.annodbg -p 4 --parallel-nodes 10 &> last_anno.log +/usr/bin/time -v -o relax.time $metagraph relax_brwt -v --relax-arity 32 -p 4 -o $out_dir/annotation_final_relaxed $out_dir/annotation_final.row_diff_int_brwt.annodbg &> relax.log + +# Note data/*.fa are the files from here: https://github.com/MitraDarja/analysis_needle/tree/main +/usr/bin/time -v -o query_1.time $metagraph query -p 4 --query-counts -i $out_dir/graph.dbg -a $out_dir/annotation_final_relaxed.row_diff_int_brwt.annodbg data/query_1.fa +/usr/bin/time -v -o query_100.time $metagraph query -p 4 --query-counts -i $out_dir/graph.dbg -a $out_dir/annotation_final_relaxed.row_diff_int_brwt.annodbg data/query_100.fa +/usr/bin/time -v -o query_1000.time $metagraph query -p 4 --query-counts -i $out_dir/graph.dbg -a $out_dir/annotation_final_relaxed.row_diff_int_brwt.annodbg data/query_1000.fa + +# Query with one thead +/usr/bin/time -v -o query_1_1.time $metagraph query -p 1 --query-counts -i $out_dir/graph.dbg -a $out_dir/annotation_final_relaxed.row_diff_int_brwt.annodbg data/query_1.fa +/usr/bin/time -v -o query_100_1.time $metagraph query -p 1 --query-counts -i $out_dir/graph.dbg -a $out_dir/annotation_final_relaxed.row_diff_int_brwt.annodbg data/query_100.fa +/usr/bin/time -v -o query_1000_1.time $metagraph query -p 1 --query-counts -i $out_dir/graph.dbg -a $out_dir/annotation_final_relaxed.row_diff_int_brwt.annodbg data/query_1000.fa + + +# Construction for smooth option + +mkdir $out_dir/clean_anno_smooth +/usr/bin/time -v -o jointbuild_smooth.time $metagraph build -p 4 -k 21 --count-kmers --count-width 32 --outfile-base $out_dir/graph_smooth single_dbgs/clean_smooth/SRR*.fasta.gz &> jointbuilt.log +/usr/bin/time -v -o annotate_joint_smooth.time $metagraph annotate --separately -p 4 -i $out_dir/graph.dbg --anno-filename --count-kmers --count-width 32 -o $out_dir/clean_anno_smooth single_dbgs/clean_smooth/SRR*.fasta.gz &> anno.log + +mkdir $out_dir/smooth_rd0 +mkdir $out_dir/smooth_rd1 +mkdir $out_dir/smooth_rd2 +/usr/bin/time -v -o rd0_smooth.time $metagraph transform_anno -v --anno-type row_diff --count-kmers --row-diff-stage 0 --mem-cap-gb 500 -o $out_dir/smooth_rd0/rd -i $out_dir/graph_smooth.dbg -p 4 --disk-swap "" $out_dir/clean_anno_smooth/*.column.annodbg &>rd0.log +/usr/bin/time -v -o rd1_smooth.time $metagraph transform_anno -v --anno-type row_diff --count-kmers --row-diff-stage 1 --mem-cap-gb 500 -o $out_dir/smooth_rd1/rd -i $out_dir/graph_smooth.dbg -p 4 --disk-swap "" $out_dir/clean_anno_smooth/*.column.annodbg &> rd1.log +/usr/bin/time -v -o rd2_smooth.time $metagraph transform_anno -v --anno-type row_diff --count-kmers --row-diff-stage 2 --mem-cap-gb 500 -o $out_dir/smooth_rd2/rd -i $out_dir/graph_smooth.dbg -p 4 --disk-swap "" $out_dir/clean_anno_smooth/*.column.annodbg &> rd2.log + +/usr/bin/time -v -o anno_smooth.time $metagraph transform_anno --anno-type row_diff_int_brwt --greedy --fast --subsample 1000000 -i $out_dir/graph_smooth.dbg -o $out_dir/annotation_final_smooth $out_dir/rd2/*.column.annodbg -p 4 --parallel-nodes 10 &> last_anno.log +/usr/bin/time -v -o relax_smooth.time $metagraph relax_brwt -v --relax-arity 32 -p 4 -o $out_dir/annotation_final_relaxed_smooth $out_dir/annotation_final_smooth.row_diff_int_brwt.annodbg &> relax.log + +# Note data/*.fa are the files from here: https://github.com/MitraDarja/analysis_needle/tree/main +/usr/bin/time -v -o query_1_smooth.time $metagraph query -p 4 --query-counts -i $out_dir/graph_smooth.dbg -a $out_dir/annotation_final_relaxed_smooth.row_diff_int_brwt.annodbg data/query_1.fa +/usr/bin/time -v -o query_100_smooth.time $metagraph query -p 4 --query-counts -i $out_dir/graph_smooth.dbg -a $out_dir/annotation_final_relaxed_smooth.row_diff_int_brwt.annodbg data/query_100.fa +/usr/bin/time -v -o query_1000_smooth.time $metagraph query -p 4 --query-counts -i $out_dir/graph_smooth.dbg -a $out_dir/annotation_final_relaxed_smooth.row_diff_int_brwt.annodbg data/query_1000.fa + +# Query with one thead +/usr/bin/time -v -o query_1_smooth_1.time $metagraph query -p 1 --query-counts -i $out_dir/graph_smooth.dbg -a $out_dir/annotation_final_relaxed_smooth.row_diff_int_brwt.annodbg data/query_1.fa +/usr/bin/time -v -o query_100_smooth_1.time $metagraph query -p 1 --query-counts -i $out_dir/graph_smooth.dbg -a $out_dir/annotation_final_relaxed_smooth.row_diff_int_brwt.annodbg data/query_100.fa +/usr/bin/time -v -o query_1000_smooth_1.time $metagraph query -p 1 --query-counts -i $out_dir/graph_smooth.dbg -a $out_dir/annotation_final_relaxed_smooth.row_diff_int_brwt.annodbg data/query_1000.fa diff --git a/utils/run_bcalm4.sh b/utils/run_bcalm4.sh new file mode 100644 index 0000000..54fefa0 --- /dev/null +++ b/utils/run_bcalm4.sh @@ -0,0 +1,9 @@ +#!/bin/bash +# Based on https://github.com/kamimrcht/REINDEER/blob/master/reproduce_manuscript_results/bcalm_2585.sh + +bcalm="Set path to bcalm2 executable" + +#get fastq.gz and launch bcalm on each file +while read -r filename; do + $bcalm -in $filename -kmer-size 21 -abundance-min 50 -nb-cores 2 -max-memory 500000 -out-tmp bcalm2 -out-dir bcalm2 +done < files.lst diff --git a/utils/run_build.sh b/utils/run_build.sh new file mode 100644 index 0000000..521c7d1 --- /dev/null +++ b/utils/run_build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu + +metagraph="Set path to metagraph executable" +# Note: You need to have a kmc_files.lst, which is a file where in each line there is a path to the kmc_files with the ending ".kmc_suf" + +mkdir single_dbgs/ +while read -r filename; do + $metagraph build --state fast --mode canonical --parallel 16 --count-kmers --count-width 32 -k 21 --mem-cap-gb 8 -o single_dbgs/$(basename ${filename}) $filename + echo $filename +done < kmc_files.lst diff --git a/utils/run_clean.sh b/utils/run_clean.sh new file mode 100644 index 0000000..3f4c322 --- /dev/null +++ b/utils/run_clean.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu + +metagraph="Set path to metagraph executable" +# Note: You need to have a dbg_files.txt, which is a file where in each line there is a path to the dbg files with the ending ".dbg" (created with run_build.sh) + +mkdir single_dbgs/clean/ + +while read -r filename; do + $metagraph clean -p4 --to-fasta --primary-kmers --smoothing-window 1 -o single_dbgs/clean/$(basename $filename) --count-kmers --count-width 32 $filename +done < dbg_files.txt diff --git a/utils/run_clean_smooth.sh b/utils/run_clean_smooth.sh new file mode 100644 index 0000000..169fcac --- /dev/null +++ b/utils/run_clean_smooth.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu + +metagraph="Set path to metagraph executable" +# Note: You need to have a dbg_files.txt, which is a file where in each line there is a path to the dbg files with the ending ".dbg" (created with run_build.sh) + +mkdir single_dbgs/clean_smooth/ + +while read -r filename; do + $metagraph clean -p 4 --to-fasta --primary-kmers --smoothing-window 1000000000 -o single_dbgs/clean_smooth/$(basename $filename) --count-kmers --count-width 32 $filename +done < dbg_files.txt diff --git a/utils/run_kmc.sh b/utils/run_kmc.sh new file mode 100644 index 0000000..cbf8c89 --- /dev/null +++ b/utils/run_kmc.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu + +kmc="Path to kmc executable" + +mkdir kmc_files +mkdir kmc_tmp +while read -r filename threshold; do + $kmc -t64 -r -k21 -ci$threshold -cs65535 -hp $filename kmc_files/$(basename $filename) kmc_tmp/ + echo $filename +done < samples.in diff --git a/utils/run_kmc4.sh b/utils/run_kmc4.sh new file mode 100644 index 0000000..ff2ab11 --- /dev/null +++ b/utils/run_kmc4.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +kmc="Set path to kmc executable" + +#get fastq.gz and launch bcalm on each file +while read -r filename; do + $kmc -t4 -r -k21 -ci50 -cs65535 -hp -m500 $filename $(basename $filename .res) kmc_tmp/ +done < files.lst diff --git a/utils/samples.in b/utils/samples.in new file mode 100644 index 0000000..a8d6f76 --- /dev/null +++ b/utils/samples.in @@ -0,0 +1,1662 @@ +SRR1023800.fastq.gz 50 +SRR1024048.fastq.gz 50 +SRR1024120.fastq.gz 50 +SRR1024121.fastq.gz 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