v0.2.1

Author: shenwei356

README.md

@@ -12,7 +12,7 @@ format. And the name was remained after adding ***seamless support for FASTA/Q f
 ## Introduction
 
 FASTA and FASTQ are basic formats for storing nucleotide and protein sequences.
-The manipulations of FASTA/Q file includes converting, clipping, searching,
+The manipulations of FASTA/Q file include converting, clipping, searching,
 filtering, deduplication, splitting, shuffling, sampling and so on.
 Existed tools only implemented parts of the functions,
 and some of them are only available for specific operating systems.
@@ -22,7 +22,8 @@ running environment also make them less friendly to common users.
 fakit is a cross-platform, efficient, and practical FASTA/Q manipulations tool
 that is friendly for researchers to complete wide ranges of FASTA file processing.
 The suite supports plain or gzip-compressed input and output
-from either standard stream or files, therefore, it could be easily used in pipelines.
+from either standard stream or files,
+therefore, it could be easily used in command-line pipe.
 
 ## Features
 
@@ -224,10 +225,10 @@ Most of the subcommands do not read whole FASTA/Q records in to memory,
 including `stat`, `fq2fa`, `fx2tab`, `tab2fx`, `grep`, `locate`, `replace`,
  `seq`, `sliding`, `subseq`. They just temporarily buffer chunks of records.
 
-However when handling big sequences, e.g. human genome, the memory is high
+However when handling big sequences, e.g. Human genome, the memory is high
 (2-3 GB) even the buffer size is 1.
-This is due to the limitation of Go programming language, it may be solved
-in the future.
+This is due to the limitation of garbage collection mechanism in
+ Go programming language, it may be solved in the future.
 
 Note that when using `subseq --gtf | --bed`, if the GTF/BED files are too
 big, the memory usage will increase.

benchmark/.Rhistory

@@ -9,22 +9,18 @@ Datasets and results are described at [http://shenwei356.github.io/fakit/benchma
 Softwares
 
 1. [fakit](https://github.com/shenwei356/fakit). (Go).
-   Version [v0.1.9](https://github.com/shenwei356/fakit/releases/tag/v0.1.9).
+   Version [v0.2.1](https://github.com/shenwei356/fakit/releases/tag/v0.2.1).
 1. [fasta_utilities](https://github.com/jimhester/fasta_utilities). (Perl).
    Version [3dcc0bc](https://github.com/jimhester/fasta_utilities/tree/3dcc0bc6bf1e97839476221c26984b1789482579).
    Lots of dependencies to install_.
 1. [fastx_toolkit](http://hannonlab.cshl.edu/fastx_toolkit/). (Perl).
    Version [0.0.13](http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2).
    Can't handle multi-line FASTA files_.
-1. [seqmagick](http://seqmagick.readthedocs.org/en/latest/index.html). (Python).
+1. [seqmagick](http://seqmagick.readthedocs.io/en/latest/index.html#installation). (Python).
    Version 0.6.1
 1. [seqtk](https://github.com/lh3/seqtk). (C).
-   Version [1.0-r82-dirty](https://github.com/lh3/seqtk/commit/4feb6e81444ab6bc44139dd3a125068f81ae4ad8).
+   Version [1.1-r92-dirty](https://github.com/lh3/seqtk/tree/fb85aad4ce1fc7b3d4543623418a1ae88fe1cea6).
 
-Not used:
-
-1. [pyfaidx](https://github.com/mdshw5/pyfaidx). (Python).
-   Version [0.4.7.1](https://pypi.python.org/packages/source/p/pyfaidx/pyfaidx-0.4.7.1.tar.gz#md5=f33604a3550c2fa115ac7d33b952127d). *Not used, because it
 
 A Python script [memusg](https://github.com/shenwei356/memusg) was used
    to computate running time and peak memory usage of a process.
@@ -45,10 +41,22 @@ The edited code is
       if $config{bar_width} < 1;
     }
 
+## Clone this repository
+
+    git clone https://github.com/shenwei356/fakit
+    cd fakit/benchmark
+
 ## Data preparation
 
 [http://shenwei356.github.io/fakit/benchmark/#datasets](http://shenwei356.github.io/fakit/benchmark/#datasets)
 
+Or download all test data [fakit-benchmark-data.tar.gz](http://bioinf.shenwei.me/fakit-benchmark-data.tar.gz)
+ (1.7G) and uncompress it, and then move them into directory `fakit/benchmark`
+
+    wget ***
+    tar -zxvf fakit-benchmark-data.tar.gz
+    mv fakit-benchmark-data/* fakit/benchmark
+
 ## Run tests
 
 A Perl scripts
@@ -76,6 +84,8 @@ To compare performance between different softwares, run:
 
     ./run.pl run_benchmark*.sh -n 3 -o benchmark.5tests.csv
 
+It costed ~50min for me.
+
 To test performance of other functions in fakit, run:
 
     ./run.pl run_test*.sh -n 1 -o benchmark.fakit.csv
@@ -86,8 +96,8 @@ R libraries `dplyr`, `ggplot2`, `scales`, `ggthemes`, `ggrepel` are needed.
 
 Plot for result of the five tests:
 
-    ./plot2.R -i benchmark.5tests.csv
+    ./plot.R -i benchmark.5tests.csv
 
-Plot for result of the stest of other functions in fakit:
+Plot for result of the tests of other functions in fakit:
 
-    ./plot2.R -i benchmark.fakit.csv --width 5 --height 3
+    ./plot.R -i benchmark.fakit.csv --width 5 --height 3

benchmark/README.md

@@ -0,0 +1,31 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Reverse complement	dataset_A.fa	biogo	100.78	1.33	35836	1226
+Reverse complement	dataset_A.fa	fakit	30.53	1.03	47684	1994
+Reverse complement	dataset_A.fa	fasta_utilities	18.87	1.36	58298	859
+Reverse complement	dataset_A.fa	seqmagick	59.68	1.56	49754	1493
+Reverse complement	dataset_A.fa	seqtk	10.06	0.53	7629	18
+Reverse complement	dataset_B.fa	biogo	93.65	2.18	1315030	53727
+Reverse complement	dataset_B.fa	fakit	26.36	1.29	1793784	75222
+Reverse complement	dataset_B.fa	fasta_utilities	27.79	3.25	1256350	92
+Reverse complement	dataset_B.fa	seqmagick	65.42	1.91	1422250	73040
+Reverse complement	dataset_B.fa	seqtk	12.25	0.95	244870	57
+Searching by ID list	dataset_A.fa	fakit	12.23	0.21	53065	2711
+Searching by ID list	dataset_A.fa	fasta_utilities	9.96	0.01	54824	3379
+Searching by ID list	dataset_A.fa	seqmagick	46.22	0.19	42166	932
+Searching by ID list	dataset_A.fa	seqtk	11.72	0.44	9954	60
+Searching by ID list	dataset_B.fa	fakit	12.02	0.06	1695814	1128
+Searching by ID list	dataset_B.fa	fasta_utilities	12.60	0.07	1256420	67
+Searching by ID list	dataset_B.fa	seqmagick	53.86	1.12	973556	36867
+Searching by ID list	dataset_B.fa	seqtk	14.22	0.27	244886	64
+Sampling by number	dataset_A.fa	fakit	28.30	0.39	44261	3344
+Sampling by number	dataset_A.fa	seqmagick	40.88	1.07	541172	912
+Sampling by number	dataset_A.fa	seqtk	4.25	0.09	1081468	1295
+Sampling by number	dataset_B.fa	fakit	31.31	0.66	1558248	149
+Sampling by number	dataset_B.fa	seqmagick	42.20	2.10	3036372	108690
+Sampling by number	dataset_B.fa	seqtk	4.99	0.11	2817700	3
+Removing duplicates by seq	dataset_A.fa	fakit	19.86	0.82	61324	2426
+Removing duplicates by seq	dataset_A.fa	seqmagick	79.47	1.87	60590	576
+Removing duplicates by seq	dataset_B.fa	fakit	16.50	0.78	1927258	133969
+Removing duplicates by seq	dataset_B.fa	seqmagick	90.29	0.67	1123858	28
+Subsequence with BED file	dataset_B.fa	fakit	9.70	0.23	2081481	163038
+Subsequence with BED file	dataset_B.fa	seqtk	6.72	0.06	246277	33

benchmark/benchmark.5tests.csv

@@ -0,0 +1,5 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Shuffling	dataset_A.fa	fakit	17.70	0.00	2843664	0
+Shuffling	dataset_B.fa	fakit	14.44	0.00	3127368	0
+Sorting by length	dataset_A.fa	fakit	18.77	0.00	2888056	0
+Sorting by length	dataset_B.fa	fakit	14.23	0.00	3254916	0

benchmark/benchmark.5tests.csv.png

@@ -0,0 +1,37 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Reverse complement	dataset_A.fa	1	38.27	0.00	45544	0
+Reverse complement	dataset_A.fa	2	31.23	0.00	45876	0
+Reverse complement	dataset_A.fa	3	30.22	0.00	42036	0
+Reverse complement	dataset_A.fa	4	32.62	0.00	48744	0
+Reverse complement	dataset_B.fa	1	38.92	0.00	1925872	0
+Reverse complement	dataset_B.fa	2	25.62	0.00	1833360	0
+Reverse complement	dataset_B.fa	3	25.02	0.00	1813708	0
+Reverse complement	dataset_B.fa	4	24.99	0.00	1925272	0
+Searching by ID list	dataset_A.fa	1	13.28	0.00	53604	0
+Searching by ID list	dataset_A.fa	2	13.01	0.00	52312	0
+Searching by ID list	dataset_A.fa	3	13.02	0.00	52572	0
+Searching by ID list	dataset_A.fa	4	13.41	0.00	56628	0
+Searching by ID list	dataset_B.fa	1	12.37	0.00	1665156	0
+Searching by ID list	dataset_B.fa	2	12.06	0.00	1585708	0
+Searching by ID list	dataset_B.fa	3	12.14	0.00	1912948	0
+Searching by ID list	dataset_B.fa	4	11.83	0.00	1912032	0
+Sampling by number	dataset_A.fa	1	33.23	0.00	47588	0
+Sampling by number	dataset_A.fa	2	28.75	0.00	44032	0
+Sampling by number	dataset_A.fa	3	29.75	0.00	42520	0
+Sampling by number	dataset_A.fa	4	30.27	0.00	47688	0
+Sampling by number	dataset_B.fa	1	36.81	0.00	1869772	0
+Sampling by number	dataset_B.fa	2	31.51	0.00	1558392	0
+Sampling by number	dataset_B.fa	3	32.99	0.00	1536872	0
+Sampling by number	dataset_B.fa	4	31.83	0.00	1604788	0
+Removing duplicates by seq content	dataset_A.fa	1	21.93	0.00	65416	0
+Removing duplicates by seq content	dataset_A.fa	2	19.45	0.00	59204	0
+Removing duplicates by seq content	dataset_A.fa	3	20.12	0.00	59924	0
+Removing duplicates by seq content	dataset_A.fa	4	19.34	0.00	59940	0
+Removing duplicates by seq content	dataset_B.fa	1	20.16	0.00	1703012	0
+Removing duplicates by seq content	dataset_B.fa	2	16.22	0.00	1780832	0
+Removing duplicates by seq content	dataset_B.fa	3	18.64	0.00	2011904	0
+Removing duplicates by seq content	dataset_B.fa	4	16.33	0.00	2150284	0
+Subsequence with BED file	dataset_B.fa	1	14.63	0.22	2105462	1846
+Subsequence with BED file	dataset_B.fa	2	9.87	0.05	2046796	105814
+Subsequence with BED file	dataset_B.fa	3	9.61	0.29	2158104	146143
+Subsequence with BED file	dataset_B.fa	4	8.85	0.27	2124036	177248

benchmark/benchmark.fakit.csv

@@ -0,0 +1,17 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Shuffling	dataset_A.fa	1	17.47	0.00	2804292	0
+Shuffling	dataset_A.fa	2	16.92	0.00	2853488	0
+Shuffling	dataset_A.fa	3	16.88	0.00	2840376	0
+Shuffling	dataset_A.fa	4	17.67	0.00	2814828	0
+Shuffling	dataset_B.fa	1	13.78	0.00	3246272	0
+Shuffling	dataset_B.fa	2	13.61	0.00	3266400	0
+Shuffling	dataset_B.fa	3	16.51	0.00	3278048	0
+Shuffling	dataset_B.fa	4	13.74	0.00	3232840	0
+Sorting by length	dataset_A.fa	1	18.27	0.00	2853268	0
+Sorting by length	dataset_A.fa	2	21.88	0.00	2856084	0
+Sorting by length	dataset_A.fa	3	19.02	0.00	2859320	0
+Sorting by length	dataset_A.fa	4	19.27	0.00	2880252	0
+Sorting by length	dataset_B.fa	1	14.72	0.00	3155324	0
+Sorting by length	dataset_B.fa	2	17.35	0.00	3141520	0
+Sorting by length	dataset_B.fa	3	14.43	0.00	3202260	0
+Sorting by length	dataset_B.fa	4	17.66	0.00	3250852	0

benchmark/benchmark.fakit.csv.png

@@ -0,0 +1 @@
+../plot.R

benchmark/fakit_multi_threads/benchmark.5tests.csv

@@ -0,0 +1 @@
+../revcom_biogo

benchmark/fakit_multi_threads/benchmark.5tests.csv.png

@@ -0,0 +1 @@
+../run.pl

benchmark/fakit_multi_threads/benchmark.fakit.csv

@@ -0,0 +1,29 @@
+#!/bin/sh
+
+echo Test: Shuffling 
+
+echo warm-up
+for f in dataset_{A,B}.fa; do echo data: $f; cat $f > /dev/null; done
+
+
+NCPUs=$(grep -c processor /proc/cpuinfo)
+for i in $(seq 1 $NCPUs); do 
+    echo == $i
+    echo recreate FASTA index file
+    for f in dataset_{A,B}.fa; do
+        if [[ -f $f.fakit.fai ]]; then
+            /bin/rm $f.fakit.fai
+            # fakit faidx $f --id-regexp "^(.+)$" -o $f.fakit.fai;
+        fi;
+    done
+
+    for f in dataset_{A,B}.fa; do
+        echo data: $f;
+        memusg -t -H fakit shuffle -2 $f > $f.fakit.shuffle;
+        # fakit stat $f.fakit.rc;
+        /bin/rm $f.fakit.shuffle;
+    done
+done
+
+
+

benchmark/fakit_multi_threads/benchmark.fakit.csv.png

@@ -0,0 +1,34 @@
+#!/bin/sh
+
+echo Test: Sorting by length
+
+echo warm-up
+for f in dataset_{A,B}.fa; do echo data: $f; cat $f > /dev/null; done
+
+
+NCPUs=$(grep -c processor /proc/cpuinfo)
+for i in $(seq 1 $NCPUs); do 
+    echo == $i
+    echo delete old FASTA index file
+    for f in dataset_{A,B}.fa; do
+        if [[ -f $f.fakit.fai ]]; then
+            /bin/rm $f.fakit.fai
+            # fakit faidx $f --id-regexp "^(.+)$" -o $f.fakit.fai;
+        fi;
+    done
+
+    for f in dataset_{A,B}.fa; do
+        echo data: $f;
+        memusg -t -H fakit sort -l -2 $f > $f.fakit.sort;
+        # fakit stat $f.fakit.rc;
+        /bin/rm $f.fakit.sort;
+    done
+done
+
+
+
+
+
+
+
+

benchmark/fakit_multi_threads/plot.R

@@ -0,0 +1,37 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Reverse complement	dataset_A.fa	1	38.27	0.00	45544	0
+Reverse complement	dataset_A.fa	2	31.23	0.00	45876	0
+Reverse complement	dataset_A.fa	3	30.22	0.00	42036	0
+Reverse complement	dataset_A.fa	4	32.62	0.00	48744	0
+Reverse complement	dataset_B.fa	1	38.92	0.00	1925872	0
+Reverse complement	dataset_B.fa	2	25.62	0.00	1833360	0
+Reverse complement	dataset_B.fa	3	25.02	0.00	1813708	0
+Reverse complement	dataset_B.fa	4	24.99	0.00	1925272	0
+Searching by ID list	dataset_A.fa	1	13.28	0.00	53604	0
+Searching by ID list	dataset_A.fa	2	13.01	0.00	52312	0
+Searching by ID list	dataset_A.fa	3	13.02	0.00	52572	0
+Searching by ID list	dataset_A.fa	4	13.41	0.00	56628	0
+Searching by ID list	dataset_B.fa	1	12.37	0.00	1665156	0
+Searching by ID list	dataset_B.fa	2	12.06	0.00	1585708	0
+Searching by ID list	dataset_B.fa	3	12.14	0.00	1912948	0
+Searching by ID list	dataset_B.fa	4	11.83	0.00	1912032	0
+Sampling by number	dataset_A.fa	1	33.23	0.00	47588	0
+Sampling by number	dataset_A.fa	2	28.75	0.00	44032	0
+Sampling by number	dataset_A.fa	3	29.75	0.00	42520	0
+Sampling by number	dataset_A.fa	4	30.27	0.00	47688	0
+Sampling by number	dataset_B.fa	1	36.81	0.00	1869772	0
+Sampling by number	dataset_B.fa	2	31.51	0.00	1558392	0
+Sampling by number	dataset_B.fa	3	32.99	0.00	1536872	0
+Sampling by number	dataset_B.fa	4	31.83	0.00	1604788	0
+Removing duplicates by seq content	dataset_A.fa	1	21.93	0.00	65416	0
+Removing duplicates by seq content	dataset_A.fa	2	19.45	0.00	59204	0
+Removing duplicates by seq content	dataset_A.fa	3	20.12	0.00	59924	0
+Removing duplicates by seq content	dataset_A.fa	4	19.34	0.00	59940	0
+Removing duplicates by seq content	dataset_B.fa	1	20.16	0.00	1703012	0
+Removing duplicates by seq content	dataset_B.fa	2	16.22	0.00	1780832	0
+Removing duplicates by seq content	dataset_B.fa	3	18.64	0.00	2011904	0
+Removing duplicates by seq content	dataset_B.fa	4	16.33	0.00	2150284	0
+Subsequence with BED file	dataset_B.fa	1	14.63	0.22	2105462	1846
+Subsequence with BED file	dataset_B.fa	2	9.87	0.05	2046796	105814
+Subsequence with BED file	dataset_B.fa	3	9.61	0.29	2158104	146143
+Subsequence with BED file	dataset_B.fa	4	8.85	0.27	2124036	177248

benchmark/fakit_multi_threads/plot2.R

@@ -0,0 +1,17 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Shuffling	dataset_A.fa	1	17.47	0.00	2804292	0
+Shuffling	dataset_A.fa	2	16.92	0.00	2853488	0
+Shuffling	dataset_A.fa	3	16.88	0.00	2840376	0
+Shuffling	dataset_A.fa	4	17.67	0.00	2814828	0
+Shuffling	dataset_B.fa	1	13.78	0.00	3246272	0
+Shuffling	dataset_B.fa	2	13.61	0.00	3266400	0
+Shuffling	dataset_B.fa	3	16.51	0.00	3278048	0
+Shuffling	dataset_B.fa	4	13.74	0.00	3232840	0
+Sorting by length	dataset_A.fa	1	18.27	0.00	2853268	0
+Sorting by length	dataset_A.fa	2	21.88	0.00	2856084	0
+Sorting by length	dataset_A.fa	3	19.02	0.00	2859320	0
+Sorting by length	dataset_A.fa	4	19.27	0.00	2880252	0
+Sorting by length	dataset_B.fa	1	14.72	0.00	3155324	0
+Sorting by length	dataset_B.fa	2	17.35	0.00	3141520	0
+Sorting by length	dataset_B.fa	3	14.43	0.00	3202260	0
+Sorting by length	dataset_B.fa	4	17.66	0.00	3250852	0

benchmark/fakit_multi_threads/revcom_biogo

@@ -0,0 +1,5 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Subsequence with BED file	dataset_B.fa	1	14.63	0.22	2105462	1846
+Subsequence with BED file	dataset_B.fa	2	9.87	0.05	2046796	105814
+Subsequence with BED file	dataset_B.fa	3	9.61	0.29	2158104	146143
+Subsequence with BED file	dataset_B.fa	4	8.85	0.27	2124036	177248

benchmark/fakit_multi_threads/run.pl

@@ -0,0 +1,37 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Reverse complement	dataset_A.fa	1	113.83	0.00	11740	0
+Reverse complement	dataset_A.fa	2	124.43	0.00	12232	0
+Reverse complement	dataset_A.fa	3	125.14	0.00	12088	0
+Reverse complement	dataset_A.fa	4	126.08	0.00	12364	0
+Reverse complement	dataset_B.fa	1	47.49	0.00	2026540	0
+Reverse complement	dataset_B.fa	2	30.09	0.00	2002564	0
+Reverse complement	dataset_B.fa	3	31.55	0.00	2254176	0
+Reverse complement	dataset_B.fa	4	29.23	0.00	2462680	0
+Searching by ID list	dataset_A.fa	1	174.38	0.00	1017628	0
+Searching by ID list	dataset_A.fa	2	168.26	0.00	979172	0
+Searching by ID list	dataset_A.fa	3	167.96	0.00	941308	0
+Searching by ID list	dataset_A.fa	4	170.26	0.00	990276	0
+Searching by ID list	dataset_B.fa	1	13.48	0.00	2250796	0
+Searching by ID list	dataset_B.fa	2	11.50	0.00	2075996	0
+Searching by ID list	dataset_B.fa	3	11.89	0.00	2445820	0
+Searching by ID list	dataset_B.fa	4	11.72	0.00	2306508	0
+Sampling by number	dataset_A.fa	1	92.26	0.00	12152	0
+Sampling by number	dataset_A.fa	2	91.47	0.00	12248	0
+Sampling by number	dataset_A.fa	3	95.17	0.00	12252	0
+Sampling by number	dataset_A.fa	4	96.31	0.00	12132	0
+Sampling by number	dataset_B.fa	1	34.73	0.00	2075620	0
+Sampling by number	dataset_B.fa	2	29.57	0.00	2076784	0
+Sampling by number	dataset_B.fa	3	31.20	0.00	1804840	0
+Sampling by number	dataset_B.fa	4	31.60	0.00	2076920	0
+Removing duplicates by seq content	dataset_A.fa	1	231.65	0.00	3428340	0
+Removing duplicates by seq content	dataset_A.fa	2	229.12	0.00	3646984	0
+Removing duplicates by seq content	dataset_A.fa	3	235.32	0.00	3451840	0
+Removing duplicates by seq content	dataset_A.fa	4	241.94	0.00	2990240	0
+Removing duplicates by seq content	dataset_B.fa	1	26.83	0.00	2322172	0
+Removing duplicates by seq content	dataset_B.fa	2	18.62	0.00	2692244	0
+Removing duplicates by seq content	dataset_B.fa	3	20.54	0.00	2836324	0
+Removing duplicates by seq content	dataset_B.fa	4	19.50	0.00	2567764	0
+Subsequence with BED file	dataset_B.fa	1	17.09	0.00	1931700	0
+Subsequence with BED file	dataset_B.fa	2	11.56	0.00	1919372	0
+Subsequence with BED file	dataset_B.fa	3	11.97	0.00	2027240	0
+Subsequence with BED file	dataset_B.fa	4	10.55	0.00	1910492	0

benchmark/fakit_multi_threads/run_benchmark_00_all.pl

@@ -0,0 +1,9 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Reverse complement	dataset_A.fa	1	38.27	0.00	45544	0
+Reverse complement	dataset_A.fa	2	31.23	0.00	45876	0
+Reverse complement	dataset_A.fa	3	30.22	0.00	42036	0
+Reverse complement	dataset_A.fa	4	32.62	0.00	48744	0
+Reverse complement	dataset_B.fa	1	38.92	0.00	1925872	0
+Reverse complement	dataset_B.fa	2	25.62	0.00	1833360	0
+Reverse complement	dataset_B.fa	3	25.02	0.00	1813708	0
+Reverse complement	dataset_B.fa	4	24.99	0.00	1925272	0

benchmark/fakit_multi_threads/run_benchmark_00_all.pl.benchmark.csv

@@ -0,0 +1,9 @@
+test	dataset	app	time_mean	time_stdev	mem_mean	mem_stdev
+Searching by ID list	dataset_A.fa	1	13.28	0.00	53604	0
+Searching by ID list	dataset_A.fa	2	13.01	0.00	52312	0
+Searching by ID list	dataset_A.fa	3	13.02	0.00	52572	0
+Searching by ID list	dataset_A.fa	4	13.41	0.00	56628	0
+Searching by ID list	dataset_B.fa	1	12.37	0.00	1665156	0
+Searching by ID list	dataset_B.fa	2	12.06	0.00	1585708	0
+Searching by ID list	dataset_B.fa	3	12.14	0.00	1912948	0
+Searching by ID list	dataset_B.fa	4	11.83	0.00	1912032	0