Command: cargo run --bin 1_beagleTA_parser
Success: true
Output:
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_█ █ █ █ █________________________________________ █ █________________ █ █ █ █ █ █______ █ █_____
_█ █____ █ █____ █ █ █____ █ █ █________ █ █ █ █__ █ █______ █ █ █________ █ █________ █ █ █ █___
_█ █ █ █ █____ █ █ █ █ █______ █ █____ █ █__ █ █__ █ █____ █ █ █ █ █______ █ █______ █ █____ █ █_
_█ █____ █ █__ █ █________ █ █ █ █______ █ █ █ █__ █ █____ █ █____________ █ █______ █ █ █ █ █ █_
_█ █ █ █ █______ █ █ █ █__ █ █ █ █ █________ █ █__ █ █ █____ █ █ █ █______ █ █______ █ █____ █ █_
_______________________________________ █ █ █ █___________________________________________________
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Package name: 'BeagleTA'.
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Package version: '1.5.11'.
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Package edition: '2021'.
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Usage: cargo run <keyword_file.txt> <corpus_dir>
🐕 Enter the path to the keyword text file: 🐕 Enter the path to the data directory: �[2K
Keyword path cannot be empty!
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Directory path cannot be empty!
[stderr]: Compiling proc-macro2 v1.0.94
Compiling unicode-ident v1.0.18
Compiling libc v0.2.171
Compiling crossbeam-utils v0.8.21
Compiling serde v1.0.219
Compiling memchr v2.7.4
Compiling zerocopy v0.8.23
Compiling rayon-core v1.12.1
Compiling utf8parse v0.2.2
Compiling cfg-if v1.0.0
Compiling anstyle-parse v0.2.6
Compiling is_terminal_polyfill v1.70.1
Compiling anstyle v1.0.10
Compiling colorchoice v1.0.3
Compiling hashbrown v0.15.2
Compiling equivalent v1.0.2
Compiling anstyle-query v1.1.2
Compiling anstream v0.6.18
Compiling aho-corasick v1.1.3
Compiling strsim v0.11.1
Compiling clap_lex v0.7.4
Compiling indexmap v2.8.0
Compiling ryu v1.0.20
Compiling itoa v1.0.15
Compiling futures v0.1.31
Compiling crossbeam-epoch v0.9.18
Compiling quote v1.0.40
Compiling crossbeam-deque v0.8.6
Compiling getrandom v0.2.15
Compiling rand_core v0.6.4
Compiling syn v2.0.100
Compiling iovec v0.1.4
Compiling num_cpus v1.16.0
Compiling crossbeam-channel v0.5.15
Compiling crossbeam-queue v0.3.12
Compiling byteorder v1.5.0
Compiling regex-syntax v0.8.5
Compiling either v1.15.0
Compiling winnow v0.7.4
Compiling serde_json v1.0.140
Compiling rayon v1.10.0
Compiling crossbeam v0.8.4
Compiling futures-cpupool v0.1.8
Compiling bytes v0.4.12
Compiling ppv-lite86 v0.2.21
Compiling clap_builder v4.5.35
Compiling rand_chacha v0.3.1
Compiling csv-core v0.1.12
Compiling fs v0.0.5
Compiling rand v0.8.5
Compiling colored v3.0.0
Compiling regex-automata v0.4.9
Compiling serde_derive v1.0.219
Compiling jwalk v0.8.1
Compiling clap v4.5.35
Compiling regex v1.11.1
Compiling serde_spanned v0.6.8
Compiling toml_datetime v0.6.8
Compiling csv v1.3.1
Compiling toml_edit v0.22.24
Compiling toml v0.8.20
Compiling BeagleTA v1.5.11 (/Users/obonhamcarter/Desktop/mini_research_TA/BeagleTA)
Finished `dev` profile [unoptimized + debuginfo] target(s) in 7.00s
Running `target/debug/1_beagleTA_parser`
Time: 7.2878 seconds
Command: cargo run --bin 2_csv_cleaner_filter/
Success: false
Output:
[stderr]: error: no bin target named `2_csv_cleaner_filter/`
Did you mean `2_csv_cleaner_filter`?
Time: 0.0611 seconds
Command: cargo run --bin 2_csv_cleaner_filter
Success: false
Output:
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___█ █ █ █ █ __█ █ _______________________________________________________________
_█ █ __________█ █ ______█ █ █ ____█ █ █ ______█ █ █ █ ______█ █ █ ____█ █ __█ █ _
_█ █ __________█ █ ____█ █ █ █ █ ______█ █ ____█ █ __█ █ __█ █ █ █ █ __█ █ █ █ ___
_█ █ __________█ █ ____█ █ ________█ █ █ █ ____█ █ __█ █ __█ █ ________█ █ _______
___█ █ █ █ █ __█ █ █ ____█ █ █ █ __█ █ █ █ █ __█ █ __█ █ ____█ █ █ █ __█ █ _______
__________________________________________________________________________________
[stderr]: Compiling BeagleTA v1.5.11 (/Users/obonhamcarter/Desktop/mini_research_TA/BeagleTA)
Finished `dev` profile [unoptimized + debuginfo] target(s) in 0.22s
Running `target/debug/2_csv_cleaner_filter`
error: the following required arguments were not provided:
--input <input>
--output <output>
--column <column>
Usage: 2_csv_cleaner_filter --input <input> --output <output> --column <column>
For more information, try '--help'.
Time: 0.4488 seconds
Command: cargo run examples/kws.txt examples/corpus_short/
Success: false
Output:
[stderr]: error: `cargo run` could not determine which binary to run. Use the `--bin` option to specify a binary, or the `default-run` manifest key.
available binaries: 1_beagleTA_parser, 2_csv_cleaner_filter, 3_csv_random_sampler
Time: 0.0413 seconds
Command: cargo run --bin -- 1_beagleTA_parser examples/kws.txt examples/corpus_short/
Success: false
Output:
[stderr]: error: "--bin" takes one argument.
Available binaries:
1_beagleTA_parser
2_csv_cleaner_filter
3_csv_random_sampler
Time: 0.0379 seconds
Command: cargo run -- --bin 1_beagleTA_parser examples/kws.txt examples/corpus_short/
Success: false
Output:
[stderr]: error: `cargo run` could not determine which binary to run. Use the `--bin` option to specify a binary, or the `default-run` manifest key.
available binaries: 1_beagleTA_parser, 2_csv_cleaner_filter, 3_csv_random_sampler
Time: 0.0331 seconds
Command: cargo run --bin 1_beagleTA_parser examples/kws.txt examples/corpus_short/
Success: true
Output:
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_█ █ █ █ █________________________________________ █ █________________ █ █ █ █ █ █______ █ █_____
_█ █____ █ █____ █ █ █____ █ █ █________ █ █ █ █__ █ █______ █ █ █________ █ █________ █ █ █ █___
_█ █ █ █ █____ █ █ █ █ █______ █ █____ █ █__ █ █__ █ █____ █ █ █ █ █______ █ █______ █ █____ █ █_
_█ █____ █ █__ █ █________ █ █ █ █______ █ █ █ █__ █ █____ █ █____________ █ █______ █ █ █ █ █ █_
_█ █ █ █ █______ █ █ █ █__ █ █ █ █ █________ █ █__ █ █ █____ █ █ █ █______ █ █______ █ █____ █ █_
_______________________________________ █ █ █ █___________________________________________________
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Package name: 'BeagleTA'.
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Package version: '1.5.11'.
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Package edition: '2021'.
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Usage: cargo run <keyword_file.txt> <corpus_dir>
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Found 63 files in the directory 'examples/corpus_short/'.
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Key words : ["2024", "ethic", "bio", "machine", "mitochondria"]
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* PMC314466.txt -> 1 of 63�[2K
* PMC314300.txt -> 2 of 63�[2K
* PMC314472.txt -> 3 of 63�[2K
* PMC193604.txt -> 4 of 63�[2K
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* PMC314465.txt -> 10 of 63�[2K
* PMC193607.txt -> 11 of 63�[2K
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* PMC314464.txt -> 13 of 63�[2K
* PMC314470.txt -> 14 of 63�[2K
* PMC314474.txt -> 15 of 63�[2K
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* PMC212689.txt -> 38 of 63�[2K
* PMC300886.txt -> 39 of 63�[2K
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* PMC261870.txt -> 43 of 63�[2K
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* PMC176546.txt -> 51 of 63�[2K
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* PMC176547.txt -> 54 of 63�[2K
* PMC314478.txt -> 55 of 63�[2K
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* PMC314469.txt -> 57 of 63�[2K
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* PMC314480.txt -> 61 of 63�[2K
✨ Run commands to create virtual environment with Python for the following commands ...
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python3 -m venv ~/Desktop/venv
source ~/Desktop/venv/bin/activate
pip install plotly matplotlib numpy pandas networkx seaborn scikit-learn pyvis
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✨ Run commands to create keyword analysis and other visualizations ...
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cd 0_out && python3 visualizations.py && cd ..
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cd 0_out && python3 interactive_network_1.py --datafile output.csv --threshold 6 && cd ..
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cd 0_out && python3 interactive_network_2.py --datafile output.csv && cd ..
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cd 0_out && python3 complete_network.py -f output.csv -t 6 -nc blue -ec green && cd ..
[stderr]: Finished `dev` profile [unoptimized + debuginfo] target(s) in 0.03s
Running `target/debug/1_beagleTA_parser examples/kws.txt examples/corpus_short/`
Time: 0.5581 seconds