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Initial upload of test data
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‎test_data/README.txt

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In each workflow folder you can find the
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reduced output files and directory systems
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of the specific workflows.
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Each folder also contains a textfile
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showing example commandline calls that
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would create the given data.
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The output is not entirely complete and
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Spice does not have a test mode. If you
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wanna generate a small Library just to
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check if it all works, you can try the
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tetraodon. The species does not have a lot
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of splicing variants annotated and the
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genome is generally small in comparison to
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other vertebrates on Ensembl.
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If you have any question you can always
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reach me via e-Mail:
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[email protected]
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Cheers,
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Christian

‎test_data/Spice_Library/Spice_Library_Workflow.txt

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Initialize library:
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python spice_library.py -s human -r 94 -o test_data/Spice_Library
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Prepare FAS SLURM Jobs
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(Start here if you come from the Spice Novel Workflow):
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python FASJobAssistant.py -L test_data/spice_lib_test_homo_sapiens_94_1ee/ -m 2 -p node_names_of_computing_cluster -d path_to_binary_directory_of_FAS -o output_directory \
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-a node_names_of_computing_cluster_used_for_annotion -A number_of_cores_that_shall_be_used_for_annotation -t path_to_annoTools_directory
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After running all FAS Jobs run this:
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python parse_domain_out.py -f test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/forward.domains -r test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/forward.domains \
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-m test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/architectures -o test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/annoTools.txt

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#linearized
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Pfam
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#normal
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fLPS
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COILS2
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SEG
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SignalP
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TMHMM
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#checked

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/fas.phyloprofile

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geneID ncbiID orthoID FAS_F FAS_B
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ENSG00000253293|ENSP00000283921|9606 ncbi9606 ENSG00000253293|ENSP00000479619|9606 0.3324 0.6492
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ENSG00000253293|ENSP00000283921|9606 ncbi9606 ENSG00000253293|ENSP00000379633|9606 0.371 0.9274
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ENSG00000253293|ENSP00000479619|9606 ncbi9606 ENSG00000253293|ENSP00000379633|9606 0.0 0.0

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/fas_index.json

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{"ENSG00000126368": "000000160.json",
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"ENSG00000183615": "000000004.json",
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"ENSG00000253293": "000000071.json"}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/fas_scores/000000004.json

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{"ENSG00000183615": {
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"ENSP00000362684": {
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"ENSP00000362684": 1.0,
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"HOMnoORFGroup": 0.0,
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"HOM4b9cf06933c8e78": 0.9986
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},
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"HOMnoORFGroup": {
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"ENSP00000362684": 0.0,
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"HOMnoORFGroup": 1.0,
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"HOM4b9cf06933c8e78": 0.0
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},
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"HOM4b9cf06933c8e78": {
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"ENSP00000362684": 0.1368,
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"HOMnoORFGroup": 0.0,
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"HOM4b9cf06933c8e78": 1.0
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}
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}}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/fas_scores/000000071.json

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{"ENSG00000253293": {
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"ENSP00000283921": {
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"ENSP00000283921": 1.0,
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"ENSP00000479619": 0.6492,
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"ENSP00000379633": 0.9274,
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"HOMnoDiamondGroup": 0.0,
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"HOMnoORFGroup": 0.0
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},
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"ENSP00000479619": {
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"ENSP00000283921": 0.3324,
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"ENSP00000479619": 1.0,
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"ENSP00000379633": 0.0,
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"HOMnoDiamondGroup": 0.0,
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"HOMnoORFGroup": 0.0
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},
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"ENSP00000379633": {
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"ENSP00000283921": 0.371,
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"ENSP00000479619": 0.0,
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"ENSP00000379633": 1.0,
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"HOMnoDiamondGroup": 0.0,
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"HOMnoORFGroup": 0.0
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},
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"HOMnoDiamondGroup": {
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"ENSP00000283921": 0.0,
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"ENSP00000479619": 0.0,
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"ENSP00000379633": 0.0,
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"HOMnoDiamondGroup": 1.0,
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"HOMnoORFGroup": 0.0
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},
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"HOMnoORFGroup": {
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"ENSP00000283921": 0.0,
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"ENSP00000479619": 0.0,
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"ENSP00000379633": 0.0,
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"HOMnoDiamondGroup": 0.0,
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"HOMnoORFGroup": 1.0
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}
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}}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/fas_data/fas_scores/000000160.json

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{"ENSG00000126368": {
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"ENSP00000246672": {
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"ENSP00000246672": 1.0,
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"HOMnoORFGroup": 0.0,
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"HOMGRP81c552f7c12b": 0.0,
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"HOMnoDiamondGroup": 0.0
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},
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"HOMnoORFGroup": {
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"ENSP00000246672": 0.0,
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"HOMnoORFGroup": 1.0,
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"HOMGRP81c552f7c12b": 0.0,
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"HOMnoDiamondGroup": 0.0
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},
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"HOMGRP81c552f7c12b": {
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"ENSP00000246672": 0.0,
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"HOMnoORFGroup": 0.0,
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"HOMGRP81c552f7c12b": 1.0,
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"HOMnoDiamondGroup": 0.0
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},
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"HOMnoDiamondGroup": {
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"ENSP00000246672": 0.0,
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"HOMnoORFGroup": 0.0,
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"HOMGRP81c552f7c12b": 0.0,
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"HOMnoDiamondGroup": 1.0
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}
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}}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/info.yaml

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commandline_args:
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copylib: null
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force: false
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keepgtf: false
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modefas: null
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outdir: test_data/Spice_Library
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release: '94'
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species: human
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info:
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collected_sequences_count: 5
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fas_mode: 1ee
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fas_scored_sequences_count: 5
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gene_count: 3
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protein_count: 5
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release: '94'
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species: test_homo_sapiens
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taxon_id: 9606
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transcript_count: 5
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init_date: '2023-06-15'
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last_edit: '2023-06-15'
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spice_version: '0.1'
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status:
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01_id_collection: true
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02_sequence_collection: true
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03_small_protein_removing: true
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04_incorrect_entry_removing: true
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05_implicit_fas_scoring: true
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06_fasta_generation: true
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07_pairing_generation: true
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08_id_tsv_generation: true
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09_sequence_annotation: false
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10_fas_scoring: false

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/paths.json

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{
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"root": "/share/gluster/spice/spice_libraries/spice_lib_homo_sapiens_94_1ee",
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"info": "info.yaml",
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"fas_data": "fas_data",
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"fas_scores": "fas_data/fas_scores",
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"fas_temp": "fas_data/tmp",
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"fas_annotation": "fas_data/annotation",
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"fas_annoTools": "fas_data/annoTools.txt",
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"fas_archtiectures": "fas_data/architectures",
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"transcript_data": "transcript_data",
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"transcript_info": "transcript_data/transcript_info.json",
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"transcript_seq": "transcript_data/sequences.json",
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"transcript_fasta": "transcript_data/transcript_set.fasta",
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"transcript_pairings": "transcript_data/transcript_pairings.json",
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"transcript_ids": "transcript_data/phyloprofile_ids.tsv",
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"self": "paths.json",
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"fas_index": "fas_data/fas_index.json"
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}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/transcript_data/genes.txt

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ENSG00000126368
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ENSG00000183615
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ENSG00000253293

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/transcript_data/phyloprofile_ids.tsv

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ENSG00000253293|ENSP00000283921|9606 ncbi9606
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ENSG00000253293|ENSP00000479619|9606 ncbi9606
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ENSG00000253293|ENSP00000379633|9606 ncbi9606

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/transcript_data/sequences.json

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{"ENSG00000126368": {
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"ENSP00000246672": "MTTLDSNNNTGGVITYIGSSGSSPSRTSPESLYSDNSNGSFQSLTQGCPTYFPPSPTGSLTQDPARSFGSIPPSLSDDGSPSSSSSSSSSSSSFYNGSPPGSLQVAMEDSSRVSPSKSTSNITKLNGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLAEMQSAMNLANNQLSSQCPLETSPTQHPTPGPMGPSPPPAPVPSPLVGFSQFPQQLTPPRSPSPEPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPPATTPHRWENQGCPPAPNDNNTLAAQRHNEALNGLRQAPSSYPPTWPPGPAHHSCHQSNSNGHRLCPTHVYAAPEGKAPANSPRQGNSKNVLLACPMNMYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLSFRVDAQ"
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},
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"ENSG00000183615": {
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"ENSP00000362684": "MSLGLLKFQAVGEEDEEDEEGESLDSVKALTAKLQLQTRRPSYLEWTAQVQSQAWRRAQAKPGPGGPGDICGFDSMDSALEWLRRELREMQAQDRQLAGQLLRLRAQLHRLKMDQACHLHQELLDEAELELELEPGAGLALAPLLRHLGLTRMNISARRFTLC"
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},
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"ENSG00000253293": {
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"ENSP00000283921": "MSARKGYLLPSPNYPTTMSCSESPAANSFLVDSLISSGRGEAGGGGGGAGGGGGGGYYAHGGVYLPPAADLPYGLQSCGLFPTLGGKRNEAASPGSGGGGGGLGPGAHGYGPSPIDLWLDAPRSCRMEPPDGPPPPPQQQPPPPPQPPQPAPQATSCSFAQNIKEESSYCLYDSADKCPKVSATAAELAPFPRGPPPDGCALGTSSGVPVPGYFRLSQAYGTAKGYGSGGGGAQQLGAGPFPAQPPGRGFDLPPALASGSADAARKERALDSPPPPTLACGSGGGSQGDEEAHASSSAAEELSPAPSESSKASPEKDSLGNSKGENAANWLTAKSGRKKRCPYTKHQTLELEKEFLFNMYLTRERRLEISRSVHLTDRQVKIWFQNRRMKLKKMNRENRIRELTANFNFS",
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"ENSP00000479619": "MSCSESPAANSFLVDSLISSGRGEAGGGGGGAGGGGGGGYYAHGGVYLPPAADLPYGLQSCGLFPTLGGKRNEAASPGSGGGGGGLGPGAHGYGPSPIDLWLDAPRSCRRRAATRGWPVPRAAPGARFRSPARASLRLGRCGPEGASPRFAAAPHAGLRQRRGLAGRRGGARVVLGRGGALPGPFREQQSLAGEGFPGQFQR",
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"ENSP00000379633": "MCQGNSKGENAANWLTAKSGRKKRCPYTKHQTLELEKEFLFNMYLTRERRLEISRSVHLTDRQVKIWFQNRRMKLKKMNRENRIRELTANFNFS"
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}}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/transcript_data/transcript_info.json

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{"ENSG00000126368": {
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"_id": "ENSG00000126368",
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"name": "NR1D1",
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"feature": "gene",
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"taxon_id": 9606,
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"chromosome": "17",
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"species": "homo_sapiens",
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"biotype": "protein_coding",
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"transcripts": {
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"ENSP00000246672": {
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"_id": "ENSP00000246672",
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"feature": "protein",
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"gene_id": "ENSG00000126368",
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"transcript_name": "NR1D1-201",
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"transcript_id": "ENST00000246672",
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"taxon_id": 9606,
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"biotype": "protein_coding",
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"tags": [
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"CCDS",
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"basic",
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"complete"
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],
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"tsl": 1
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}
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}
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},
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"ENSG00000183615": {
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"_id": "ENSG00000183615",
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"name": "FAM167B",
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"feature": "gene",
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"taxon_id": 9606,
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"chromosome": "1",
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"species": "homo_sapiens",
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"biotype": "protein_coding",
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"transcripts": {
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"ENSP00000362684": {
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"_id": "ENSP00000362684",
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"feature": "protein",
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"gene_id": "ENSG00000183615",
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"transcript_name": "FAM167B-201",
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"transcript_id": "ENST00000373582",
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"taxon_id": 9606,
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"biotype": "protein_coding",
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"tags": [
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"CCDS",
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"basic",
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"complete"
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],
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"tsl": 1
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}
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}
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},
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"ENSG00000253293": {
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"_id": "ENSG00000253293",
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"name": "HOXA10",
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"feature": "gene",
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"taxon_id": 9606,
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"chromosome": "7",
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"species": "homo_sapiens",
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"biotype": "protein_coding",
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"transcripts": {
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"ENSP00000283921": {
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"_id": "ENSP00000283921",
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"feature": "protein",
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"gene_id": "ENSG00000253293",
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"transcript_name": "HOXA10-201",
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"transcript_id": "ENST00000283921",
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"taxon_id": 9606,
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"biotype": "protein_coding",
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"tags": [
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"CCDS",
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"basic",
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"complete"
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],
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"tsl": 1
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},
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"ENSP00000479619": {
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"_id": "ENSP00000479619",
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"feature": "protein",
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"gene_id": "ENSG00000253293",
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"transcript_name": "HOXA10-206",
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"transcript_id": "ENST00000613671",
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"taxon_id": 9606,
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"biotype": "protein_coding",
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"tags": [
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"basic",
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"complete"
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],
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"tsl": 5
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},
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"ENSP00000379633": {
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"_id": "ENSP00000379633",
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"feature": "protein",
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"gene_id": "ENSG00000253293",
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"transcript_name": "HOXA10-202",
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"transcript_id": "ENST00000396344",
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"taxon_id": 9606,
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"biotype": "protein_coding",
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"tags": [
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"basic",
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"complete"
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],
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"tsl": 1
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}
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}
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}}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/transcript_data/transcript_pairings.json

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{"ENSG00000253293": "ENSG00000253293|ENSP00000283921|9606\tENSG00000253293|ENSP00000479619|9606\nENSG00000253293|ENSP00000283921|9606\tENSG00000253293|ENSP00000379633|9606\nENSG00000253293|ENSP00000479619|9606\tENSG00000253293|ENSP00000379633|9606"}

‎test_data/Spice_Library/spice_lib_test_homo_sapiens_94_1ee/transcript_data/transcript_set.fasta

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>ENSG00000126368|ENSP00000246672|9606
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MTTLDSNNNTGGVITYIGSSGSSPSRTSPESLYSDNSNGSFQSLTQGCPTYFPPSPTGSLTQDPARSFGSIPPSLSDDGSPSSSSSSSSSSSSFYNGSPPGSLQVAMEDSSRVSPSKSTSNITKLNGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLAEMQSAMNLANNQLSSQCPLETSPTQHPTPGPMGPSPPPAPVPSPLVGFSQFPQQLTPPRSPSPEPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPPATTPHRWENQGCPPAPNDNNTLAAQRHNEALNGLRQAPSSYPPTWPPGPAHHSCHQSNSNGHRLCPTHVYAAPEGKAPANSPRQGNSKNVLLACPMNMYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLSFRVDAQ
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>ENSG00000183615|ENSP00000362684|9606
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MSLGLLKFQAVGEEDEEDEEGESLDSVKALTAKLQLQTRRPSYLEWTAQVQSQAWRRAQAKPGPGGPGDICGFDSMDSALEWLRRELREMQAQDRQLAGQLLRLRAQLHRLKMDQACHLHQELLDEAELELELEPGAGLALAPLLRHLGLTRMNISARRFTLC
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>ENSG00000253293|ENSP00000283921|9606
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MSARKGYLLPSPNYPTTMSCSESPAANSFLVDSLISSGRGEAGGGGGGAGGGGGGGYYAHGGVYLPPAADLPYGLQSCGLFPTLGGKRNEAASPGSGGGGGGLGPGAHGYGPSPIDLWLDAPRSCRMEPPDGPPPPPQQQPPPPPQPPQPAPQATSCSFAQNIKEESSYCLYDSADKCPKVSATAAELAPFPRGPPPDGCALGTSSGVPVPGYFRLSQAYGTAKGYGSGGGGAQQLGAGPFPAQPPGRGFDLPPALASGSADAARKERALDSPPPPTLACGSGGGSQGDEEAHASSSAAEELSPAPSESSKASPEKDSLGNSKGENAANWLTAKSGRKKRCPYTKHQTLELEKEFLFNMYLTRERRLEISRSVHLTDRQVKIWFQNRRMKLKKMNRENRIRELTANFNFS
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>ENSG00000253293|ENSP00000479619|9606
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MSCSESPAANSFLVDSLISSGRGEAGGGGGGAGGGGGGGYYAHGGVYLPPAADLPYGLQSCGLFPTLGGKRNEAASPGSGGGGGGLGPGAHGYGPSPIDLWLDAPRSCRRRAATRGWPVPRAAPGARFRSPARASLRLGRCGPEGASPRFAAAPHAGLRQRRGLAGRRGGARVVLGRGGALPGPFREQQSLAGEGFPGQFQR
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>ENSG00000253293|ENSP00000379633|9606
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MCQGNSKGENAANWLTAKSGRKKRCPYTKHQTLELEKEFLFNMYLTRERRLEISRSVHLTDRQVKIWFQNRRMKLKKMNRENRIRELTANFNFS

‎test_data/Spice_Library/spice_novlib_test_homo_sapiens_94_1ee/fas_data/annoTools.txt

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#linearized
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Pfam
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#normal
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fLPS
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COILS2
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SEG
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SignalP
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TMHMM
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#checked

‎test_data/Spice_Library/spice_novlib_test_homo_sapiens_94_1ee/fas_data/fas.phyloprofile

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geneID ncbiID orthoID FAS_F FAS_B
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ENSG00000126368|ENSP00000246672|9606 ncbi9606 ENSG00000126368|HOMGRP81c552f7c12b|9606 0.0 0.0
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ENSG00000183615|ENSP00000362684|9606 ncbi9606 ENSG00000183615|HOM4b9cf06933c8e78|9606 0.1368 0.9986
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ENSG00000253293|ENSP00000283921|9606 ncbi9606 ENSG00000253293|ENSP00000479619|9606 0.3324 0.6492
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ENSG00000253293|ENSP00000283921|9606 ncbi9606 ENSG00000253293|ENSP00000379633|9606 0.371 0.9274
6+
ENSG00000253293|ENSP00000479619|9606 ncbi9606 ENSG00000253293|ENSP00000379633|9606 0.0 0.0

‎test_data/Spice_Library/spice_novlib_test_homo_sapiens_94_1ee/fas_data/fas_index.json

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{"ENSG00000126368": "000000160.json",
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"ENSG00000183615": "000000004.json",
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"ENSG00000253293": "000000071.json"}

‎test_data/Spice_Library/spice_novlib_test_homo_sapiens_94_1ee/fas_data/fas_scores/000000004.json

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{"ENSG00000183615": {
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"ENSP00000362684": {
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"ENSP00000362684": 1.0,
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"HOMnoORFGroup": 0.0,
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"HOM4b9cf06933c8e78": 0.9986
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},
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"HOMnoORFGroup": {
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"ENSP00000362684": 0.0,
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"HOMnoORFGroup": 1.0,
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"HOM4b9cf06933c8e78": 0.0
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},
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"HOM4b9cf06933c8e78": {
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"ENSP00000362684": 0.1368,
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"HOMnoORFGroup": 0.0,
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"HOM4b9cf06933c8e78": 1.0
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}
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}}

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