tandem_repeat_annotation_defaults_2.ini

[sequencewise_parallel_flow]
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/seq
    retag = sp_(\d+)
[TRDwise_parallel_flow]
    PFAM = Hmmer
    T-REKS = deNovo
    XSTREAM = deNovo
    HHrepID = deNovo
    TRUST = deNovo
[split_sequence_file]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/split_sequence_file.py
    input = /scratch/cluster/monthly/eschaper/tral/sp_test/data/seq/uniprot_sprot.fasta
    output = /scratch/cluster/monthly/eschaper/tral/sp_test/data/seq/split/sp_
    extra = -f fasta -n 1000
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/split_sequence_file
    stdout = stdout.log
    stderr = stderr.log
[create_and_annotate_sequence_pickles]
    activated = False
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/create_and_annotate_sequence_pickles.py
    input = /scratch/cluster/monthly/eschaper/tral/sp_test/data/seq/split
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/seq
    extra = -a /scratch/cluster/monthly/eschaper/tral/sp_test/data/PFAM/uniprot-database-type-pfamA-AND-reviewed.pickle
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/create_and_annotate_sequence_pickles
    stdout = stdout.log
    stderr = stderr.log
[create_hmm_pickles]
    activated = False
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/create_hmm_pickles.py
    input = /scratch/cluster/monthly/eschaper/tral/sp_test/data/PFAM/Pfam-A.hmm
    output = /scratch/cluster/monthly/eschaper/tral/sp_test/data/PFAM/split
    extra =
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/create_hmm_pickles
    stdout = stdout.log
    stderr = stderr.log
[annotate_TRs_from_hmmer]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py annotate_TRs_from_hmmer
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/seq/sp_$N.pickle
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/1_detection/PFAM/sp_$N.pickle
    extra = -hmm /scratch/cluster/monthly/eschaper/tral/sp_test/data/PFAM/split
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/annotate_TRs_from_hmmer_$N
    stdout = stdout.log
    stderr = stderr.log
[annotate_de_novo]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py annotate_de_novo
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/seq/sp_$N.pickle
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/1_detection/$TRD/sp_$N.pickle
    extra = -d $TRD
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/annotate_de_novo_$N_$TRD
    stdout = stdout.log
    stderr = stderr.log
[calculate_significance]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py calculate_significance
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/1_detection/$TRD/sp_$N.pickle
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/2_significance/$TRD/sp_$N.pickle
    extra =
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/calculate_significance_$N_$TRD
    stdout = stdout.log
    stderr = stderr.log
[merge_and_basic_filter]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py merge_and_basic_filter
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/seq/sp_$N.pickle
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/3_merge/sp_$N.pickle
    extra =  -rep /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/2_significance/HHrepID/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/2_significance/TRUST/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/2_significance/T-REKS/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/2_significance/XSTREAM/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/2_significance/PFAM/sp_$N.pickle
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/merge_and_basic_filter_$N
    stdout = stdout.log
    stderr = stderr.log
[calculate_overlap]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py calculate_overlap
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/3_merge/sp_$N.pickle
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/4_overlap/sp_$N.pickle
    extra = -ov common_ancestry shared_char
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/calculate_overlap_$N
    stdout = stdout.log
    stderr = stderr.log
[refine_denovo]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py refine_denovo
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/4_overlap/sp_$N.pickle
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/5_refine_denovo/sp_$N.pickle
    extra =
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/refine_denovo_$N
    stdout = stdout.log
    stderr = stderr.log
[serialize_annotations]
    script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py serialize_annotations
    input = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/5_refine_denovo
    output = /scratch/cluster/monthly/eschaper/tral/sp_test_1/results/6_serialize_annotations/out.txt
    extra = -f tsv
    logdir = /scratch/cluster/monthly/eschaper/tral/sp_test_1/output/serialize_annotations
    stdout = stdout.log
    stderr = stderr.log