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tandem_repeat_annotation_defaults_tiny.ini
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tandem_repeat_annotation_defaults_tiny.ini
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required_memory = 5
[sequencewise_parallel_flow]
input = /scratch/cluster/monthly/eschaper/tral/sp_tiny/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_tiny/data/seq/uniprot_sprot.fasta
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/data/seq/split/sp_
extra = -f fasta -n 10
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/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_tiny/data/seq/split
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/seq
extra = -a /scratch/cluster/monthly/eschaper/tral/sp_tiny/data/PFAM/uniprot-database-type-pfamA-AND-reviewed.pickle
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/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_tiny/data/PFAM/Pfam-A.hmm
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/data/PFAM/split
extra =
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/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_tiny/results/seq/sp_$N.pickle
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/1_detection/PFAM/sp_$N.pickle
extra = -hmm /scratch/cluster/monthly/eschaper/tral/sp_test/data/PFAM/split
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/output/annotate_TRs_from_hmmer_$N
stdout = stdout.log
stderr = stderr.log
required_memory = 50
[annotate_de_novo]
script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py annotate_de_novo
input = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/seq/sp_$N.pickle
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/1_detection/$TRD/sp_$N.pickle
extra = -d $TRD
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/output/annotate_de_novo_$N_$TRD
stdout = stdout.log
stderr = stderr.log
required_memory = 50
[calculate_significance]
script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py calculate_significance
input = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/1_detection/$TRD/sp_$N.pickle
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/2_significance/$TRD/sp_$N.pickle
extra =
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/output/calculate_significance_$N_$TRD
stdout = stdout.log
stderr = stderr.log
[merge_and_basic_filter]
script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py merge_and_basic_filter
input = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/seq/sp_$N.pickle
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/3_merge/sp_$N.pickle
extra = -rep /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/2_significance/HHrepID/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/2_significance/TRUST/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/2_significance/T-REKS/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/2_significance/XSTREAM/sp_$N.pickle /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/2_significance/PFAM/sp_$N.pickle
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/output/merge_and_basic_filter_$N
stdout = stdout.log
stderr = stderr.log
[calculate_overlap]
script = /software/bin/python3 /home/eschaper/Python_projects/TandemRepeats/tandemrepeats/scripts/detect_tandem_repeats_in_sequence.py calculate_overlap
input = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/3_merge/sp_$N.pickle
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/4_overlap/sp_$N.pickle
extra = -ov common_ancestry shared_char
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/output/calculate_overlap_$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_tiny/results/4_overlap/sp_$N.pickle
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/5_refine_denovo/sp_$N.pickle
extra =
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/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_tiny/results/5_refine_denovo
output = /scratch/cluster/monthly/eschaper/tral/sp_tiny/results/6_serialize_annotations/out.txt
extra = -f tsv
logdir = /scratch/cluster/monthly/eschaper/tral/sp_tiny/output/serialize_annotations
stdout = stdout.log
stderr = stderr.log