Mercurial > repos > tduigou > sculpt_sequences
changeset 1:a0cd867780ec draft default tip
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
| author | tduigou |
|---|---|
| date | Thu, 17 Jul 2025 13:24:49 +0000 |
| parents | 0c7f75a2338b |
| children | |
| files | sculpt_sequences.py sculpt_sequences.xml test-data/test_json_workflow2.json |
| diffstat | 3 files changed, 195 insertions(+), 55 deletions(-) [+] |
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--- a/sculpt_sequences.py Mon Jul 07 13:11:42 2025 +0000 +++ b/sculpt_sequences.py Thu Jul 17 13:24:49 2025 +0000 @@ -1,4 +1,6 @@ import argparse +import json +import sys import os import re import dnacauldron @@ -175,16 +177,20 @@ parser.add_argument("--outdir_unscul", required=True, help="unscul file dir") parser.add_argument("--use_file_names_as_id", type=lambda x: x.lower() == 'true', default=True, help="Use file names as IDs (True/False)") - parser.add_argument("--avoid_patterns", required=True, + parser.add_argument("--avoid_patterns", required=False, help="List of patterns to avoid (comma-separated, e.g., 'BsaI_site,BsmBI_site')") - parser.add_argument("--gc_constraints", required=True, + parser.add_argument("--gc_constraints", required=False, help="GC content constraints as 'min;max;window' (space-separated, e.g., '0.3;0.7;100 0.1;0.3;100')") - parser.add_argument("--DnaOptimizationProblemClass", required=True, + parser.add_argument("--DnaOptimizationProblemClass", required=False, help="the class to use for DnaOptimizationProblem") - parser.add_argument("--hairpin_constraints", required=True, + parser.add_argument("--hairpin_constraints", required=False, help="Hairpin constraints as 'stem_size;window_size' (space-separated, e.g., '20;200 30;250')") - parser.add_argument("--kmer_size", required = True, + parser.add_argument("--kmer_size", required = False, help="K-mer uniqueness size (e.g., '15')") + parser.add_argument("--json_params", required=False, + help="JSON params for the tool") + parser.add_argument("--use_json_param", required=True, + help="If use JSON as param source") return parser.parse_args() @@ -206,19 +212,78 @@ # 4. k-mer size: single value or list kmer_size = [int(k.strip()) for k in args.kmer_size.strip().split(',') if k.strip()] if args.kmer_size.strip() else [] - return avoid_patterns, hairpin_constraints, gc_constraints, kmer_size + # 5. DnaOptimizationProblemClass (as string) + DnaOptimizationProblemClass = args.DnaOptimizationProblemClass if args.DnaOptimizationProblemClass else None + + return avoid_patterns, hairpin_constraints, gc_constraints, kmer_size, DnaOptimizationProblemClass +def load_constraints_from_json(json_path): + with open(json_path, 'r') as f: + params = json.load(f) + + def split_lines(val): + if isinstance(val, str): + return [line.strip() for line in val.strip().split('\n') if line.strip()] + return val + + avoid_patterns = split_lines(params.get("avoid_patterns", "")) + hairpin_constraints = split_lines(params.get("hairpin_constraints", "")) + gc_constraints = split_lines(params.get("gc_constraints", "")) + kmer_size = [int(k.strip()) for k in str(params.get("kmer_size", "")).split(',') if k.strip()] + DnaOptimizationProblemClass = params.get("DnaOptimizationProblemClass", None) + + return { + "avoid_patterns": avoid_patterns, + "hairpin_constraints": hairpin_constraints, + "gc_constraints": gc_constraints, + "kmer_size": kmer_size, + "DnaOptimizationProblemClass": DnaOptimizationProblemClass + } if __name__ == "__main__": args = parse_command_line_args() - avoid_patterns, hairpin_constraints, gc_constraints, kmer_size, = extract_constraints_from_args(args) + avoid_patterns, hairpin_constraints, gc_constraints, kmer_size, DnaOptimizationProblemClass = extract_constraints_from_args(args) + + # Check if the flag --use_json_param is present and set to true + if "--use_json_param" in sys.argv: + use_json_index = sys.argv.index("--use_json_param") + 1 + use_json = sys.argv[use_json_index].lower() == "true" + else: + use_json = False + + # Now only check --json_params if use_json is True + if use_json: + if "--json_params" in sys.argv: + json_index = sys.argv.index("--json_params") + 1 + json_file = sys.argv[json_index] + if json_file.lower() != "none": + json_constraints = load_constraints_from_json(json_file) + avoid_patterns = json_constraints["avoid_patterns"] + hairpin_constraints = json_constraints["hairpin_constraints"] + gc_constraints = json_constraints["gc_constraints"] + kmer_size = json_constraints["kmer_size"] + DnaOptimizationProblemClass = json_constraints["DnaOptimizationProblemClass"] + + params = { + "files_to_sculpt": args.files_to_sculpt, + "file_name_mapping": args.file_name_mapping, + "outdir_unscul": args.outdir_unscul, + "outdir_scul": args.outdir_scul, + "use_file_names_as_id": args.use_file_names_as_id, + "avoid_patterns": avoid_patterns, + "hairpin_constraints": hairpin_constraints, + "gc_constraints": gc_constraints, + "kmer_size": kmer_size, + "DnaOptimizationProblemClass": DnaOptimizationProblemClass + } + sculpt_sequances( args.files_to_sculpt, args.file_name_mapping, args.outdir_scul, args.outdir_unscul, args.use_file_names_as_id, avoid_patterns, - gc_constraints, args.DnaOptimizationProblemClass, + gc_constraints, DnaOptimizationProblemClass, kmer_size, hairpin_constraints )
--- a/sculpt_sequences.xml Mon Jul 07 13:11:42 2025 +0000 +++ b/sculpt_sequences.xml Thu Jul 17 13:24:49 2025 +0000 @@ -18,14 +18,24 @@ <requirement type="package" version="3.1.5">dna_features_viewer</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - #set avoid_list = [line.strip() for line in str($avoid_patterns).strip().split('\n') if line.strip()] - #set avoid_patterns = ','.join($avoid_list) + #if str($json_use.use_json_param) == "false": + #set avoid_list = [line.strip() for line in str($avoid_patterns).strip().split('\n') if line.strip()] + #set avoid_patterns = ','.join($avoid_list) + + #set hairpin_lines = [line.strip() for line in str($json_use.hairpin_constraints).strip().split('\n') if line.strip()] + #set hairpin_constraints = '__cn__'.join($hairpin_lines) - #set hairpin_lines = [line.strip() for line in str($adv.hairpin_constraints).strip().split('\n') if line.strip()] - #set hairpin_constraints = '__cn__'.join($hairpin_lines) + #set gc_lines = [line.strip() for line in str($json_use.gc_constraints).strip().split('\n') if line.strip()] + #set gc_constraints = '__cn__'.join($gc_lines) + + #set kmer_size = $json_use.kmer_size - #set gc_lines = [line.strip() for line in str($adv.gc_constraints).strip().split('\n') if line.strip()] - #set gc_constraints = '__cn__'.join($gc_lines) + #else: + #set avoid_patterns = '' + #set hairpin_constraints = '' + #set gc_constraints = '' + #set kmer_size = '' + #end if #set genbank_file_paths = ','.join([str(f) for f in $genbank_files]) #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files]) @@ -33,30 +43,42 @@ mkdir 'outdir_scul' && mkdir 'outdir_unscul' && python '$__tool_directory__/sculpt_sequences.py' + --use_json_param '$json_use.use_json_param' --files_to_sculpt '$genbank_file_paths' --file_name_mapping '$file_name_mapping' --outdir_scul 'outdir_scul' --outdir_unscul 'outdir_unscul' - --use_file_names_as_id '$adv.use_file_names_as_ids' + --use_file_names_as_id '$use_file_names_as_ids' --avoid_patterns '$avoid_patterns' - --gc_constraints '$adv.gc_constraints' - --DnaOptimizationProblemClass '$DnaOptimizationProblemClass' - --kmer_size '$adv.kmer_size' - --hairpin_constraints '$adv.hairpin_constraints' + --gc_constraints '$gc_constraints' + --kmer_size '$kmer_size' + --hairpin_constraints '$hairpin_constraints' + #if $json_use.use_json_param: + --json_params '$json_use.json_params' + #else: + --json_params '' + --DnaOptimizationProblemClass '$json_use.DnaOptimizationProblemClass' + #end if ]]></command> <inputs> <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/> - <param name="DnaOptimizationProblemClass" type="select" label="DnaOptimizationProblem Calss" help="select the assambly class"> - <option value="DnaOptimizationProblem" selected="True">DnaOptimizationProblem</option> - <option value="CircularDnaOptimizationProblem">CircularDnaOptimizationProblem</option> - </param> - <param name="avoid_patterns" type="text" area="true" label="Pattern to Avoid" helps="Each pattern on a line" /> - <section name="adv" title="Advanced Options" expanded="false"> - <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/> - <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/> - <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/> - <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" /> - </section> + <conditional name='json_use'> + <param name="use_json_param" type="boolean" checked="false" label="Use parameter from a JSON file" /> + <when value="false"> + <param name="DnaOptimizationProblemClass" type="select" label="DnaOptimizationProblem Calss" help="select the assambly class"> + <option value="DnaOptimizationProblem" selected="True">DnaOptimizationProblem</option> + <option value="CircularDnaOptimizationProblem">CircularDnaOptimizationProblem</option> + </param> + <param name="avoid_patterns" type="text" area="true" label="Avoid Pattern Constraints" help="Each pattern on a line" /> + <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/> + <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/> + <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/> + </when> + <when value="true"> + <param name="json_params" type="data" format="json" optional="true" label="JSON parameters file" help="Contains tool's parameters" /> + </when> + </conditional> + <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" /> </inputs> <outputs> <collection name="scul" type="list" label="scul group" > @@ -68,7 +90,7 @@ </outputs> <tests> <test> - <!-- test for DnaOptimizationProblem --> + <!-- test for DnaOptimizationProblem --> <param name="genbank_files"> <collection type="list"> <element name="p15_PuroR" value="10_emma_genbanks/p15_PuroR.gb" /> @@ -83,23 +105,26 @@ <element name="HC_Amp_ccdB" value="10_emma_genbanks/HC_Amp_ccdB.gb" /> </collection> </param> - <param name="DnaOptimizationProblemClass" value="DnaOptimizationProblem" /> - <param name="adv|use_file_names_as_ids" value="True" /> - <!-- AvoidPatterns --> - <param name="avoid_patterns" value="BsaI_site - NotI_site - XbaI_site - ClaI_site - 8x1mer" /> - <!-- EnforceGCContent --> - <param name="adv|gc_constraints" value="mini=0.1, maxi=0.9, window=50"/> + <conditional name="json_use"> + <param name="use_json_param" value="false" /> + <param name="DnaOptimizationProblemClass" value="DnaOptimizationProblem" /> + <!-- AvoidPatterns --> + <param name="avoid_patterns" value="BsaI_site + NotI_site + XbaI_site + ClaI_site + 8x1mer" /> + <!-- EnforceGCContent --> + <param name="gc_constraints" value="mini=0.1, maxi=0.9, window=50"/> + </conditional> + <param name="use_file_names_as_ids" value="True" /> <output_collection name="scul" count="10"> </output_collection> <output_collection name="unscul" count="10"> </output_collection> </test> <test> - <!-- test for CircularDnaOptimizationProblem --> + <!-- test for CircularDnaOptimizationProblem --> <param name="genbank_files"> <collection type="list"> <element name="p15_PuroR" value="10_emma_genbanks/p15_PuroR.gb" /> @@ -114,19 +139,48 @@ <element name="HC_Amp_ccdB" value="10_emma_genbanks/HC_Amp_ccdB.gb" /> </collection> </param> - <param name="DnaOptimizationProblemClass" value="CircularDnaOptimizationProblem" /> - <param name="adv|use_file_names_as_ids" value="True" /> - <!-- AvoidPatterns --> - <param name="avoid_patterns" value="BsaI_site - NotI_site - XbaI_site - ClaI_site - 8x1mer" /> - <!-- EnforceGCContent --> - <param name="adv|gc_constraints" value="mini=0.1, maxi=0.9 - mini-0.3, maxi=0.7, window=50"/> - <param name="adv|hairpin_constraints" value="stem_size=20, hairpin_window=200 - stem_size=10, hairpin_window=100"/> + <conditional name="json_use"> + <param name="use_json_param" value="false" /> + <param name="DnaOptimizationProblemClass" value="CircularDnaOptimizationProblem" /> + <!-- AvoidPatterns --> + <param name="avoid_patterns" value="BsaI_site + NotI_site + XbaI_site + ClaI_site + 8x1mer" /> + <!-- EnforceGCContent --> + <param name="gc_constraints" value="mini=0.1, maxi=0.9 + mini=0.3, maxi=0.7, window=50"/> + <param name="hairpin_constraints" value="stem_size=20, hairpin_window=200 + stem_size=10, hairpin_window=100"/> + </conditional> + <param name="use_file_names_as_ids" value="True" /> + <output_collection name="scul" count="10"> + </output_collection> + <output_collection name="unscul" count="10"> + </output_collection> + </test> + <test> + <!-- test json params --> + <param name="genbank_files"> + <collection type="list"> + <element name="p15_PuroR" value="10_emma_genbanks/p15_PuroR.gb" /> + <element name="p9_PuroR" value="10_emma_genbanks/p9_PuroR.gb" /> + <element name="p15_Pup9_mTagBFP2roR" value="10_emma_genbanks/p9_mTagBFP2.gb" /> + <element name="p15_p9_BSDRPuroR" value="10_emma_genbanks/p9_BSDR.gb" /> + <element name="p8_Linker1" value="10_emma_genbanks/p8_Linker1.gb" /> + <element name="p7_L7Ae-Weiss" value="10_emma_genbanks/p7_L7Ae-Weiss.gb" /> + <element name="p6_Nt-IgKLsequence" value="10_emma_genbanks/p6_Nt-IgKLsequence.gb" /> + <element name="p6_Kozak-ATG" value="10_emma_genbanks/p6_Kozak-ATG.gb" /> + <element name="p4_Kt-L7Ae-Weiss" value="10_emma_genbanks/p4_Kt-L7Ae-Weiss.gb" /> + <element name="HC_Amp_ccdB" value="10_emma_genbanks/HC_Amp_ccdB.gb" /> + </collection> + </param> + <conditional name="json_use"> + <param name="use_json_param" value="true" /> + <param name="json_params" value="test_json_workflow2.json" /> + </conditional> + <param name="use_file_names_as_ids" value="True" /> <output_collection name="scul" count="10"> </output_collection> <output_collection name="unscul" count="10"> @@ -142,6 +196,9 @@ **Parameters**: --------------- * **GenBank File(s)**: List of GenBank files to be processed. +* **Use parameter from a JSON file**: + Yes/No parameter to indicate if user want to set parameter manually or using a json file + If Yes, user should provide a JSON file contains all parameters * **DnaOptimizationProblem Class**: - "DnaOptimizationProblem": is the class to define and solve an optimization problems. Its methods implement all the solver logics. - "CircularDnaOptimizationProblem": is a variant of DnaOptimizationProblem whose optimization algorithm assumes that the sequence is circular.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_json_workflow2.json Thu Jul 17 13:24:49 2025 +0000 @@ -0,0 +1,18 @@ +{ + "DnaOptimizationProblemClass":"DnaOptimizationProblem", + "avoid_patterns": "BsaI_site\nNotI_site\nXbaI_site\nClaI_site\n8x1mer", + "hairpin_constraints": "stem_size=20, hairpin_window=200\nstem_size=10, hairpin_window=100", + "gc_constraints": "mini=0.1, maxi=0.9\nmini=0.3, maxi=0.7, window=50", + "kmer_size": "15", + "methylation_protection":"methylation_protection", + "allow_edits":"True", + "assembly_plan_name": "Type2sRestrictionAssembly", + "topology": "circular", + "enzyme": "auto", + "execution": "true", + "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "table": "sample", + "fragment_column": "fragment", + "sequence_column": "sequence", + "annotation_column": "annotation" +} \ No newline at end of file