Mercurial > repos > guerler > springsuite
changeset 9:4ac5d5a9b21c draft
"planemo upload commit f465445ebca0307953f59938494a2244ca8ea23c"
| author | guerler |
|---|---|
| date | Sat, 01 Aug 2020 02:13:31 -0400 |
| parents | f2f38991c36f |
| children | 860bd6f8f480 |
| files | spring_minz.py spring_minz.xml |
| diffstat | 2 files changed, 10 insertions(+), 7 deletions(-) [+] |
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--- a/spring_minz.py Sat Aug 01 00:35:20 2020 -0400 +++ b/spring_minz.py Sat Aug 01 02:13:31 2020 -0400 @@ -18,7 +18,7 @@ crossreference[core] = [] crossreference[core].append(partner) print ("Loaded cross reference from `%s`." % args.crossreference) - targets = get_template_scores(args.target, args.minscore) + targets = get_template_scores(args.target, args.minscore, args.idx) interactions = [] if not targets: print("No targets found `%s`" % args.target) @@ -27,7 +27,7 @@ for name in names: input_directory = args.inputs.rstrip("/") input_file = "%s/%s" % (input_directory, name) - templates = get_template_scores(input_file, args.minscore) + templates = get_template_scores(input_file, args.minscore, args.idx) minz = 0 for t in targets: if t in crossreference: @@ -45,15 +45,16 @@ for i in interactions: output_file.write("%s %s\n" % (i[0], i[1])) -def get_template_scores(hhr_file, min_score): +def get_template_scores(hhr_file, min_score, identifier_length): result = {} + identifier_length = identifier_length + 4 if os.path.isfile(hhr_file): with open(hhr_file) as file: for index, line in enumerate(file): if index > 8: if not line.strip(): break - template_id = line[4:10] + template_id = line[4:identifier_length] template_score = float(line[57:63]) if template_score > min_score: result[template_id] = template_score @@ -63,8 +64,9 @@ parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.') parser.add_argument('-t', '--target', help='HHR target file result', required=True) parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True) + parser.add_argument('-x', '--idx', help='Length of identifier', type=int, default=6) parser.add_argument('-l', '--list', help='Text file containing identifiers.', required=True) - parser.add_argument('-i', '--inputs', help='Directory containing `hhr/X/Y.hhr` files', required=True) + parser.add_argument('-i', '--inputs', help='Directory containing `hhr` files', required=True) parser.add_argument('-o', '--output', help='Output file containing minZ-scores`', required=True) parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=10) args = parser.parse_args()
--- a/spring_minz.xml Sat Aug 01 00:35:20 2020 -0400 +++ b/spring_minz.xml Sat Aug 01 02:13:31 2020 -0400 @@ -7,13 +7,14 @@ link '${str(input)}' 'inputs/${input.element_identifier}' && echo '${input.element_identifier}' >> 'input_list' && #end for - python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs + python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs ]]></command> <inputs> <param format="txt" name="target" type="data" label="Target Profile" help="Homology search result of target/query profile `hhr`."/> <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/> - <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins pairs from SPRING database protocol."/> + <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/> + <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="10" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/> </inputs> <outputs> <data format="txt" name="output" />