Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
changeset 3:a2953ef09fe1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
| author | iuc |
|---|---|
| date | Mon, 12 Oct 2020 13:47:03 +0000 |
| parents | b3710e492ee4 |
| children | 157a5c9ea72a |
| files | data_manager/install_primer_scheme_bedfiles.py data_manager/install_primer_scheme_bedfiles.xml test-data/sample1.bed |
| diffstat | 3 files changed, 21 insertions(+), 15 deletions(-) [+] |
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--- a/data_manager/install_primer_scheme_bedfiles.py Mon Jun 22 18:26:10 2020 -0400 +++ b/data_manager/install_primer_scheme_bedfiles.py Mon Oct 12 13:47:03 2020 +0000 @@ -18,7 +18,7 @@ DATA_TABLE_NAME = "primer_scheme_bedfiles" -def write_good_bed(input_file, bed_output_filename): +def write_artic_style_bed(input_file, bed_output_filename): with open(bed_output_filename, "w") as bed_output_file: for line in input_file: fields = line.split("\t") @@ -27,10 +27,16 @@ exit("invalid format in BED file: {}".format(line.rstrip())) try: # try and parse field 5 as a number - float(fields[4]) + score = float(fields[4]) except ValueError: - # ARTIC with broken BED, set field 5 to 60 - fields[4] = "60" + # Alright, this is an ARTIC-style bed, + # which is actually against the specs, but required by the + # ARTIC pipeline. + pass + else: + # This is a regular bed with numbers in the score column. + # We need to "fix" it for the ARTIC pipeline. + fields[4] = '_{0}'.format(score) bed_output_file.write("\t".join(fields)) @@ -56,7 +62,7 @@ ) exit(response.status_code) bed_output_filename = os.path.join(output_directory, name + ".bed") - write_good_bed(StringIO(response.text), bed_output_filename) + write_artic_style_bed(StringIO(response.text), bed_output_filename) description = name[:-2] + " " + name[-2:] + " primer set" data.append(dict(value=name, path=bed_output_filename, description=description)) return data @@ -68,7 +74,7 @@ name = re.sub(r"\W", "", str(primer_name).replace(" ", "_")) output_filename = os.path.join(output_directory, name + ".bed") with open(input_filename) as input_file: - write_good_bed(input_file, output_filename) + write_artic_style_bed(input_file, output_filename) data = [dict(value=name, description=primer_description, path=output_filename)] return data
--- a/data_manager/install_primer_scheme_bedfiles.xml Mon Jun 22 18:26:10 2020 -0400 +++ b/data_manager/install_primer_scheme_bedfiles.xml Mon Oct 12 13:47:03 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.11" tool_type="manage_data" profile="19.05"> +<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.12" tool_type="manage_data" profile="19.05"> <requirements> <requirement type="package" version="2.24.0">requests</requirement> </requirements> @@ -61,7 +61,7 @@ </test> </tests> <help><![CDATA[ - Amplicon sequencing for viral pathogens using the `PrimalSeq and iVar`_ relies on + Amplicon sequencing for viral pathogens using the ARTIC_ pipeline or `PrimalSeq and iVar`_ relies on identifying primer locations in a reference sequence using BED format files. This data manager populates a Galaxy tool data table, either from files provided via a history or via the ARTIC_ network Github repository.
--- a/test-data/sample1.bed Mon Jun 22 18:26:10 2020 -0400 +++ b/test-data/sample1.bed Mon Oct 12 13:47:03 2020 +0000 @@ -1,7 +1,7 @@ -MN908947.3 30 54 nCoV-2019_1_LEFT 60 + -MN908947.3 385 410 nCoV-2019_1_RIGHT 60 - -MN908947.3 320 342 nCoV-2019_2_LEFT 60 + -MN908947.3 704 726 nCoV-2019_2_RIGHT 60 - -MN908947.3 642 664 nCoV-2019_3_LEFT 60 + -MN908947.3 1004 1028 nCoV-2019_3_RIGHT 60 - -MN908947.3 943 965 nCoV-2019_4_LEFT 60 + +MN908947.3 30 54 nCoV-2019_1_LEFT nCoV-2019_1 + +MN908947.3 385 410 nCoV-2019_1_RIGHT nCoV-2019_1 - +MN908947.3 320 342 nCoV-2019_2_LEFT nCoV-2019_2 + +MN908947.3 704 726 nCoV-2019_2_RIGHT nCoV-2019_2 - +MN908947.3 642 664 nCoV-2019_3_LEFT nCoV-2019_1 + +MN908947.3 1004 1028 nCoV-2019_3_RIGHT nCoV-2019_1 - +MN908947.3 943 965 nCoV-2019_4_LEFT nCoV-2019_2 +