Mercurial > repos > mvdbeek > dapars
changeset 2:47b0044bc7f8 draft
planemo upload for repository https://github.com/mvdbeek/dapars commit a02ced0b40d8946aa78a58321bd8f9771148391e-dirty
| author | mvdbeek |
|---|---|
| date | Wed, 28 Oct 2015 05:56:52 -0400 |
| parents | 1b20ba32b4c5 |
| children | aca85eb3eb5b |
| files | dapars.py dapars.xml |
| diffstat | 2 files changed, 2 insertions(+), 23 deletions(-) [+] |
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--- a/dapars.py Wed Oct 28 05:32:30 2015 -0400 +++ b/dapars.py Wed Oct 28 05:56:52 2015 -0400 @@ -33,7 +33,7 @@ help="minimum coverage in each aligment to be considered for determining breakpoints") parser.add_argument("-b", "--breakpoint_bed", required=False, type=argparse.FileType('w'), help="Write bedfile with coordinates of breakpoint positions to supplied path.") - parser.add_argument("-v", "--version", action='version', version='%(prog)s 0.1.4') + parser.add_argument("-v", "--version", action='version', version='%(prog)s 0.1.5') return parser.parse_args() @@ -127,25 +127,6 @@ utr_dict[gene] = utr_d return utr_dict - def get_utr_coverage(self): - """ - Returns a dict: - { UTR : [coverage_aligment1, ...]} - """ - utr_coverages = {} - for utr, utr_d in self.utr_dict.iteritems(): - if utr_d["chr"] in self.available_chromosomes: - if utr_d["strand"] == "+": - is_reverse = False - else: - is_reverse = True - utr_coverage = [] - for bam in self.all_alignments: - bp_coverage = get_bp_coverage(bam, utr_d["chr"], utr_d["new_start"], utr_d["new_end"], is_reverse) - utr_coverage.append(bp_coverage) - utr_coverages[utr] = utr_coverage - return utr_coverages - def get_coverage_weights(self): """ Return weights for normalizing coverage. @@ -230,8 +211,6 @@ return res_control, res_treatment - - def breakpoint_to_result(res, utr, utr_d, breakpoint, breakpoint_type, abundances, is_reverse, num_samples, num_control, num_treatment): """
--- a/dapars.xml Wed Oct 28 05:32:30 2015 -0400 +++ b/dapars.xml Wed Oct 28 05:56:52 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="dapars" name="dapars" version="0.1.4"> +<tool id="dapars" name="dapars" version="0.1.5"> <description>infer de-novo alternative polyadenylation from rna-seq</description> <requirements> <requirement type="package" version="1.9">numpy</requirement>