Commit 7d081506 authored by BeatriceTan's avatar BeatriceTan
Browse files

Fixed split errors.

parent a61e8e72
from Reports import ReportTools
import ReportTools
import os.path
import datetime
......@@ -24,11 +24,10 @@ rule report_tools:
biomart_info=os.path.join(workflow.basedir, config["biomart_genes"]) if config["biomart_genes"].startswith("input_files") else config["biomart_genes"],
ref=config["reference"]
run:
ReportTools(input.gistic, input.rubic_gain, input.rubic_loss,
params.census, params.known, params.ref, params.biomart_info,
output.tools, output.table_regions, output.venn, output.overlap,
output.swarmplot,
output.genes_both, output.genes_gistic, output.genes_rubic)
ReportTools.make_report(input.gistic, input.rubic_gain, input.rubic_loss,
params.census, params.known, params.ref, params.biomart_info,
output.tools, output.table_regions, output.venn, output.overlap, output.swarmplot,
output.genes_both, output.genes_gistic, output.genes_rubic)
rule bed_intersect:
"""Intersect the recurrent regions detected by RUBIC and GISTIC2.0."""
......
from Reports import ReportSegmentation
import ReportSegments
rule firehose:
"""Download copy number profiles for a cancer type of choice from firehose."""
......@@ -53,7 +53,7 @@ rule report_seg:
output:
"Reports/Segments.txt"
run:
ReportSegmentation(input[0], output[0])
ReportSegments.make_report(input[0], output[0])
......
from Reports import ReportSizes
import ReportSizes
from SampleSizes import SegFile
from Rubic import MarkerFile
......@@ -62,4 +62,4 @@ rule report_sizes:
reps=config["repeats"],
ref=config["reference"]
run:
ReportSizes(input[0], params.census, params.known, params.reps, params.ref, output.report, output.plots)
ReportSizes.make_report(input[0], params.census, params.known, params.reps, params.ref, output.report, output.plots)
from Reports import ReportControl
import ReportControl
rule run_gistic_control:
"""Run GISTIC2 for the tumor segmentation data with data from control samples included."""
......@@ -27,4 +27,4 @@ rule report_control:
known=config["prev_found_genes"],
ref=config["reference"]
run:
ReportControl(input.control, input.nocontrol, output[0], params.census, params.known, params.ref)
ReportControl.make_report(input.control, input.nocontrol, output[0], params.census, params.known, params.ref)
......@@ -10,7 +10,7 @@ import pyensembl
from ParseResults import parse, get_stats, install_ensembl
from collections import OrderedDict
class make_report(gistic_results, rubic_gain_results, rubic_loss_results,
def make_report(gistic_results, rubic_gain_results, rubic_loss_results,
census_genes, known_genes, ref_genome, biomart_file,
file_tools, file_regions, file_venn, file_overlap, file_swarmplot,
file_genes_both, file_genes_GISTIC, file_genes_RUBIC):
......
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