| Previous changeset 24:fcc1021bd496 (2017-05-31) Next changeset 26:df42241d3731 (2017-07-03) |
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Commit message:
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty |
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modified:
tool_dependencies.xml util/subtools.py |
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| diff -r fcc1021bd496 -r 99dad5f9444c tool_dependencies.xml --- a/tool_dependencies.xml Wed May 31 11:35:16 2017 -0400 +++ b/tool_dependencies.xml Fri Jun 02 17:36:24 2017 -0400 |
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| @@ -19,11 +19,11 @@ <repository changeset_revision="a819439b6d76" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="ucsc_bigbed" version="340"> - <repository changeset_revision="b23d341df89d" name="package_ucsc_bigbed_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e3faf2af4e59" name="package_ucsc_bigbed_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="ucsc_bigwig" version="340"> - <repository changeset_revision="b1fb46f92da0" name="package_ucsc_bigwig_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5ba6d8812c60" name="package_ucsc_bigwig_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
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| diff -r fcc1021bd496 -r 99dad5f9444c util/subtools.py --- a/util/subtools.py Wed May 31 11:35:16 2017 -0400 +++ b/util/subtools.py Fri Jun 02 17:36:24 2017 -0400 |
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| @@ -11,6 +11,7 @@ import subprocess import sys import string +import tempfile class PopenError(Exception): def __init__(self, cmd, error, return_code): @@ -128,7 +129,9 @@ :param gene_pred_file_name: :return: """ - array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name] + valid_gff3_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gff3") + validateGff(input_gff3_file_name, valid_gff3_file.name) + array_call = ['gff3ToGenePred', valid_gff3_file.name, gene_pred_file_name] p = _handleExceptionAndCheckCall(array_call) return p @@ -256,3 +259,19 @@ sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename]) sanitize_name = "gonramp_" + sanitize_name return sanitize_name + +def validateGff(orig_gff3, valid_gff3): + """ + Remove extra meta line: ##gff-version 3 + """ + valid = open(valid_gff3, 'w') + num = 0 + with open(orig_gff3, 'r') as f: + for line in f: + if '##gff-version 3' in line: + if num == 0: + num += 1 + else: + continue + valid.write(line) + |