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Improve user feedback #459

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merged 3 commits into from
Dec 4, 2018
Merged

Improve user feedback #459

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eda541f
Improved message when specific locus incorrectly specified
mihailefter Dec 4, 2018
10b6cd6
Fix typo in about page
mihailefter Dec 4, 2018
2ab226e
Update broken external link (#454)
mihailefter Dec 4, 2018
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2 changes: 1 addition & 1 deletion extras/soap-tools/sp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# Example SOAP client for the Mutalyzer web service in Python using the
# SOAPpy library.
#
# See http://www.mutalyzer.nl/2.0/webservices
# See https://mutalyzer.nl/webservices
#
# Usage:
# python sp.py
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27 changes: 21 additions & 6 deletions mutalyzer/variantchecker.py
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Expand Up @@ -1605,12 +1605,25 @@ def process_variant(mutator, description, record, output):
# Todo: message?
gene = record.record.geneList[0]
else:
output.addMessage(__file__, 4, "EINVALIDGENE",
"No gene specified. Please choose from: %s" % ", ".join(genes))
if len(genes) < 10:
output.addMessage(__file__, 4, "EINVALIDGENE",
"No gene specified. Please choose from: %s" %
", ".join(genes))
else:
output.addMessage(__file__, 4, "EINVALIDGENE",
"No gene specified. Specify one of the %s genes "
"that are present the reference." % len(genes))

else:
output.addMessage(__file__, 4, "EINVALIDGENE",
"Gene %s not found. Please choose from: %s" % (
gene_symbol, ", ".join(genes)))
if len(genes) < 10:
output.addMessage(__file__, 4, "EINVALIDGENE",
"Gene %s not found. Please choose from: %s" % (
gene_symbol, ", ".join(genes)))
else:
output.addMessage(__file__, 4, "EINVALIDGENE",
"Gene %s not found. Specify one of the %s genes that "
"are present in the reference. " % (
gene_symbol, len(genes)))

if gene:
# Find transcript.
Expand Down Expand Up @@ -1799,7 +1812,9 @@ def check_variant(description, output):
gene_symbol, transcript_id = transcript_info
else:
output.addMessage(__file__, 4, 'EINVALIDTRANSVAR',
'Invalid name for transcript variant identifier.')
'%s is not annotated on %s.' % (
'.'.join(parsed_description.AccNoTransVar),
record_id))

# Add recordType to output for output formatting.
output.addOutput('recordType', filetype)
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2 changes: 1 addition & 1 deletion mutalyzer/website/templates/about.html
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Expand Up @@ -45,7 +45,7 @@ <h2>Open Source</h2>

<p>
Contributions to Mutalyzer are very welcome! They can be feature requests, bug
reports, bug fixes, unit tests, documentation updates, or anything els you may
reports, bug fixes, unit tests, documentation updates, or anything else you may
come up with.
</p>

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