Commit d774c18f authored by Alisa Muraveva's avatar Alisa Muraveva
Browse files

Some grammar mistakes were fixed

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@736 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
parent f6565c21
......@@ -517,7 +517,9 @@ class GBparser():
record.chromOffset = int(accInfo[2].split('.')[0])
#if
for i in biorecord.features :
print i
if i.qualifiers :
if i.type == "source" :
if i.qualifiers.has_key("mol_type") :
if i.qualifiers["mol_type"][0] in ["mRNA", \
......@@ -537,7 +539,6 @@ class GBparser():
fakeGene.CDS = PList()
fakeGene.CDS.location = self.__location2pos(i.location)
#if
if i.qualifiers.has_key("gene") :
geneName = i.qualifiers["gene"][0]
if i.type == "gene" :
......@@ -622,7 +623,7 @@ class GBparser():
else:
if not i.gene in myTranscript.nonusableList:
output.addMessage(__file__, 2, 'WPOSITION',
"The gene's {0} coordinates extend beyound transcript".format(i.gene))
"The gene's {0} coordinates extend beyond transcript".format(i.gene))
myTranscript.nonusableList.append(i.gene)
#for
for i in myGene.cdsList :
......
......@@ -1520,7 +1520,7 @@ def process_variant(mutator, description, record, output):
else:
output.addMessage(__file__, 4, "EINVALIDGENE",
"Gene %s not found. Please choose from: %s" % (
gene_symbol, ", ".join(locus)))
gene_symbol, ", ".join(genes)))
if gene:
# Find transcript.
......@@ -1883,6 +1883,7 @@ def check_variant(description, output):
# level descriptions.
for gene in record.record.geneList:
if gene.locus:
name = gene.locus
else:
name = gene.name
......
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