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Parsing bugs
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@murphycj
murphycj committed Nov 7, 2017
1 parent 885c858 commit 8b5f841
Showing 1 changed file with 39 additions and 37 deletions.
76 changes: 39 additions & 37 deletions agfusion/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,9 @@ def __init__(self,infile,logger):
for line in fin.readlines():
if re.findall('^#',line):
line = line.rstrip().split('\t')
assert line[0]=='#FusionName', 'Unrecognized STAR-Fusion input'
if line[0]!='#FusionName' and line[0]!='#fusion_name':
raise AssertionError('Unrecognized STAR-Fusion input for first column in header. Should be #FusionName or #fusion_name.')

assert line[4]=='LeftGene', 'Unrecognized STAR-Fusion input'
assert line[5]=='LeftBreakpoint', 'Unrecognized STAR-Fusion input'
assert line[6]=='RightGene', 'Unrecognized STAR-Fusion input'
Expand All @@ -54,12 +56,12 @@ def __init__(self,infile,logger):
gene_3prime_junction = int(line[7].split(':')[1])
self.fusions.append(
{
'ensembl_5prime':gene_5prime,
'ensembl_3prime':gene_3prime,
'gene5prime':gene_5prime,
'gene3prime':gene_3prime,
'alternative_name_5prime':gene_5prime_name,
'alternative_name_3prime':gene_3prime_name,
'junction_5prime':gene_5prime_junction,
'junction_3prime':gene_3prime_junction
'gene5prime_junction':gene_5prime_junction,
'gene3prime_junction':gene_3prime_junction
}
)
fin.close()
Expand All @@ -85,12 +87,12 @@ def __init__(self,infile,logger):
gene_3prime_junction = int(line[6])
self.fusions.append(
{
'ensembl_5prime':None,
'ensembl_3prime':None,
'gene5prime':None,
'gene3prime':None,
'alternative_name_5prime':gene_5prime_name,
'alternative_name_3prime':gene_3prime_name,
'junction_5prime':gene_5prime_junction,
'junction_3prime':gene_3prime_junction
'gene5prime_junction':gene_5prime_junction,
'gene3prime_junction':gene_3prime_junction
}
)
fin.close()
Expand All @@ -114,12 +116,12 @@ def __init__(self,infile,logger):
line = line.strip().split('\t')
self.fusions.append(
{
'ensembl_5prime':line[10],
'ensembl_3prime':line[11],
'gene5prime':line[10],
'gene3prime':line[11],
'alternative_name_5prime':line[0],
'alternative_name_3prime':line[1],
'junction_5prime':int(line[8].split(':')[1]),
'junction_3prime':int(line[9].split(':')[1])
'gene5prime_junction':int(line[8].split(':')[1]),
'gene3prime_junction':int(line[9].split(':')[1])
}
)
fin.close()
Expand All @@ -141,12 +143,12 @@ def __init__(self,infile,logger):
if gene1 is not None and gene2 is not None:
self.fusions.append(
{
'ensembl_5prime':None,
'ensembl_3prime':None,
'gene5prime':None,
'gene3prime':None,
'alternative_name_5prime':gene1,
'alternative_name_3prime':gene2,
'junction_5prime':int(gene1_junction),
'junction_3prime':int(gene2_junction)
'gene5prime_junction':int(gene1_junction),
'gene3prime_junction':int(gene2_junction)
}
)

Expand All @@ -160,12 +162,12 @@ def __init__(self,infile,logger):
if gene1 is not None and gene2 is not None:
self.fusions.append(
{
'ensembl_5prime':None,
'ensembl_3prime':None,
'gene5prime':None,
'gene3prime':None,
'alternative_name_5prime':gene1,
'alternative_name_3prime':gene2,
'junction_5prime':int(gene1_junction),
'junction_3prime':int(gene2_junction)
'gene5prime_junction':int(gene1_junction),
'gene3prime_junction':int(gene2_junction)
}
)

Expand Down Expand Up @@ -193,12 +195,12 @@ def __init__(self,infile,logger):
if gene1 is not None and gene2 is not None:
self.fusions.append(
{
'ensembl_5prime':None,
'ensembl_3prime':None,
'gene5prime':None,
'gene3prime':None,
'alternative_name_5prime':gene1,
'alternative_name_3prime':gene2,
'junction_5prime':int(gene1_junction),
'junction_3prime':int(gene2_junction)
'gene5prime_junction':int(gene1_junction),
'gene3prime_junction':int(gene2_junction)
}
)

Expand All @@ -224,12 +226,12 @@ def __init__(self,infile,logger):
gene_3prime_junction = int(line[8])
self.fusions.append(
{
'ensembl_5prime':None,
'ensembl_3prime':None,
'gene5prime':None,
'gene3prime':None,
'alternative_name_5prime':gene_5prime_name,
'alternative_name_3prime':gene_3prime_name,
'junction_5prime':gene_5prime_junction,
'junction_3prime':gene_3prime_junction
'gene5prime_junction':gene_5prime_junction,
'gene3prime_junction':gene_3prime_junction
}
)
fin.close()
Expand All @@ -255,12 +257,12 @@ def __init__(self,infile,logger):
gene_3prime_junction = int(line[2])
self.fusions.append(
{
'ensembl_5prime':None,
'ensembl_3prime':None,
'gene5prime':None,
'gene3prime':None,
'alternative_name_5prime':gene_5prime_name,
'alternative_name_3prime':gene_3prime_name,
'junction_5prime':gene_5prime_junction,
'junction_3prime':gene_3prime_junction
'gene5prime_junction':gene_5prime_junction,
'gene3prime_junction':gene_3prime_junction
}
)
fin.close()
Expand All @@ -283,12 +285,12 @@ def __init__(self,infile,logger):
gene_3prime_junction = int(line[6])
self.fusions.append(
{
'ensembl_5prime':gene_5prime,
'ensembl_3prime':gene_3prime,
'gene5prime':gene_5prime,
'gene3prime':gene_3prime,
'alternative_name_5prime':gene_5prime_name,
'alternative_name_3prime':gene_3prime_name,
'junction_5prime':gene_5prime_junction,
'junction_3prime':gene_3prime_junction
'gene5prime_junction':gene_5prime_junction,
'gene3prime_junction':gene_3prime_junction
}
)
fin.close()
Expand Down

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