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Bug fix with free text being put into more than one column #58

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Apr 21, 2016
Merged

Bug fix with free text being put into more than one column #58

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49 changes: 29 additions & 20 deletions ariba/report.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import sys
import pymummer

columns = [
Expand All @@ -15,20 +16,20 @@
'var_type', # 11 The type of variant. Currently only SNP supported
'var_seq_type', # 12 if known_var=1, n|p for nucleotide or protein
'known_var_change', # 13 if known_var=1, the wild/variant change, eg I42L
'has_known_var', # 13 if known_var=1, 1|0 for whether or not the assembly has the variant
'ref_ctg_change', # 14 amino acid or nucleotide change between reference and contig, eg I42L
'ref_ctg_effect', # 15 effect of change between reference and contig, eg SYS, NONSYN (amino acid changes only)
'ref_start', # 16 start position of variant in contig
'ref_end', # 17 end position of variant in contig
'ref_nt', # 18 nucleotide(s) in contig at variant position
'ctg_start', # 19 start position of variant in contig
'ctg_end', # 20 end position of variant in contig
'ctg_nt', # 21 nucleotide(s) in contig at variant position
'smtls_total_depth', # 22 total read depth at variant start position in contig, reported by mpileup
'smtls_alt_nt', # 23 alt nucleotides on contig, reported by mpileup
'smtls_alt_depth', # 24 alt depth on contig, reported by mpileup
'var_description', # 25 description of variant from reference metdata
'free_text', # 26 other free text about reference sequence, from reference metadata
'has_known_var', # 14 if known_var=1, 1|0 for whether or not the assembly has the variant
'ref_ctg_change', # 15 amino acid or nucleotide change between reference and contig, eg I42L
'ref_ctg_effect', # 16 effect of change between reference and contig, eg SYS, NONSYN (amino acid changes only)
'ref_start', # 17 start position of variant in contig
'ref_end', # 18 end position of variant in contig
'ref_nt', # 19 nucleotide(s) in contig at variant position
'ctg_start', # 20 start position of variant in contig
'ctg_end', # 21 end position of variant in contig
'ctg_nt', # 22 nucleotide(s) in contig at variant position
'smtls_total_depth', # 23 total read depth at variant start position in contig, reported by mpileup
'smtls_alt_nt', # 24 alt nucleotides on contig, reported by mpileup
'smtls_alt_depth', # 25 alt depth on contig, reported by mpileup
'var_description', # 26 description of variant from reference metdata
'free_text', # 27 other free text about reference sequence, from reference metadata
]


Expand Down Expand Up @@ -141,9 +142,9 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
]

if cluster.ref_sequence.id in cluster.refdata.metadata and len(cluster.refdata.metadata[cluster.ref_sequence.id]['.']) > 0:
free_text_columns = [x.free_text for x in cluster.refdata.metadata[cluster.ref_sequence.id]['.']]
free_text_column = ';'.join([x.free_text for x in cluster.refdata.metadata[cluster.ref_sequence.id]['.']])
else:
free_text_columns = ['.']
free_text_column = ';'.join(['.'])

if cluster.assembled_ok and contig_name in cluster.assembly_variants and len(cluster.assembly_variants[contig_name]) > 0:
for (position, var_seq_type, ref_ctg_change, var_effect, contributing_vars, matching_vars_set, metainfo_set) in cluster.assembly_variants[contig_name]:
Expand Down Expand Up @@ -208,15 +209,15 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
if samtools_columns is None:
samtools_columns = [['.'] * 9]

lines.append('\t'.join(common_first_columns + var_columns + samtools_columns + [matching_vars_column] + free_text_columns))
lines.append('\t'.join(common_first_columns + var_columns + samtools_columns + [matching_vars_column] + [free_text_column]))
else:
lines.append('\t'.join(
common_first_columns + var_columns + \
samtools_columns + \
[matching_vars_column] + free_text_columns
[matching_vars_column] + [free_text_column]
))
else:
lines.append('\t'.join(common_first_columns + ['.'] * (len(columns) - len(common_first_columns) - 1) + free_text_columns))
lines.append('\t'.join(common_first_columns + ['.'] * (len(columns) - len(common_first_columns) - 1) + [free_text_column]))

return lines

Expand All @@ -236,8 +237,16 @@ def report_lines(cluster):
contig_pymummer_variants = [x for x in pymummer_variants if x.qry_name == contig_name]
lines.extend(_report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, contig_pymummer_variants))

lines_ok = True

for line in lines:
assert len(line.split('\t')) == len(columns)
if len(line.split('\t')) != len(columns):
print('Error making report - wrong number of columns. Expected', len(columns), 'but got', len(line.split('\t')), file=sys.stderr)
print(line, file=sys.stderr)
lines_ok = False

if not lines_ok:
raise Error('Error making report. Cannot continue')

return lines if len(lines) > 0 else None