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import: made ngsfilter file parsing more resilient and switching to

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version 3.0.1b19
This commit is contained in:
mercierc
2022-07-15 16:02:21 +12:00
parent ef9d9674b0
commit 55ada80500
2 changed files with 14 additions and 13 deletions
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25
python/obitools3/parsers/ngsfilter.pyx
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@ -48,24 +48,25 @@ def ngsfilterIterator(lineiterator,
all_lines.insert(0, firstline) all_lines.insert(0, firstline)
# Insert header for column names # Insert header for column names
column_names = [b"experiment", b"sample", b"forward_tag", b"reverse_tag", b"forward_primer", b"reverse_primer",b"additional_info"] column_names = [b"experiment", b"sample", b"forward_tag", b"reverse_tag", b"forward_primer", b"reverse_primer"] #,b"additional_info"]
header = out_sep.join(column_names) header = out_sep.join(column_names)
new_lines.append(header) new_lines.append(header)
for line in all_lines: for line in all_lines:
split_line = line.split(maxsplit=5) split_line = line.split(maxsplit=5)
tags = split_line.pop(2) if split_line:
tags = tags.split(b":") tags = split_line.pop(2)
for t_idx in range(len(tags)): tags = tags.split(b":")
if tags[t_idx]==b"-" or tags[t_idx]==b"None" or tags[t_idx]==b"": for t_idx in range(len(tags)):
tags[t_idx] = nastring if tags[t_idx]==b"-" or tags[t_idx]==b"None" or tags[t_idx]==b"":
if len(tags) == 1: # Forward and reverse tags are the same tags[t_idx] = nastring
tags.append(tags[0]) if len(tags) == 1: # Forward and reverse tags are the same
split_line.insert(2, tags[0]) tags.append(tags[0])
split_line.insert(3, tags[1]) split_line.insert(2, tags[0])
new_lines.append(out_sep.join(split_line[0:7])) split_line.insert(3, tags[1])
new_lines.append(out_sep.join(split_line[0:6]))
return tabIterator(iter(new_lines), return tabIterator(iter(new_lines),
header = True, header = True,
sep = out_sep, sep = out_sep,

2
python/obitools3/version.py
View File

@ -1,5 +1,5 @@
major = 3 major = 3
minor = 0 minor = 0
serial= '1b18' serial= '1b19'
version ="%d.%d.%s" % (major,minor,serial) version ="%d.%d.%s" % (major,minor,serial)