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Fasta more dict-like behaviour #156

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merged 7 commits into from
Dec 10, 2019
Merged

Fasta more dict-like behaviour #156

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a6a1253
Fasta more dict-like behaviour
Maarten-vd-Sande Dec 9, 2019
99a9f69
add keys, values, items to Fasta class
Maarten-vd-Sande Dec 10, 2019
cede320
minor keys bug fix and list comprehension to dict comprehension
Maarten-vd-Sande Dec 10, 2019
2f82d43
remove debugging print
Maarten-vd-Sande Dec 10, 2019
990a22c
Add some debugging for #156 failing test
mdshw5 Dec 10, 2019
8995223
Fix for record insertion order in #156
mdshw5 Dec 10, 2019
80ad273
Bump version for release
mdshw5 Dec 10, 2019
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19 changes: 14 additions & 5 deletions pyfaidx/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -997,13 +997,13 @@ def __init__(self,
sequence_always_upper=sequence_always_upper,
rebuild=rebuild,
build_index=build_index)
self.keys = self.faidx.index.keys
if not self.mutable:
self.records = dict(
[(rname, FastaRecord(rname, self)) for rname in self.keys()])
self.records = {rname: FastaRecord(rname, self)
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Great! You can ignore my previous comment.

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It seems like dictionary key insertion order is the issue, and I will update here to do something similar to what the Fasta.keys method currently relies on:

pyfaidx/pyfaidx/__init__.py

Line 399 in f1668d2

self.index = OrderedDict()

for rname in self.faidx.index.keys()}
elif self.mutable:
self.records = dict([(rname, MutableFastaRecord(rname, self))
for rname in self.keys()])
self.records = {rname: MutableFastaRecord(rname, self)
for rname in self.faidx.index.keys()}


def __contains__(self, rname):
"""Return True if genome contains record."""
Expand Down Expand Up @@ -1060,6 +1060,15 @@ def get_spliced_seq(self, name, intervals, rc=False):
# len(Sequence.seq) != end - start
return Sequence(name=name, seq=seq, start=None, end=None)

def keys(self):
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I agree that this brings clarity to the methods.

return self.records.keys()

def values(self):
return self.records.values()

def items(self):
return self.records.items()

def close(self):
self.__exit__()

Expand Down