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Added a function to calculate GC content of a sequence #68

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merged 3 commits into from
Feb 19, 2018
Merged

Added a function to calculate GC content of a sequence #68

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edd743e
add gc content function to fasta class
Feb 16, 2018
55a32cc
update version number
Feb 16, 2018
abeb7e0
make loop more efficient. Fix Martin's crazy grammar requirements.
Feb 19, 2018
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8 changes: 5 additions & 3 deletions pyfastaq/sequences.py
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Original file line number Diff line number Diff line change
Expand Up @@ -470,7 +470,7 @@ def gc_content(self, as_decimal=True):
This method ignores N when calculating the length of the sequence.
It does not, however ignore other ambiguous bases. It also only
includes the ambiguous base S (G or C). In this sense the method is
conservative with it's calculation.
conservative with its calculation.
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👍


Args:
as_decimal (bool): Return the result as a decimal. Setting to False
Expand All @@ -484,15 +484,17 @@ def gc_content(self, as_decimal=True):
"""
gc_total = 0.0
num_bases = 0.0
n_tuple = tuple('nN')
accepted_bases = tuple('cCgGsS')

# counter sums all unique characters in sequence. Case insensitive.
for base, count in Counter(self.seq).items():

# dont count N in the number of bases
if base not in tuple('nN'):
if base not in n_tuple:
num_bases += count

if base in tuple('cCgGsS'): # S is a G or C
if base in accepted_bases: # S is a G or C
gc_total += count

gc_content = gc_total / num_bases
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