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Edinburgh-Genome-Foundry / DnaChisel

:pencil2: A versatile DNA sequence optimizer
https://edinburgh-genome-foundry.github.io/DnaChisel/
MIT License
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Unable to load customized `codon_usage_table` #4

Closed y9c closed 5 years ago

y9c commented 5 years ago 
Note that the species can be omited if a ``codon_usage_table`` is provided instead

However, when omitting the species args, this error message will occur.

TypeError: sequence item 0: expected str instance, NoneType found
Exception ignored in: <function tqdm.__del__ at 0x7fd3e5262620>
y9c commented 5 years ago

Both these forms of codon_table are not work.

{'GGG': 0.256110452118628, 'GGA': 0.412721063810386, 'GGU': 0.430997493208316, 'GGC': 0.40017099086267, 'GAG': 0.760047053318429, 'GAA': 0.739952946681571, 'GAU': 0.786485991985531, 'GAC': 0.713514008014469, 'GUG': 0.54740452571466, 'GUA': 0.215292374185063, 'GUU': 0.393379530920203, 'GUC': 0.343923569180074, 'GCG': 0.162936328377505, 'GCA': 0.387106765783236, 'GCU': 0.493975795446384, 'GCC': 0.455981110392875, 'AGG': 0.305245686703522, 'AGA': 0.479456098742338, 'AGU': 0.235979502119684, 'AGC': 0.287505540000549, 'AAG': 0.771696692775617, 'AAA': 0.728303307224383, 'AAU': 0.718941094197242, 'AAC': 0.781058905802758, 'AUG': 1.5, 'AUA': 0.296443738433726, 'AUU': 0.569630307114663, 'AUC': 0.633925954451611, 'ACG': 0.189293372854481, 'ACA': 0.452611743917297, 'ACU': 0.428123264324363, 'ACC': 0.429971618903859, 'UGG': 1.5, 'UGA': 0.644679695982628, 'UGU': 0.797714008072064, 'UGC': 0.702285991927936, 'UAG': 0.382871878393051, 'UAA': 0.472448425624321, 'UAU': 0.70675415915354, 'UAC': 0.79324584084646, 'UUG': 0.275886067566318, 'UUA': 0.21190875879034, 'UUU': 0.746633795400179, 'UUC': 0.753366204599821, 'UCG': 0.107797440215462, 'UCA': 0.258036250550349, 'UCU': 0.332094921083291, 'UCC': 0.278586346030666, 'CGG': 0.174723999131495, 'CGA': 0.159182352646435, 'CGU': 0.177112387887696, 'CGC': 0.204279474888514, 'CAG': 0.893197290460588, 'CAA': 0.606802709539412, 'CAU': 0.741894530984379, 'CAC': 0.758105469015621, 'CUG': 0.454500516940046, 'CUA': 0.142923218073301, 'CUU': 0.197073988009875, 'CUC': 0.21770745062012, 'CCG': 0.184769320887825, 'CCA': 0.496246609532784, 'CCU': 0.467625017509455, 'CCC': 0.351359052069936, 'GGT': 0.430997493208316, 'GAT': 0.786485991985531, 'GTG': 0.54740452571466, 'GTA': 0.215292374185063, 'GTT': 0.393379530920203, 'GTC': 0.343923569180074, 'GCT': 0.493975795446384, 'AGT': 0.235979502119684, 'AAT': 0.718941094197242, 'ATG': 1.5, 'ATA': 0.296443738433726, 'ATT': 0.569630307114663, 'ATC': 0.633925954451611, 'ACT': 0.428123264324363, 'TGG': 1.5, 'TGA': 0.644679695982628, 'TGT': 0.797714008072064, 'TGC': 0.702285991927936, 'TAG': 0.382871878393051, 'TAA': 0.472448425624321, 'TAT': 0.70675415915354, 'TAC': 0.79324584084646, 'TTG': 0.275886067566318, 'TTA': 0.21190875879034, 'TTT': 0.746633795400179, 'TTC': 0.753366204599821, 'TCG': 0.107797440215462, 'TCA': 0.258036250550349, 'TCT': 0.332094921083291, 'TCC': 0.278586346030666, 'CGT': 0.177112387887696, 'CAT': 0.741894530984379, 'CTG': 0.454500516940046, 'CTA': 0.142923218073301, 'CTT': 0.197073988009875, 'CTC': 0.21770745062012, 'CCT': 0.467625017509455, 'best_frequencies': {'A': 0.493975795446384, 'R': 0.479456098742338, 'N': 0.781058905802758, 'D': 0.786485991985531, 'C': 0.797714008072064, 'Q': 0.893197290460588, 'E': 0.760047053318429, 'G': 0.430997493208316, 'H': 0.758105469015621, 'I': 0.633925954451611, 'L': 0.454500516940046, 'F': 0.753366204599821, 'P': 0.496246609532784, 'S': 0.332094921083291, 'T': 0.452611743917297, 'Y': 0.79324584084646, 'V': 0.54740452571466, 'W': 1.5, 'M': 1.5, 'K': 0.771696692775617, '*': 0.644679695982628}}
{'GGG': 0.256110452118628, 'GGA': 0.412721063810386, 'GGU': 0.430997493208316, 'GGC': 0.40017099086267, 'GAG': 0.760047053318429, 'GAA': 0.739952946681571, 'GAU': 0.786485991985531, 'GAC': 0.713514008014469, 'GUG': 0.54740452571466, 'GUA': 0.215292374185063, 'GUU': 0.393379530920203, 'GUC': 0.343923569180074, 'GCG': 0.162936328377505, 'GCA': 0.387106765783236, 'GCU': 0.493975795446384, 'GCC': 0.455981110392875, 'AGG': 0.305245686703522, 'AGA': 0.479456098742338, 'AGU': 0.235979502119684, 'AGC': 0.287505540000549, 'AAG': 0.771696692775617, 'AAA': 0.728303307224383, 'AAU': 0.718941094197242, 'AAC': 0.781058905802758, 'AUG': 1.5, 'AUA': 0.296443738433726, 'AUU': 0.569630307114663, 'AUC': 0.633925954451611, 'ACG': 0.189293372854481, 'ACA': 0.452611743917297, 'ACU': 0.428123264324363, 'ACC': 0.429971618903859, 'UGG': 1.5, 'UGA': 0.644679695982628, 'UGU': 0.797714008072064, 'UGC': 0.702285991927936, 'UAG': 0.382871878393051, 'UAA': 0.472448425624321, 'UAU': 0.70675415915354, 'UAC': 0.79324584084646, 'UUG': 0.275886067566318, 'UUA': 0.21190875879034, 'UUU': 0.746633795400179, 'UUC': 0.753366204599821, 'UCG': 0.107797440215462, 'UCA': 0.258036250550349, 'UCU': 0.332094921083291, 'UCC': 0.278586346030666, 'CGG': 0.174723999131495, 'CGA': 0.159182352646435, 'CGU': 0.177112387887696, 'CGC': 0.204279474888514, 'CAG': 0.893197290460588, 'CAA': 0.606802709539412, 'CAU': 0.741894530984379, 'CAC': 0.758105469015621, 'CUG': 0.454500516940046, 'CUA': 0.142923218073301, 'CUU': 0.197073988009875, 'CUC': 0.21770745062012, 'CCG': 0.184769320887825, 'CCA': 0.496246609532784, 'CCU': 0.467625017509455, 'CCC': 0.351359052069936, 'GGT': 0.430997493208316, 'GAT': 0.786485991985531, 'GTG': 0.54740452571466, 'GTA': 0.215292374185063, 'GTT': 0.393379530920203, 'GTC': 0.343923569180074, 'GCT': 0.493975795446384, 'AGT': 0.235979502119684, 'AAT': 0.718941094197242, 'ATG': 1.5, 'ATA': 0.296443738433726, 'ATT': 0.569630307114663, 'ATC': 0.633925954451611, 'ACT': 0.428123264324363, 'TGG': 1.5, 'TGA': 0.644679695982628, 'TGT': 0.797714008072064, 'TGC': 0.702285991927936, 'TAG': 0.382871878393051, 'TAA': 0.472448425624321, 'TAT': 0.70675415915354, 'TAC': 0.79324584084646, 'TTG': 0.275886067566318, 'TTA': 0.21190875879034, 'TTT': 0.746633795400179, 'TTC': 0.753366204599821, 'TCG': 0.107797440215462, 'TCA': 0.258036250550349, 'TCT': 0.332094921083291, 'TCC': 0.278586346030666, 'CGT': 0.177112387887696, 'CAT': 0.741894530984379, 'CTG': 0.454500516940046, 'CTA': 0.142923218073301, 'CTT': 0.197073988009875, 'CTC': 0.21770745062012, 'CCT': 0.467625017509455}
Zulko commented 5 years ago

Thanks for the report, I'll have a look in ~1h.

y9c commented 5 years ago

I think there is a quick solution to solute this issue temporarily by exposing codons_usage_dir option in this line. https://github.com/Edinburgh-Genome-Foundry/DnaChisel/blob/7b3d90a08804d09e34ad2b97830c46c6abd1dfd8/dnachisel/biotools/biotables.py#L50

Zulko commented 5 years ago

I have patched it, it should work now. just upgrade (probably with pip install --upgrade dnachisel) and let me know how it works.

y9c commented 5 years ago

It works now.

Zulko commented 5 years ago

Awesome. Closing this.