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convert nucleic sequence in protein sequence

License: MIT License

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bioinformatics dna go protein-sequences translation

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ayang64 shammishailaj ayllonbe minghao2016 wangdi2014 jokendo-collab pyspider anyihu liuchen92 adeslatt

gotranseq's Issues

dna ambiguity

Hi Feliixx,

I have encountered an error when running gotranseq in my data. The error is the following:

WARNING: invalid char in sequence SAGAGTCATCTCCTATGCAGGCTGCCTGACTCAGATGTCTCTCTTTGCCATTTKTGGAGGCATGGAAGAGAGACATGCTCCTGAGTGTGATGGCCTATGGCCGGTTTGTAGCCATCTGTCACCCTCTATATCGTTCAGCCATCTTGAACCCATGTTTCTGTGGCTTCCTAGATTTGTTGTCTTCGTTTTGTTTTGTTTTGTTTTTCTCAGTCTTTTAGACTCCCAGCTGCACAACTTGATTGCCTTACAAATGACCGGCTTCAAGGATGTGGAATTCCTAATTTCTTCTGGGAACCTTCTCAACTCCCCATCTTGCATGTTGTGACACCTTCACCAGGAACATCAACCTGTATTTCCCTGCTGCCGTATTTGGTTTTCTTCCCATCTTGGGGACCTTTTCTCTTACTGTAAAATTGTTTCCTCCATTCTGAGGGTTTCATCATCAGGTGGGAAGTATAAACCTTCTCCACCTGTGGGTCTCACCTGCCAGTTGTTTGCTGATTTTGTGGAACAGGTGTTGGAGGGTACCTTGGTTCAGATGTGTCATCTTCCCCAAGAAAGAGTGCAGTGCCCTCAGTGATGTACCCGGTGGTCACCTCC: S, ignoringWARNING: invalid char in sequence SKTGGAGGCATGGAAGAGAGACATGCTCCTGAGTGTGATGGCCTATGGCCGGTTTGTAGCCATCTGTCACCCTCTATATCGTTCAGCCATCTTGAACCCATGTTTCTGTGGCTTCCTAGATTTGTTGTCTTCGTTTTGTTTTGTTTTGTTTTTCTCAGTCTTTTAGACTCCCAGCTGCACAACTTGATTGCCTTACAAATGACCGGCTTCAAGGATGTGGAATTCCTAATTTCTTCTGGGAACCTTCTCAACTCCCCATCTTGCATGTTGTGACACCTTCACCAGGAACATCAACCTGTATTTCCCTGCTGCCGTATTTGGTTTTCTTCCCATCTTGGGGACCTTTTCTCTTACTGTAAAATTGTTTCCTCCATTCTGAGGGTTTCATCATCAGGTGGGAAGTATAAACCTTCTCCACCTGTGGGTCTCACCTGCCAGTTGTTTGCTGATTTTGTGGAACAGGTGTTGGAGGGTACCTTGGTTCAGATGTGTCATCTTCCCCAAGAAAGAGTGCAGTGCCCTCAGTGATGTACCCGGTGGTCACCTCC: K, ignoringpanic: runtime error: index out of range [4915971] with length 263173

goroutine 21 [running]:
github.com/feliixx/gotranseq/transeq.(*writer).translate3Frames(0xc000980000, 0xc00005e600, 0x2f6, 0x5b6)
	/home/runner/work/gotranseq/gotranseq/transeq/writer.go:99 +0x89a
github.com/feliixx/gotranseq/transeq.(*writer).translate(0xc000980000, 0xc00005e600, 0x2f6, 0x5b6)
	/home/runner/work/gotranseq/gotranseq/transeq/writer.go:60 +0x71
github.com/feliixx/gotranseq/transeq.Translate.func1(0xc00010c150, 0xc000280000, 0x1, 0x0, 0x0, 0x0, 0x0, 0x0, 0x5858585858585800, 0x10fe62d, ...)
	/home/runner/work/gotranseq/gotranseq/transeq/transeq.go:149 +0x318
created by github.com/feliixx/gotranseq/transeq.Translate
	/home/runner/work/gotranseq/gotranseq/transeq/transeq.go:135 +0x3da

I think the reason is that there are ambiguous characters in my data. In this case, the character "S" represents the possibility of finding cytosine or guanine. Is there any solution to this issue?

Here are the nucleotide sequences in fasta format:

test.fa.txt

fatal error: all goroutines are asleep - deadlock!

I've had gotranseq randomly crash with this error. Used current master branch and parameters --frame 6 and -n 1, if that matters. Crash does not appear to be deterministic: re-ran the tool on the same file and it went fine. Could be related with -n 1 not being enforced sometimes, as CPU usage can be >100%.

lower case fasta seqeunces no recognised

Hi Feliix,

thanks for gotranseq, I've hit an issue with some of my fasta DNA sequences being in lower case letters whcih are all replaced with 'N' (see below), and I end up with no translation for that sequence. Is this something you can rectify in the future?

WARNING: invalid char in sequence >sakai_stx2a-A.fasta: 't' ( pos 503), replacing with 'N'

Thanks,

DeenSm

the results is not full

i have 2840 uniq dna sequence, but the results only output 1930 rows with default. It makes me very puzzled.

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