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jnovembre / ENCprime

ENCprime : Command-line utility for measuring codon bias
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Totals column from SeqCount -n are off by 2 #4

Open jolespin opened 4 years ago

jolespin commented 4 years ago

Computed by SeqCount:

cat test.ffn.codcnt
26
64
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT CTC CTA CTG CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG GGT GGC GGA GGG
contig_1_1_373_+>6 2 5 5 1 2 3 0 2 1 0 0 2 1 0 1 1 0 1 2 0 0 1 0 4 0 1 2 0 0 0 0 5 3 2 3 6 0 2 0 7 4 9 0 3 1 2 1 8 0 3 0 4 1 1 1 3 1 4 3 0 1 2 0
contig_2_33_194_+>1 0 1 0 1 0 1 0 3 0 0 0 4 0 0 0 0 0 0 0 3 0 1 0 0 0 1 0 0 0 1 0 0 0 2 1 3 1 0 0 2 0 1 4 1 0 3 0 3 0 4 0 0 0 2 0 1 0 1 0 2 0 4 0
contig_3_1_279_+>5 1 1 4 0 1 3 0 3 1 0 0 2 0 0 0 1 0 0 2 0 0 0 0 2 1 0 1 0 0 0 0 8 1 0 0 0 1 0 2 3 2 10 4 0 1 1 1 1 0 1 1 1 2 2 1 5 1 10 4 0 0 1 0
contig_4_1_333_+>2 0 3 1 0 0 4 0 3 0 0 0 4 0 0 0 6 1 2 0 1 0 1 0 1 0 0 1 0 0 0 0 4 1 6 3 2 2 1 0 1 0 9 2 3 3 5 0 4 0 5 1 0 0 2 0 6 3 5 2 2 1 6 1
contig_5_1_445_+>4 2 0 1 4 1 1 0 7 3 0 0 2 0 0 1 1 2 0 0 2 0 3 0 1 1 2 0 0 2 0 0 3 5 11 2 6 4 4 2 6 5 11 6 1 0 1 0 5 0 1 0 3 2 3 0 4 4 8 1 1 1 7 0
contig_6_1_260_+>1 0 1 2 0 1 1 1 1 1 0 0 0 0 0 2 1 0 3 3 0 0 1 0 1 0 4 3 0 1 0 0 0 2 1 5 1 3 3 1 1 2 4 1 2 3 2 0 2 0 0 0 4 3 1 1 5 1 5 1 1 1 1 0
contig_7_1_301_+>2 0 1 0 3 0 1 0 5 1 0 0 0 1 0 1 2 1 2 1 0 0 1 0 1 0 1 0 0 0 0 0 1 1 4 2 2 1 0 0 2 1 3 11 1 0 1 3 0 0 4 0 10 2 1 2 5 3 4 5 0 1 3 2
contig_8_1_354_+>5 1 1 3 1 0 0 0 2 2 0 0 1 1 0 3 5 0 0 0 0 1 0 1 0 4 4 2 1 0 2 1 2 2 5 3 2 2 0 3 5 3 8 3 0 0 2 0 1 0 4 0 2 1 3 1 5 5 8 3 0 2 1 0
contig_9_49_297_->2 2 2 3 3 5 0 0 2 0 0 0 0 0 0 0 1 0 1 2 0 2 0 0 0 1 0 0 2 1 0 0 8 1 1 2 0 1 1 1 1 2 3 3 0 0 1 0 3 1 3 1 1 1 0 1 10 1 2 1 2 0 0 0
contig_10_1_200_->2 3 0 0 2 1 0 0 3 1 0 0 0 1 0 0 4 0 0 1 0 0 0 3 0 0 1 0 0 0 0 0 3 0 0 2 2 2 1 0 2 0 1 3 0 1 1 0 2 0 2 2 1 0 1 1 4 3 2 2 4 0 2 0
contig_11_1_201_+>0 2 0 0 2 2 0 0 2 2 0 0 1 0 0 2 1 2 0 3 4 0 0 0 1 4 1 2 1 3 0 0 0 0 0 1 0 0 1 1 1 2 3 1 0 4 0 0 0 1 0 2 2 0 0 0 1 2 2 0 3 4 0 0
contig_12_1_83_+>0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 2 0 0 2 0 1 0 0 1 0 0 0 2 1 0 0 1 1 0 0 1 0 0 2 0 0 2 0 2 0 1 0 0 0 0 0 0 1 1 1 1 1 0 0
contig_12_132_323_+>0 3 0 0 2 0 0 0 2 2 0 0 0 0 0 0 1 1 0 0 2 1 0 0 0 1 0 2 5 2 0 0 0 2 0 1 0 0 2 0 2 0 3 5 0 1 0 0 2 1 0 0 4 0 3 0 1 0 0 3 5 3 0 0
contig_13_1_118_+>2 3 0 2 1 0 0 1 0 0 0 0 0 0 0 2 1 0 1 1 0 1 0 0 0 0 2 0 1 1 1 0 2 0 0 0 0 0 0 1 1 1 4 1 0 0 0 0 1 1 0 0 0 1 2 0 0 1 1 1 0 0 0 0
contig_14_1_395_+>7 1 4 0 1 0 0 0 7 1 0 0 1 0 0 0 5 0 2 1 2 0 0 1 3 1 1 0 0 0 0 0 4 0 3 6 8 0 2 0 3 0 7 3 2 0 5 1 4 0 4 1 4 0 3 0 5 3 11 5 2 0 4 3
contig_15_1_265_+>3 1 1 0 2 0 2 1 5 0 0 0 0 0 0 2 0 2 0 0 1 0 0 0 0 1 4 0 3 3 0 0 1 1 3 2 2 1 4 0 2 4 5 2 3 0 0 0 2 0 1 0 1 1 2 0 4 3 5 2 1 3 1 0
contig_16_1_244_+>4 2 4 5 6 3 2 2 1 2 0 0 1 0 0 4 5 3 1 1 7 1 0 0 1 2 3 6 2 3 0 0 5 2 3 4 3 2 4 2 6 2 6 3 0 0 3 1 8 1 4 2 7 4 3 1 2 5 5 2 1 4 3 3
contig_17_1_279_+>2 2 2 2 4 1 0 2 0 1 0 0 0 0 0 3 3 0 1 0 4 1 0 0 1 1 1 5 2 2 0 0 2 1 2 3 2 0 3 1 4 1 3 1 0 0 0 0 5 0 3 1 6 2 1 1 0 1 1 0 1 3 2 2
contig_18_1_282_+>6 0 0 2 1 1 2 1 4 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 0 1 1 0 1 0 0 2 1 1 2 1 1 6 0 3 0 3 7 1 0 1 0 0 2 4 2 0 2 2 2 3 2 4 8 3 0 4 2
contig_19_1_622_+>2 1 8 1 5 0 2 1 9 1 0 0 0 0 0 4 2 0 1 0 2 0 7 0 1 0 3 0 2 1 1 0 6 0 3 0 9 3 7 2 14 2 19 5 4 1 3 0 6 3 12 0 7 0 2 0 7 3 19 3 6 0 7 0
contig_20_1_212_+>3 0 2 3 3 0 1 0 5 0 0 0 0 0 0 1 1 0 1 2 1 0 0 0 1 0 0 0 0 0 0 0 4 1 4 4 2 0 4 0 3 0 2 1 2 0 1 1 0 1 3 2 3 0 0 0 2 1 0 1 2 0 1 1
contig_21_1_254_+>2 3 1 1 2 0 1 2 3 2 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 1 1 2 0 0 1 0 8 0 2 2 0 0 1 1 4 1 3 2 0 1 2 1 3 1 1 0 3 1 1 1 4 1 6 1 2 3 2 0
contig_22_1_297_+>0 1 1 2 3 1 0 1 3 0 0 0 0 0 0 1 4 1 0 0 3 0 2 1 1 0 2 6 0 1 1 0 5 1 1 4 3 0 2 1 1 2 7 3 5 1 1 0 1 1 2 1 5 1 4 0 1 0 4 1 1 0 3 1
contig_23_1_218_+>1 1 1 4 0 0 2 0 1 0 0 0 0 0 0 0 2 2 0 1 0 0 1 1 1 1 1 2 1 2 0 0 0 0 2 4 1 1 2 1 5 3 1 1 2 1 0 0 1 1 2 0 4 1 1 1 3 1 3 3 0 1 0 0
contig_24_1_228_+>3 3 0 0 0 1 1 2 1 1 0 0 0 0 0 0 3 4 0 2 0 1 1 1 0 1 0 1 2 0 2 1 0 2 2 2 1 0 1 4 1 2 3 0 1 0 0 0 0 3 2 1 1 0 1 3 3 4 4 0 0 2 0 1
Totals> 65 34 39 41 47 20 27 14 74 22 0 0 18 5 0 27 51 19 17 25 35 8 19 11 21 21 34 36 23 23 9 2 75 28 58 58 57 26 51 23 81 39 128 74 31 18 37 9 64 17 66 17 73 25 41 17 84 50 115 53 40 31 54 16

Computed manually: 

python encprime_preprocessing.py -i test.ffn -c

101
64
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT CTC CTA CTG CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG GGT GGC GGA GGG
contig_1_1_373_+>6 2 5 5 1 2 3 0 2 1 0 0 2 1 0 1 1 0 1 2 0 0 1 0 4 0 1 2 0 0 0 0 5 3 2 3 6 0 2 0 7 4 9 0 3 1 2 1 8 0 3 0 4 1 1 1 3 1 4 3 0 1 2 0
contig_2_33_194_+>1 0 1 0 1 0 1 0 3 0 0 0 4 0 0 0 0 0 0 0 3 0 1 0 0 0 1 0 0 0 1 0 0 0 2 1 3 1 0 0 2 0 1 4 1 0 3 0 3 0 4 0 0 0 2 0 1 0 1 0 2 0 4 0
contig_3_1_279_+>5 1 1 4 0 1 3 0 3 1 0 0 2 0 0 0 1 0 0 2 0 0 0 0 2 1 0 1 0 0 0 0 8 1 0 0 0 1 0 2 3 2 10 4 0 1 1 1 1 0 1 1 1 2 2 1 5 1 10 4 0 0 1 0
contig_4_1_333_+>2 0 3 1 0 0 4 0 3 0 0 0 4 0 0 0 6 1 2 0 1 0 1 0 1 0 0 1 0 0 0 0 4 1 6 3 2 2 1 0 1 0 9 2 3 3 5 0 4 0 5 1 0 0 2 0 6 3 5 2 2 1 6 1
contig_5_1_445_+>4 2 0 1 4 1 1 0 7 3 0 0 2 0 0 1 1 2 0 0 2 0 3 0 1 1 2 0 0 2 0 0 3 5 11 2 6 4 4 2 6 5 11 6 1 0 1 0 5 0 1 0 3 2 3 0 4 4 8 1 1 1 7 0
contig_6_1_260_+>1 0 1 2 0 1 1 1 1 1 0 0 0 0 0 2 1 0 3 3 0 0 1 0 1 0 4 3 0 1 0 0 0 2 1 5 1 3 3 1 1 2 4 1 2 3 2 0 2 0 0 0 4 3 1 1 5 1 5 1 1 1 1 0
contig_7_1_301_+>2 0 1 0 3 0 1 0 5 1 0 0 0 1 0 1 2 1 2 1 0 0 1 0 1 0 1 0 0 0 0 0 1 1 4 2 2 1 0 0 2 1 3 11 1 0 1 3 0 0 4 0 10 2 1 2 5 3 4 5 0 1 3 2
contig_8_1_354_+>5 1 1 3 1 0 0 0 2 2 0 0 1 1 0 3 5 0 0 0 0 1 0 1 0 4 4 2 1 0 2 1 2 2 5 3 2 2 0 3 5 3 8 3 0 0 2 0 1 0 4 0 2 1 3 1 5 5 8 3 0 2 1 0
contig_9_49_297_->2 2 2 3 3 5 0 0 2 0 0 0 0 0 0 0 1 0 1 2 0 2 0 0 0 1 0 0 2 1 0 0 8 1 1 2 0 1 1 1 1 2 3 3 0 0 1 0 3 1 3 1 1 1 0 1 10 1 2 1 2 0 0 0
contig_10_1_200_->2 3 0 0 2 1 0 0 3 1 0 0 0 1 0 0 4 0 0 1 0 0 0 3 0 0 1 0 0 0 0 0 3 0 0 2 2 2 1 0 2 0 1 3 0 1 1 0 2 0 2 2 1 0 1 1 4 3 2 2 4 0 2 0
contig_11_1_201_+>0 2 0 0 2 2 0 0 2 2 0 0 1 0 0 2 1 2 0 3 4 0 0 0 1 4 1 2 1 3 0 0 0 0 0 1 0 0 1 1 1 2 3 1 0 4 0 0 0 1 0 2 2 0 0 0 1 2 2 0 3 4 0 0
contig_12_1_83_+>0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 2 0 0 2 0 1 0 0 1 0 0 0 2 1 0 0 1 1 0 0 1 0 0 2 0 0 2 0 2 0 1 0 0 0 0 0 0 1 1 1 1 1 0 0
contig_12_132_323_+>0 3 0 0 2 0 0 0 2 2 0 0 0 0 0 0 1 1 0 0 2 1 0 0 0 1 0 2 5 2 0 0 0 2 0 1 0 0 2 0 2 0 3 5 0 1 0 0 2 1 0 0 4 0 3 0 1 0 0 3 5 3 0 0
contig_13_1_118_+>2 3 0 2 1 0 0 1 0 0 0 0 0 0 0 2 1 0 1 1 0 1 0 0 0 0 2 0 1 1 1 0 2 0 0 0 0 0 0 1 1 1 4 1 0 0 0 0 1 1 0 0 0 1 2 0 0 1 1 1 0 0 0 0
contig_14_1_395_+>7 1 4 0 1 0 0 0 7 1 0 0 1 0 0 0 5 0 2 1 2 0 0 1 3 1 1 0 0 0 0 0 4 0 3 6 8 0 2 0 3 0 7 3 2 0 5 1 4 0 4 1 4 0 3 0 5 3 11 5 2 0 4 3
contig_15_1_265_+>3 1 1 0 2 0 2 1 5 0 0 0 0 0 0 2 0 2 0 0 1 0 0 0 0 1 4 0 3 3 0 0 1 1 3 2 2 1 4 0 2 4 5 2 3 0 0 0 2 0 1 0 1 1 2 0 4 3 5 2 1 3 1 0
contig_16_1_244_+>2 0 2 3 2 2 2 0 1 1 0 0 1 0 0 1 2 3 0 1 3 0 0 0 0 1 2 1 0 1 0 0 3 1 1 1 1 2 1 1 2 1 3 2 0 0 3 1 3 1 1 1 1 2 2 0 2 4 4 2 0 1 1 1
contig_17_1_279_+>2 2 2 2 4 1 0 2 0 1 0 0 0 0 0 3 3 0 1 0 4 1 0 0 1 1 1 5 2 2 0 0 2 1 2 3 2 0 3 1 4 1 3 1 0 0 0 0 5 0 3 1 6 2 1 1 0 1 1 0 1 3 2 2
contig_18_1_282_+>6 0 0 2 1 1 2 1 4 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 0 1 1 0 1 0 0 2 1 1 2 1 1 6 0 3 0 3 7 1 0 1 0 0 2 4 2 0 2 2 2 3 2 4 8 3 0 4 2
contig_19_1_622_+>2 1 8 1 5 0 2 1 9 1 0 0 0 0 0 4 2 0 1 0 2 0 7 0 1 0 3 0 2 1 1 0 6 0 3 0 9 3 7 2 14 2 19 5 4 1 3 0 6 3 12 0 7 0 2 0 7 3 19 3 6 0 7 0
contig_20_1_212_+>3 0 2 3 3 0 1 0 5 0 0 0 0 0 0 1 1 0 1 2 1 0 0 0 1 0 0 0 0 0 0 0 4 1 4 4 2 0 4 0 3 0 2 1 2 0 1 1 0 1 3 2 3 0 0 0 2 1 0 1 2 0 1 1
contig_21_1_254_+>2 3 1 1 2 0 1 2 3 2 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 1 1 2 0 0 1 0 8 0 2 2 0 0 1 1 4 1 3 2 0 1 2 1 3 1 1 0 3 1 1 1 4 1 6 1 2 3 2 0
contig_22_1_297_+>0 1 1 2 3 1 0 1 3 0 0 0 0 0 0 1 4 1 0 0 3 0 2 1 1 0 2 6 0 1 1 0 5 1 1 4 3 0 2 1 1 2 7 3 5 1 1 0 1 1 2 1 5 1 4 0 1 0 4 1 1 0 3 1
contig_23_1_218_+>1 1 1 4 0 0 2 0 1 0 0 0 0 0 0 0 2 2 0 1 0 0 1 1 1 1 1 2 1 2 0 0 0 0 2 4 1 1 2 1 5 3 1 1 2 1 0 0 1 1 2 0 4 1 1 1 3 1 3 3 0 1 0 0
contig_24_1_228_+>3 3 0 0 0 1 1 2 1 1 0 0 0 0 0 0 3 4 0 2 0 1 1 1 0 1 0 1 2 0 2 1 0 2 2 2 1 0 1 4 1 2 3 0 1 0 0 0 0 3 2 1 1 0 1 3 3 4 4 0 0 2 0 1
Totals> 63 32 37 39 43 19 27 12 74 21 0 0 18 5 0 24 48 19 16 25 31 7 19 11 20 20 33 31 21 21 9 2 73 27 56 55 55 26 48 22 77 38 125 73 31 18 37 9 59 17 63 16 67 23 40 16 84 49 114 53 39 28 52 14
jnovembre commented 2 years ago

Can you share the operating system and would you be willing to share the file so I can see if it replicates here?

jolespin commented 2 years ago 
(base) -bash-4.2$ uname -a
Linux lsub1 3.10.0-1160.24.1.el7.x86_64 #1 SMP Thu Apr 8 19:51:47 UTC 2021 x86_64 GNU/Linux

I've been using this instead of ENCPrime: https://github.com/BioinfoHR/coRdon

jolespin commented 2 years ago

I would have been willing to share the file but I've moved on from this project a few years ago. I wouldn't even know which file I was using for this error. Good luck.

jnovembre commented 2 years ago

Ok - thanks for noting the issue.