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Description
While adding some tests to check for the GFF output (in order to fix #18) I noticed that the start score of some genes were deviating from the Prodigal reference results. This was not verified before since the GFF format is the only output format to contain these statistics. This change in start score affects the may score and the confidence of each gene marginally.
Genes scored with Prodigal:
NODE_23_length_79939_cov_26.984653 Prodigal_v2.6.3 CDS 1 177 8.4 - 0 ID=1_1;partial=10;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.237;conf=90.13;score=9.62;cscore=10.74;sscore=-1.12;rscore=-5.22;uscore=-1.07;tscore=3.94;
NODE_23_length_79939_cov_26.984653 Prodigal_v2.6.3 CDS 168 386 25.1 - 0 ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.251;conf=99.77;score=26.33;cscore=27.03;sscore=-0.70;rscore=-6.04;uscore=0.68;tscore=3.41;
NODE_23_length_79939_cov_26.984653 Prodigal_v2.6.3 CDS 389 1483 186.7 - 0 ID=1_3;partial=00;start_type=ATG;rbs_motif=GGAGG;rbs_spacer=5-10bp;gc_cont=0.254;conf=99.99;score=186.70;cscore=168.23;sscore=18.47;rscore=14.49;uscore=0.04;tscore=3.94;
NODE_23_length_79939_cov_26.984653 Prodigal_v2.6.3 CDS 1632 2981 218.9 - 0 ID=1_4;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=3-4bp;gc_cont=0.296;conf=99.99;score=218.26;cscore=200.52;sscore=17.74;rscore=14.49;uscore=-0.04;tscore=3.94;
NODE_23_length_79939_cov_26.984653 Prodigal_v2.6.3 CDS 3569 3925 25.5 + 0 ID=1_5;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.266;conf=99.72;score=25.49;cscore=21.09;sscore=4.41;rscore=1.46;uscore=-1.00;tscore=3.94;
Genes scored with Pyrodigal v0.6.4:
NODE_23_length_79939_cov_26.984653_1 pyrodigal_v0.6.4 CDS 1 177 8.4 - 0 ID=1_1;partial=10;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.237;conf=90.13;score=9.62;cscore=10.74;sscore=-1.12;rscore=-5.22;uscore=-1.07;tscore=3.94;
NODE_23_length_79939_cov_26.984653_2 pyrodigal_v0.6.4 CDS 168 386 25.1 - 0 ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.251;conf=99.77;score=26.33;cscore=27.03;sscore=-0.70;rscore=-6.04;uscore=0.68;tscore=3.41;
NODE_23_length_79939_cov_26.984653_3 pyrodigal_v0.6.4 CDS 389 1483 186.7 - 0 ID=1_3;partial=00;start_type=ATG;rbs_motif=GGAGG;rbs_spacer=5-10bp;gc_cont=0.254;conf=99.99;score=186.70;cscore=168.23;sscore=18.47;rscore=14.49;uscore=0.04;tscore=3.94;
NODE_23_length_79939_cov_26.984653_4 pyrodigal_v0.6.4 CDS 1632 2981 218.9 - 0 ID=1_4;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=3-4bp;gc_cont=0.296;conf=99.99;score=218.26;cscore=200.52;sscore=17.74;rscore=14.49;uscore=-0.04;tscore=3.94;
NODE_23_length_79939_cov_26.984653_5 pyrodigal_v0.6.4 CDS 3569 3925 25.5 + 0 ID=1_5;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.266;conf=99.72;score=25.49;cscore=21.09;sscore=4.41;rscore=1.46;uscore=-1.00;tscore=3.94;
Genes scored with Pyrodigal v1.1.2:
NODE_23_length_79939_cov_26.984653_1 pyrodigal_v1.1.2 CDS 1 177 8.4 - 0 ID=1_1;partial=10;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.237;conf=87.32;score=8.39;cscore=10.74;sscore=-2.35;rscore=-5.22;uscore=-1.07;tscore=3.94
NODE_23_length_79939_cov_26.984653_2 pyrodigal_v1.1.2 CDS 168 386 25.1 - 0 ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.251;conf=99.69;score=25.07;cscore=27.03;sscore=-1.96;rscore=-6.04;uscore=0.68;tscore=3.41
NODE_23_length_79939_cov_26.984653_3 pyrodigal_v1.1.2 CDS 389 1483 186.7 - 0 ID=1_3;partial=00;start_type=ATG;rbs_motif=GGAGG;rbs_spacer=5-10bp;gc_cont=0.254;conf=99.99;score=186.70;cscore=168.23;sscore=18.47;rscore=14.49;uscore=0.04;tscore=3.94
NODE_23_length_79939_cov_26.984653_4 pyrodigal_v1.1.2 CDS 1632 2981 218.9 - 0 ID=1_4;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=3-4bp;gc_cont=0.296;conf=99.99;score=218.91;cscore=200.52;sscore=18.39;rscore=14.49;uscore=-0.04;tscore=3.94
NODE_23_length_79939_cov_26.984653_5 pyrodigal_v1.1.2 CDS 3569 3925 25.5 + 0 ID=1_5;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.266;conf=99.72;score=25.49;cscore=21.09;sscore=4.41;rscore=1.46;uscore=-1.00;tscore=3.94
After bissecting, I found that the bug was introduced between v0.6.4 and v0.7.0.