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kircherlab / CADD-SV

CADD-SV – a framework to score the effect of structural variants
https://cadd-sv.bihealth.org
MIT License
14 stars 3 forks source link

Missing header in output #10

Closed Han-Cao closed 11 months ago

Han-Cao commented 1 year ago

Hi,

I found the output drop column name of "CADD-SV raw score", resulting in the incorrect header for columns after phred-score.

For example:

<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

chr | start | end | type | name | CADDSV-score | raw-score-span | raw-score-flank | CADD_max | CADD_sum | PhastCons100_max | PhastCons100_sum | PhastCons30_max | PhastCons30_sum | PhastCons20_max | PhastCons20_sum | CADD_count | CCR | E1_poised | E2_repressed | E3_dead | E4_dead | E5_repressed | E6_repressed | E7_weak | E8_gene | E9_gene | E10_gene | E11_gene | E12_distal | E13_distal | E14_distal | E15_weak | E16_tss | E17_proximal | E18_proximal | E19_tss | E20_poised | E21_dead | E22_repressed | E23_weak | E24_distal | E25_distal | nr_ctcf_BS | ctcf_nr_bases | ctcf_fraction | DI_min | DI_max | DNase.seq_max | DNase.seq_sum | H2AFZ_max | H2AFZ_sum | H3K27ac_max | H3K27ac_sum | H3K27me3_max | H3K27me3_sum | H3K36me3_max | H3k36me3_sum | H3K4me1_max | H3K4me1_sum | H3K4me2_max | H3K4me2_sum | H3K4me3_max | H3K4me3_sum | H3K79me2_max | H3K79me2_sum | H3K9ac_max | H3K9ac_sum | H3K9me3_max | H3K9me3_sum | H4K20me1_max | H4k20me1_sum | totalRNA.seq_max | totalRNA.seq_sum | EP_intra | EP_boundary | EP_ext | EP_distance | FIRE_gm12878_max | FIRE_gm12878_min | FIRE_msc_max | FIRE_msc_min | FIRE_mes_max | FIRE_mes_min | FIRE_imr90_max | FIRE_imr90_min | FIRE_h1_max | FIRE_h1_min | perc_gc | exon | transcript | gene | start_codon | stop_codon | X3utr | X5utr | cds | gerp_max | gerp_count | A549_nested_intra | A549_nested_boundary | A549_nested_ext | A549_nested_dist | A549_tad_intra | A549_tad_boundary | A549_tad_ext | A549_tad_dist | caki2_nested_intra | caki2_nested_boundary | caki2_nested_ext | caki2_nested_dist | caki2_tad_intra | caki2_tad_boundary | caki2_tad_ext | caki2_tad_dist | escTAD_intra | escTAD_boundary | escTAD_ext | escTAD_distance | microsyn_intra | miscrosyn_boundary | microsyn_ext | microsyn_distance | MPC | pli | exon_dist | gene_dist | start_codon_dist | remapTF | f5_enhancers | DDD_HaploInsuf | deepC_saliencie | nr_uc_elements | nr_uc_bases | uc_fraction | LINSIGHT |   -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- 1 | 85440802 | 85440877 | DEL | test_chr1:85440802-85440877 | 31 | 0.975740902 | 0.532292662 | 0.975740902 | 0.174320632 | 0.303273 | 0.822741 | 0.084122 | 0.8488 | 0.032106 | 0.895259 | 0.060158 | 0.530481 | -0.2139 | -0.33748 | -0.33745 | -0.45738 | -0.05991 | -0.41814 | -0.20909 | -0.46126 | -0.3204 | -0.26107 | -0.21539 | 0.417095 | 0.016964 | 1.325423 | -0.50277 | 0.367497 | -0.17066 | -0.0228 | -0.24288 | -0.22054 | -0.16873 | -0.62871 | -0.34196 | -0.39717 | 0.06043 | 0.051632 | -0.03945 | -0.03863 | -0.11431 | -1.19839 | 0.620707 | -0.20368 | -0.50226 | -0.24892 | -0.32348 | -0.18769 | -0.24996 | -0.2734 | -0.28793 | -0.24038 | -0.24553 | -0.26375 | -0.27039 | -0.18971 | -0.20456 | -0.1624 | -0.18504 | -0.13963 | -0.14453 | -0.15676 | -0.20269 | -0.51219 | -0.53241 | -0.13505 | -0.13807 | -0.0655 | -0.23268 | 2.144238 | -1.93954 | -0.17975 | -1.33003 | 3.74549 | 3.843992 | -0.22831 | -0.22929 | -0.16531 | -0.16611 | -0.23986 | -0.24024 | -0.16786 | -0.16823 | 0.485743 | -0.46569 | 0.066885 | 0.066885 | -0.04038 | -0.03648 | -0.03951 | -0.03662 | 0.414916 | 1.755174 | 1.032673 | 0.382543 | -0.37654 | -0.05909 | 1.491063 | 0.456313 | -0.43993 | -0.10131 | 0.088538 | 0.357634 | -0.35285 | -0.05164 | 1.415113 | 0.438994 | -0.42199 | -0.10261 | 0.097749 | 0.310279 | -0.29444 | -0.08969 | -0.59891 | -0.1938 | 0.197384 | -0.03608 | -0.64139 | -0.28562 | -0.49435 | 0.3137 | -0.79463 | -0.21424 | -0.21832 | -0.03453 | 1.698594 | -0.16982 | -0.0319 | 0.619747 | 4.451285 | 0.682787

Thanks, Han

varunkas commented 1 year ago

I too have this issue...

CatonaO commented 11 months ago

Hello, Thank you for pointing that out, we have now fixed this issue with the header, for this to work effectively please download the dependencies again, other than just pulling the git repository to update, also remove the run.caddsv environment and create it again from the updated "environment.yaml". Best, Orazio