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sahammond / gnavigator

Use cDNA alignments with or without genetic map information to evaluate the completeness and correctness of a de novo genome or transcriptome assembly.
GNU General Public License v3.0
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Fix to genetic map JIRA-formatted report #13

Closed lcoombe closed 5 years ago

lcoombe commented 5 years ago

Looks like there was a small bug in the JIRA report format for the genetic map:

[lcoombe@hpce704 WS-cDNAs]$ cat Q903-scaffolds.tigmint_1000plus-genetic-map-scaffold-results.jira
## Gnavigator command was: /projects/btl/lcoombe/git/gnavigator/gnavigator.py -p Q903-scaffolds.tigmint_1000plus -t24 -m Pglauca_geneticMap_v2.GCATfilter.tsv GCAT_WS-3.3.cluseq.noGaps.simple.fa Q903-scaffolds.tigmint_1000plus.fa
||1 complete cDNA||2+ complete cDNAs||Same LG, expected order||Same LG, unexpected order||Different LG||Same LG, undetermined order||
|5297 (95.72%)|5534 (4.28%)|210 (3.79%)|3 (0.05%)|24 (0.43%)|0 (0.0%)|

[lcoombe@hpce704 WS-cDNAs]$ cat Q903-scaffolds.tigmint_1000plus-genetic-map-scaffold-results.tsv
## Gnavigator command was: /projects/btl/lcoombe/git/gnavigator/gnavigator.py -p Q903-scaffolds.tigmint_1000plus -t24 -m Pglauca_geneticMap_v2.GCATfilter.tsv GCAT_WS-3.3.cluseq.noGaps.simple.fa Q903-scaffolds.tigmint_1000plus.fa
    1 complete cDNA 2+ complete cDNAs   Same LG, expected order Same LG, unexpected order   Different LG    Same LG, undetermined order
Number  5297    237 210 3   24  0
Percent 95.72   4.28    3.79    0.05    0.43    0.0

This should fix it!

sahammond commented 5 years ago

Good catch! Thanks for the fix, Lauren!