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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Mingraph-Cactus final GFA file format #1243

Closed Xuelei-Dai closed 11 months ago

Xuelei-Dai commented 11 months ago

Hi Glenn,

I run the cactus-pangenome, but the gfa file format in our final results is different, so I can not to stat some nodes and bp et. from the gfa file, the W line in the final gfa file as follows: commad grep -e '^W' Chr26-pg.gfa | cut -f2-6 | awk '{ print $1 "#" $2 "#" $3 ":" $4 "-" $5 }' |head

Assembly1#0#JABTCH010000015.1:0-130387
Assembly1#0#JABTCH010000015.1:186361-3471095
Assembly1#0#JABTCH010000130.1:0-51597
Assembly1#0#JABTCH010000139.1:0-19670
Assembly1#0#JABTCH010000139.1:37995-545999
Assembly1#0#JABTCH010000139.1:564286-576836
Assembly1#0#JABTCH010000400.1:0-76533
Assembly1#0#JABTCH010000400.1:117564-135237
Assembly1#0#JABTCH010000406.1:0-648325
Assembly1#0#JABTCH010000406.1:659015-1930337

For the human pangenome gfa format is like:

CHM13#0#chr1:0-16173080
CHM13#0#chr1:16184045-121670597
CHM13#0#chr1:126701173-126908079
CHM13#0#chr1:142241657-145181159
CHM13#0#chr1:145446240-145852542
CHM13#0#chr1:146366933-148479713
CHM13#0#chr1:148680951-248387328

so for my gfa file is there some wrong or how can I change this?

Best wishes!

glennhickey commented 11 months ago

Sorry, I don't understand your question.