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Old 06-27-2012, 06:40 AM   #1
cllorens
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Default Program edit an ace file to simultaneously extract read information from all contig?

Hi guys

I need to extract the read names composition of all contigs from an ace file of an assembly. I know tablet and other tools do this but only browsing the file contig by contig by my ace has 65000 contigs (UGG). Doe anyone knows
a tool capable to let to edit the ace and extract this particular info from all
contigs simultanously?? perhaps converting the ace to bam??

Thanks in advance

Carlos
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Old 06-27-2012, 07:52 AM   #2
cllorens
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forget it i already have the solution which quite easy
thankl you anyway
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Old 06-27-2012, 08:05 AM   #3
maubp
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And what was your solution?

I would try parsing the ACE file with Biopython to get the read names - but you could probably do it with a regular expression at the Unix command line too.
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Old 06-27-2012, 08:20 AM   #4
cllorens
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Yes, i will make a small perl or php script to parse the file.
I wrote the question so fastly i guess because i wrongly though that .ace cannot be edit as a plane file. So there is no problem to parse it with any script.
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