User: Yotam ConstantiniBiostar

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Posts by Yotam ConstantiniBiostar

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Turning pairwise alignment description in XML/JSON to a multiline string
... I ended up just writing it in PL/SQL, if you ever need to translate to another programming language, here it is: function pretty_pairwise_alignment( ALIGN_LEN integer, query_from INTEGER, query_to INTEGER, hit_from INTEGER, hit_to INTEGER, qseq C ...
written 8 weeks ago by Yotam ConstantiniBiostar0
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Comment: C: Turning pairwise alignment description in XML/JSON to a multiline string
... Thank you for the quick reply. I need a solution for the input I've written, as I can only use the JSON data I'm getting. I'm looking for some actual source code I can rewrite into my application ...
written 8 weeks ago by Yotam ConstantiniBiostar0
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Comment: C: Convert Xml Alignment To Aln Format
... too bad this was closed.. [I reopened a parallel question][1] [1]: https://www.biostars.org/p/431199/ ...
written 8 weeks ago by Yotam ConstantiniBiostar0
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Turning pairwise alignment description in XML/JSON to a multiline string
... Hey all, I'm getting blastp results in a JSON, and want to turn them into a readable format to display on a website to formulate this as a general question about pairwise alignment, I'm looking for a function (don't matter which programming language) that takes in the following arguments: Positions ...
alignment blast written 8 weeks ago by Yotam ConstantiniBiostar0
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Comment: C: Bam header editing
... I ended up using addreplacerg, and wrapped it in a fun loop.. for file in PATH/TO/INPUTS/*.bam; do base_name=$(basename $file .bam); samtools addreplacerg -r "ID:${base_name}\tSM:${base_name}" -o PATH/TO/OUTPUT/${base_name}.bam $file; done ...
written 4 months ago by Yotam ConstantiniBiostar0

Latest awards to Yotam ConstantiniBiostar

Scholar 8 weeks ago, created an answer that has been accepted. For A: Turning pairwise alignment description in XML/JSON to a multiline string

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