[Biopython-dev] [Biopython (old issues only) - Bug #2929] (Migrated) NCBIXML PSI-Blast parser should gather all information from XML blastgpg output

[redmine at redmine.open-bio.org]

Issue #2929 has been updated by Peter Cock.

Description updated
Status changed from New to Migrated
URL set to https://github.com/biopython/biopython/issues/1723

Migrated to GitHub as https://github.com/biopython/biopython/issues/1723

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Bug #2929: NCBIXML PSI-Blast parser should gather all information from XML blastgpg output
https://redmine.open-bio.org/issues/2929#change-15415

* Author: Miguel empty
* Status: Migrated
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.52
* URL: https://github.com/biopython/biopython/issues/1723
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With the problems encountered while parsing plain text output from blastpgp, perhaps an answer would be to use the XML output of this program. The XML output seems to have evolved in recent versions of blastpgp and now all the info gets in a single proper XML file (not several concatenated files) and, in principle, it would seem that all the information in the plain text format can also be found in the XML one.

I will attach an XML output for a PSI-Blast search that converges after 3 passes.

---Files--------------------------------
blast.xml (59.2 KB)


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