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This queue is for tickets about the Bio-LITE-Taxonomy-NCBI-Gi2taxid CPAN distribution.

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Id: 107026
Status: new
Priority: 0/
Queue: Bio-LITE-Taxonomy-NCBI-Gi2taxid

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Owner: Nobody in particular
Requestors: zhangsenchao [...] honortech.cn
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Subject: taxid isn't all correct
Date: Fri, 11 Sep 2015 11:10:19 +0800
To: bug-Bio-LITE-Taxonomy-NCBI-Gi2taxid <bug-Bio-LITE-Taxonomy-NCBI-Gi2taxid [...] rt.cpan.org>
From: 张森超 <zhangsenchao [...] honortech.cn>
Hi, Thanks for the module helping me a lot. The module is efficient to convert GI to taxid, so I need it in my work. Recently, I Meet a problem when use the module. Compared with the original file(download from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz), Taxid converted isn't all correct. For example, I test 54 Gis and 6 Gi's taxid isn't correct. Command: perl gi2tax.pl 2 3 4 36907497 36907498 36907499 87102679 87102680 87102681 145715279 145715280 145715281 184496190 184496191 184496192 258288903 258288904 258288905 308437015 308437016 308437017 352560229 352560230 352560231 396689468 396689469 396689470 450556407 450556408 450556409 506984014 506984015 506984016 561373688 561373689 561373690 615261913 615261914 615261915 669242497 669242498 669242499 709940630 709940631 709940632 758499405 758499406 758499407 796667246 796667247 796667248 847342571 847342572 847342573 > test.out Not correct Gi2taxid: 758499405 758499406 758499407 796667246 796667247 796667248 Content of gi2tax.pl perl script : #!/usr/bin/perl use strict; use warnings; use Bio::LITE::Taxonomy::NCBI::Gi2taxid qw/new_dict/; new_dict (in => "/data/database/ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp", out => "gi_taxid_nucl.bin"); my $dict = Bio::LITE::Taxonomy::NCBI::Gi2taxid->new(dict=>"gi_taxid_nucl.bin"); foreach (@ARGV){ my $taxid = $dict->get_taxid($_); print "$_=>$taxid\n"; } Bio::LITE::Taxonomy::NCBI::Gi2taxid version: v0.13 perl version : v5.10.1 Operating System vendor and version: Linux mu01 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux best, search.
Download Catch.jpg
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Catch.jpg
Download gi_taxid_nucl_correct.txt
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Download test.out
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