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stxmjh / interproscan

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tsv output of ver5 is not compatible with ver4 #10

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. run both instances (4.8 and 5RC1) of iprscan with output format 'tsv' and 
ask for goterms.

What is the expected output? What do you see instead?

example of expected output:
orf00004_892-3075_-1_2181   00CB64BAA0249C13    727 HMMPfam PF00403 HMA 15  65  5.7e-13
    T   02-Jul-2012 IPR006121   Heavy metal-associated domain, HMA  Biological Process: 
metal ion transport (GO:0030001), Molecular Function: metal ion binding 
(GO:0046872)

output we get:
orf00004_892-3075_-1_2181   346cdeb0fd70c925b4586322dd709bf6    727 Pfam    PF00403 Heav
y-metal-associated domain   15  65  5.7E-13 T   04-07-2012  IPR006121   Heavy 
metal-associated domain, HMA    GO:0030001|GO:0046872

What version of the product are you using? On what operating system?
current RC1 on Linux rserv01.vital-it.ch 2.6.32-220.17.1.el6.x86_64 #1 SMP Wed 
May 16 00:01:37 BST 2012 x86_64 x86_64 x86_64 GNU/Linux

Please provide any additional information below.

Would you have a ipr5->4 converter or any option to force ipr4 output?
Thanks

Laurent Falquet
laurent.falquet@unil.ch

Original issue reported on code.google.com by lfalq...@gmail.com on 4 Jul 2012 at 11:06

GoogleCodeExporter commented 9 years ago 
Dear Laurent,
First of all sorry for the late reply.

It is true the TSV outputs between version 4.8 and 5 are slightly different. 
First of all we moved from crc64 to md5 checksums (column 2), which is a step 
forwards. Secondly we changed the formatting of the date column for some reason 
I cannot tell you. Thirdly the structure of GO annotation column changed as 
well. Thanks for pointing that out. I think it makes sense to go back to pipe 
separated version as it is easier to parse.

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 27 Mar 2013 at 3:01

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 Aug 2013 at 11:14

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 Aug 2013 at 11:14

GoogleCodeExporter commented 9 years ago 
We've added a migration page. Please find it here: 
https://code.google.com/p/interproscan/wiki/MigratingInterProScanVersions

Original comment by Maxim.Sc...@gmail.com on 5 Nov 2013 at 12:18