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Add gbk2pf converter. #30

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ArnaudBelcour opened this issue Aug 15, 2019 · 4 comments
Open

Add gbk2pf converter. #30

ArnaudBelcour opened this issue Aug 15, 2019 · 4 comments
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enhancement New feature or request

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@ArnaudBelcour
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As genbank formats created by different tools are different, we can have errors during PathoLogic. To solve these errors, we could convert genbank into PathoLogic Format.

The idea is to add a new argument:

mpwt gbk2pf -i input_folder -o output_folder --cpu number_cpu

This command takes as argument a folder containing the genbank (in the same structure than the input_folder of mpwt -f) and an output folder. It will then generates the PathoLogic Format files from the genbank.
@ArnaudBelcour ArnaudBelcour added the enhancement New feature or request label Aug 15, 2019
@ArnaudBelcour ArnaudBelcour self-assigned this Aug 15, 2019
ArnaudBelcour added a commit that referenced this issue Aug 15, 2019
@ArnaudBelcour
Add draft of gbk2pf converter (issue #30).
60bafe0
ArnaudBelcour added a commit that referenced this issue Aug 15, 2019
@ArnaudBelcour
Improve gbk2pf: better gene ID/Name and GO handling (issue #30).
dc01b3c
@ArnaudBelcour
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It could also be useful to have a gff2pf converter.

So I will create a new command:

mpwt topf -i input_folder -o output_folder

ArnaudBelcour added a commit that referenced this issue Oct 17, 2019
@ArnaudBelcour
Rename gbk2pf in to_pf (issue #30).
09e2669 
Add GFF support for to_pf (need more tests).
@ArnaudBelcour ArnaudBelcour mentioned this issue Oct 17, 2019
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Added in #32 but need more polishing in 0.5.3.

ArnaudBelcour added a commit that referenced this issue Nov 18, 2019
@ArnaudBelcour
Fix issue with variable name in topf function (issue #30).
da8a774
ArnaudBelcour added a commit that referenced this issue Nov 22, 2019
@ArnaudBelcour
Fix issue with topf and PF as input (issue #30).
24140ee 
Add test for topf (issue #30).
ArnaudBelcour added a commit that referenced this issue Nov 22, 2019
@ArnaudBelcour
Add topf in Readme (issue #30).
1f0bbd4
ArnaudBelcour added a commit that referenced this issue Nov 26, 2019
@ArnaudBelcour
Fix issue with PathoLogic file creation when using GFF (issue #30).
12c94ce 
Fix link in Readme.
ArnaudBelcour added a commit that referenced this issue Nov 26, 2019
@ArnaudBelcour
Fix issue with GO terms in topf (issue #30).
d7154f2
@ArnaudBelcour ArnaudBelcour mentioned this issue Jan 9, 2020
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@ArnaudBelcour
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Fix some issues but it needs more testing and polishing in 0.5.4.

ArnaudBelcour added a commit that referenced this issue Jan 31, 2020
@ArnaudBelcour
Better handling of RNAs and CDS in topf (issue #30).
5a91a82
ArnaudBelcour added a commit that referenced this issue Feb 7, 2020
@ArnaudBelcour
Fix issue with .gbk and .pf files in topf (issue #30).
275fc2b
ArnaudBelcour added a commit that referenced this issue Feb 26, 2020
@ArnaudBelcour
Add DBLINK in topf (issue #30).
27527ed
ArnaudBelcour added a commit that referenced this issue Feb 27, 2020
@ArnaudBelcour
Add check for gene name lenght in topf (issue #30).
4e0e0d7
@ArnaudBelcour ArnaudBelcour mentioned this issue Apr 10, 2020
Merged
ArnaudBelcour added a commit that referenced this issue May 13, 2020
@ArnaudBelcour
Add pseudogene mRNA in topf when using a genbank (issue #30).
a3e5d62
@ArnaudBelcour ArnaudBelcour mentioned this issue May 27, 2020
Merged
ArnaudBelcour added a commit that referenced this issue Jun 11, 2020
@ArnaudBelcour
Remove use of genbank function qualifier in topf (issue #30)..
d08b677
ArnaudBelcour added a commit that referenced this issue Jun 12, 2020
@ArnaudBelcour
Fix issue in start and end location in topf (issue #30).
2c9d394
ArnaudBelcour added a commit that referenced this issue Jun 12, 2020
@ArnaudBelcour
Avoid duplication between NAME and IN in topf (issue #30).
5becc44
@ArnaudBelcour ArnaudBelcour mentioned this issue Jul 28, 2020
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Fix numerous issues in #50.

ArnaudBelcour added a commit that referenced this issue Aug 21, 2020
@ArnaudBelcour
New script to_pathologic.py for topf (issue #30).
0987770 
Fix issue in topf with pf files.
ArnaudBelcour added a commit that referenced this issue Sep 2, 2020
@ArnaudBelcour
Fix an issue with taxon_id.tsv creation in topf (issue #30).
289eb4a
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