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0.1.0 #26

Merged
merged 27 commits into from
Jan 24, 2023
Merged

0.1.0 #26

merged 27 commits into from
Jan 24, 2023

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trvinh
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@trvinh trvinh commented Jan 24, 2023

  • convert main codes to python
  • rename data folders
  • improve runtime
  • simplify parameters

@trvinh
create v0.1.0
daec73c
@trvinh
simplfying hamstr.pl
8872cee
@trvinh
first python conversion
71c8636
@trvinh
modified addTaxon and addTaxa
08d7e64
@trvinh
first final version
43797e3
@trvinh
fixed undefined var
e0d35d3
@trvinh
fixed github_build
139f4a1
@trvinh
added install/check dependencies
a202294
@trvinh
added install/check dependencies
ba0efba
@trvinh
added install/check dependencies
b62dce6
@trvinh
added install/check dependencies
770b1ce
@trvinh
added install/check dependencies
45702d4
@trvinh
added install/check dependencies
94fd00d
@trvinh
added install/check dependencies
b6b8974
@trvinh
added install/check dependencies
1efcb43
@trvinh
added install/check dependencies
1ed85d5
@trvinh
added install/check dependencies
6723e8a
@trvinh
added install/check dependencies
2e3d924
@trvinh
added install/check dependencies
1986b40
@trvinh
added install/check dependencies
ea20fa7
@trvinh
fixed parameters of create_genome
e2124b7
@trvinh
modified github_build
8eb9a2e
@trvinh
rename data folders
dcc3e84
@trvinh
fixed github_build
9681324
@trvinh
fixed github_build
5323541
@trvinh
fixed bug when searching in refspec
bf8eace
@trvinh
added runtime for core complilation
49fa477
@trvinh trvinh requested a review from mueli94 January 24, 2023 09:06
@trvinh trvinh merged commit 055051f into master Jan 24, 2023
@trvinh trvinh deleted the 0.1.0 branch January 24, 2023 09:22
This was referenced Jan 24, 2023
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@elfring
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elfring commented Jan 24, 2023

💭 I find it interesting that Perl code was replaced by Python code.

@trvinh
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trvinh commented Jan 24, 2023

Hello @elfring,
Our plan was to improve the program (modularisation, solve issues with the incompatible perl versions, improve the runtime by reducing I/O processing, etc.). It is easier for us to implement again from scratch than to modify the old Perl code :-P And we chose Python for this since it is the main language in our group currently.
Many thanks for your interest :)

mueli94 added a commit that referenced this pull request Oct 24, 2023
@mueli94
Squashed commit of the following:
7f666b7 
commit 3f2929b
Merge: 7fb439f 959e0a0
Author: Hannah Muelbaier <47216555+mueli94@users.noreply.github.com>
Date:   Mon Oct 23 15:06:29 2023 +0200

    Merge pull request #2 from BIONF/master

    deactivate fas config output

commit 7fb439f
Author: mueli94 <hannah.muelbaier@gmail.com>
Date:   Fri Oct 20 10:05:26 2023 +0200

    Revert "Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly"

    This reverts commit d688bbb, reversing
    changes made to 5068b7a.

commit d0d359f
Merge: 5068b7a d688bbb
Author: mueli94 <hannah.muelbaier@gmail.com>
Date:   Fri Oct 20 10:05:01 2023 +0200

    Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly

commit d688bbb
Merge: 5068b7a 3b62945
Author: mueli94 <hannah.muelbaier@gmail.com>
Date:   Thu Oct 19 16:28:55 2023 +0200

    Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly

commit 5068b7a
Author: mueli94 <hannah.muelbaier@gmail.com>
Date:   Thu Oct 19 16:20:18 2023 +0200

    contig fasta files where delited from the tmp folder to save memory

commit 3b62945
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Thu Sep 21 16:31:17 2023 +0200

    further updates to adapt fDOG-Assembly to the new fDOG version. Additionally bugfix in co-ortholog detection if MSA crashed due to too many sequences.

commit 41660e6
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Wed Sep 20 10:34:56 2023 +0200

    fixed augustus version

commit 5d77522
Author: mueli94 <hannah.muelbaier@gmail.com>
Date:   Tue Sep 19 15:02:57 2023 +0200

    Bugfix muscle v5 command in fdog.addCoreGroup

commit 959e0a0
Author: trvinh <trvinh@gmail.com>
Date:   Tue Sep 19 14:49:48 2023 +0200

    deactivate fas config output

commit ea40a0c
Merge: 3140fc4 3cc809c
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Mon Sep 18 17:27:04 2023 +0200

    Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly

commit 3140fc4
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Mon Sep 18 17:25:39 2023 +0200

    script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file

commit 3cc809c
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Mon Sep 18 17:21:07 2023 +0200

    script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file

commit ef5acb7
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Mon Sep 18 17:20:09 2023 +0200

    further changes to adapt to new fDOG version

commit a832824
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Mon Sep 18 13:17:11 2023 +0200

    adjustments to new muscle version and fDOG version

commit 8df8a73
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Mon Sep 18 11:38:06 2023 +0200

    added fDOG-Assembly dependencies

commit fc0ea45
Author: Hannah <47216555+mueli94@users.noreply.github.com>
Date:   Mon Sep 18 10:58:18 2023 +0200

    added fDOG-Assembly workflow

commit 5ccf824
Author: trvinh <trvinh@gmail.com>
Date:   Wed Aug 16 13:33:40 2023 +0200

    check valid rank for refspec only

commit deeda8a
Author: Vinh Tran <trvinh@gmail.com>
Date:   Wed Aug 16 13:19:31 2023 +0200

    Update CHANGELOG.md

commit eb902a6
Author: trvinh <trvinh@gmail.com>
Date:   Wed Aug 16 12:03:36 2023 +0200

    option to not added all taxa

commit e6ce3d1
Author: trvinh <trvinh@gmail.com>
Date:   Wed Aug 16 11:50:10 2023 +0200

    changed orthID NA to fdogMA for manually added taxa

commit 5cb0946
Author: trvinh <trvinh@gmail.com>
Date:   Wed Aug 16 09:57:26 2023 +0200

    added all searchTaxa to phyloprofile

commit 3e0859b
Author: trvinh <trvinh@gmail.com>
Date:   Tue Aug 15 15:39:54 2023 +0200

    added check for invalid min-/maxDist; works with fasta36.3.8g

commit b7ec6fa
Author: trvinh <trvinh@gmail.com>
Date:   Tue Aug 15 15:19:36 2023 +0200

    fixed worrking with old fasta36

commit 553cdaa
Author: trvinh <trvinh@gmail.com>
Date:   Tue Aug 15 12:44:18 2023 +0200

    added check for invalid min-/maxDist; works with fasta36.3.8g

commit c756ab0
Author: trvinh <trvinh@gmail.com>
Date:   Tue Aug 15 11:48:59 2023 +0200

    added check for invalid min-/maxDist; works with fasta36.3.8g

commit a746c8f
Author: trvinh <trvinh@gmail.com>
Date:   Tue Aug 15 11:32:45 2023 +0200

    added check for invalid min-/maxDist; works with fasta36.3.8g

commit 48372cf
Author: trvinh <trvinh@gmail.com>
Date:   Tue Jul 18 11:11:37 2023 +0200

    added warning for no hmm hit

commit a8541f8
Author: trvinh <trvinh@gmail.com>
Date:   Thu Jun 15 16:24:24 2023 +0200

    set seqlen limit for muscle5

commit b06b3a1
Author: trvinh <trvinh@gmail.com>
Date:   Mon Jun 12 14:09:09 2023 +0200

    fixed mapping file for addTaxon

commit c5ca07c
Author: trvinh <trvinh@gmail.com>
Date:   Thu May 25 14:13:45 2023 +0200

    fixed output filename for muscle5

commit b014157
Author: trvinh <trvinh@gmail.com>
Date:   Thu May 11 13:13:19 2023 +0200

    check empty tmp dir before deleting in addTaxon

commit 052cf70
Author: trvinh <trvinh@gmail.com>
Date:   Fri Mar 10 15:42:15 2023 +0100

    muscle5,checkBlast,ignoreAnnoCheck

commit 7e6bfbc
Author: trvinh <trvinh@gmail.com>
Date:   Wed Feb 22 09:57:23 2023 +0100

    adapt evalue

commit 56995b1
Author: trvinh <trvinh@gmail.com>
Date:   Wed Feb 22 09:56:40 2023 +0100

    adapt evalue

commit 7798d15
Author: trvinh <trvinh@gmail.com>
Date:   Mon Feb 20 13:50:31 2023 +0100

    rename log fdogs.run

commit 03c9038
Author: trvinh <trvinh@gmail.com>
Date:   Fri Feb 17 14:29:03 2023 +0100

    fix number of hmmhits core compilation

commit f7c4cf8
Author: trvinh <trvinh@gmail.com>
Date:   Tue Feb 14 12:47:09 2023 +0100

    fix check for pathconfig file

commit 5785980
Author: trvinh <trvinh@gmail.com>
Date:   Tue Feb 14 11:14:23 2023 +0100

    fix sorting hmm hits

commit bb185a3
Author: trvinh <trvinh@gmail.com>
Date:   Mon Feb 6 14:14:52 2023 +0100

    add several options to work with data paths; resolves: #28

commit 8bd2359
Author: trvinh <trvinh@gmail.com>
Date:   Mon Feb 6 14:04:01 2023 +0100

    add several options to work with data paths; resolves: #28

commit 7c3191a
Author: trvinh <trvinh@gmail.com>
Date:   Mon Feb 6 13:59:31 2023 +0100

    add several options to work with data paths

commit ab5491b
Author: trvinh <trvinh@gmail.com>
Date:   Fri Feb 3 15:46:46 2023 +0100

    option to use different names for data folders

commit 198393d
Author: trvinh <trvinh@gmail.com>
Date:   Fri Feb 3 15:07:49 2023 +0100

    add option to update json file to checkData

commit 4339bad
Author: trvinh <trvinh@gmail.com>
Date:   Thu Feb 2 17:17:34 2023 +0100

    accept old folder names

commit bfbc324
Author: trvinh <trvinh@gmail.com>
Date:   Thu Feb 2 16:39:34 2023 +0100

    added fn desc

commit ad8741d
Author: trvinh <trvinh@gmail.com>
Date:   Thu Feb 2 10:17:29 2023 +0100

    v0.1.5 version bump

commit ad2cbbd
Author: trvinh <trvinh@gmail.com>
Date:   Thu Feb 2 10:06:53 2023 +0100

    sort hmm hits using domain scores; correct tree walking; setup force not delete data; correct profile output with fasOff

commit 206def0
Author: trvinh <trvinh@gmail.com>
Date:   Thu Feb 2 10:04:18 2023 +0100

    sort hmm hits using domain scores; correct tree walking; setup force not delete data; correct profile output with fasOff

commit 1edad42
Author: trvinh <trvinh@gmail.com>
Date:   Fri Jan 27 09:33:58 2023 +0100

    version bump

commit 8855db4
Author: trvinh <trvinh@gmail.com>
Date:   Fri Jan 27 09:33:38 2023 +0100

    reduce evalue for identify seed ID

commit 8332690
Author: trvinh <trvinh@gmail.com>
Date:   Thu Jan 26 14:48:27 2023 +0100

    fix bug identify seed ID with reuseCore

commit 9edaf9e
Author: trvinh <trvinh@gmail.com>
Date:   Thu Jan 26 10:47:14 2023 +0100

    speed up preparation in fdogs.run

commit 2405698
Author: trvinh <trvinh@gmail.com>
Date:   Thu Jan 26 10:24:23 2023 +0100

    save core jobs for fdogs.run to file

commit e728252
Author: trvinh <trvinh@gmail.com>
Date:   Thu Jan 26 09:51:00 2023 +0100

    fix path to refspec fa; add amino to hmmbuild

commit f984b26
Author: trvinh <trvinh@gmail.com>
Date:   Wed Jan 25 14:41:09 2023 +0100

    added preparation runtime to fdogs.run

commit 8624f7d
Author: trvinh <trvinh@gmail.com>
Date:   Tue Jan 24 14:23:03 2023 +0100

    fixed kimura distance devide by 0

commit dd9a45c
Author: trvinh <trvinh@gmail.com>
Date:   Tue Jan 24 10:57:38 2023 +0100

    updated README

commit 055051f
Author: Vinh Tran <trvinh@gmail.com>
Date:   Tue Jan 24 10:21:08 2023 +0100

    0.1.0 (#26)

    * create v0.1.0

    * simplfying hamstr.pl

    * first python conversion

    * modified addTaxon and addTaxa

    * added install/check dependencies

    * rename data folders

    * added runtime for core complilation

commit d8eea1f
Author: trvinh <trvinh@gmail.com>
Date:   Wed Oct 12 09:10:56 2022 +0200

    fixed addTaxon replacing pipe

commit 20aa839
Author: trvinh <trvinh@gmail.com>
Date:   Mon Jun 13 10:19:40 2022 +0200

    removed fdog assembly files

commit a0747e0
Author: trvinh <trvinh@gmail.com>
Date:   Tue Mar 15 14:19:32 2022 +0100

    fdogs accepts dots in seed filename
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@trvinh @elfring