alignproteome added by martin-steinegger · Pull Request #875 · soedinglab/MMseqs2

martin-steinegger · 2024-08-18T08:51:22Z

No description provided.

martin-steinegger · 2024-08-18T08:52:26Z

src/MMseqsBase.cpp

I would improve this text.

martin-steinegger · 2024-08-18T08:52:45Z

src/MMseqsBase.cpp

Please add you @Gyuuul2

martin-steinegger · 2024-08-18T08:53:35Z

src/commons/ClusterSpecies.cpp

This file looks incomplete

martin-steinegger · 2024-08-18T08:53:55Z

src/commons/ClusterSpecies.h

martin-steinegger · 2024-08-18T08:54:28Z

src/commons/DBReader.cpp

I would remove this print out.

martin-steinegger · 2024-08-18T08:55:03Z

src/commons/DBReader.cpp

I would remove this print out.

martin-steinegger · 2024-08-18T08:55:08Z

src/commons/DBReader.cpp

I would remove this print out.

martin-steinegger · 2024-08-18T09:02:00Z

src/commons/CMakeLists.txt

Please remove it.

martin-steinegger · 2024-08-18T09:02:59Z

src/alignment/Matcher.h

Why is this needed?

martin-steinegger · 2024-08-18T09:03:40Z

src/util/alignall.cpp


-    DBReader<unsigned int> tdbr(par.db1.c_str(), par.db1Index.c_str(), par.threads, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);
+    // DBReader<unsigned int> tdbr(par.db1.c_str(), par.db1Index.c_str(), par.threads, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);
+    DBReader<unsigned int> tdbr(par.db1.c_str(), par.db1Index.c_str(), par.threads, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_LOOKUP);


I assume this is not needed anymore

martin-steinegger · 2024-08-18T09:03:46Z

src/util/alignall.cpp

martin-steinegger · 2024-08-18T09:12:43Z

src/util/alignproteome.cpp

MemberProteinEntry

milot-mirdita · 2024-08-19T08:54:09Z

src/commons/DBReader.h

I would name this getSourceTotalLen or getSetTotalLen to be consistent with the .source naming

milot-mirdita · 2024-08-19T08:55:37Z

src/workflow/EasyAlignproteome.cpp

You need to implement this whenever you use the createParameterString(..., true) parameter. Or it won't get passed along.

milot-mirdita · 2024-08-19T08:56:16Z

src/workflow/EasyAlignproteome.cpp

CLUSTER_PAR, THREADS_PAR etc are missing

milot-mirdita · 2024-08-19T08:57:35Z

src/workflow/EasyAlignproteome.cpp

You need to pop_back() the output path too and pass it as an environment variable. Or else it will also be passed to createdb.

…of different fasta files

…usage to createdb and easy-search in MMseqsBase.cpp.

milot-mirdita · 2024-08-27T15:57:40Z

src/commons/IndexReader.h

    ) : sequenceReader(NULL), index(NULL) {
        int targetDbtype = FileUtil::parseDbType(dataName.c_str());
        if (Parameters::isEqualDbtype(targetDbtype, Parameters::DBTYPE_INDEX_DB)) {
-            index = new DBReader<unsigned int>(dataName.c_str(), (dataName + ".index").c_str(), 1, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);


what happened here?

milot-mirdita · 2024-08-27T16:01:48Z

src/util/proteomecluster.cpp

style: please add spaces around if:
if[space](...)[space]{

milot-mirdita · 2024-08-27T16:03:23Z

src/util/proteomecluster.cpp

double ;

also careful about bool vectors. They are not multi-threading friendly. Here its fine, as you don't do any multi-threading

milot-mirdita · 2024-08-27T16:03:36Z

src/util/proteomecluster.cpp

style: missing space after the for

milot-mirdita · 2024-08-27T16:03:52Z

src/util/proteomecluster.cpp

+    for (size_t idx = 0; idx < ProteomeList.size(); idx++){
+        if (ProteomeList[idx].isCovered()) {
+            continue;
+        }else{


style: missing spaces around else

milot-mirdita · 2024-08-27T16:05:58Z

src/util/proteomecluster.cpp

style: should be lowercase: proteomeList

milot-mirdita · 2024-08-27T16:07:02Z

src/util/proteomecluster.cpp

You can avoid the explicit allocation here:

SubstitutionMatrix subMat(par.scoringMatrixFile.values.aminoacid().c_str(), 2.0, par.scoreBias); ...

milot-mirdita · 2024-08-27T16:08:16Z

src/util/proteomecluster.cpp

if you use __sync_fetch_and_add inside incrementMemCount you don't need the critical

milot-mirdita · 2024-08-27T16:09:38Z

src/util/proteomecluster.cpp

here you might need the critical as atomic floats can be tricky to do correctly

milot-mirdita · 2024-08-27T16:10:08Z

src/util/proteomecluster.cpp

if you rewrite the subMat init above, you can remove this

…mber proteome is detected)

…teome handling update

alignproteome added

1cb2074

martin-steinegger commented Aug 18, 2024

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src/MMseqsBase.cpp Outdated

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martin-steinegger Aug 18, 2024

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I would improve this text.

martin-steinegger commented Aug 18, 2024

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src/MMseqsBase.cpp Outdated

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Please add you @Gyuuul2

martin-steinegger commented Aug 19, 2024

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add workflow, revise based on feedback

12c0c81

milot-mirdita reviewed Aug 19, 2024

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src/workflow/EasyAlignproteome.cpp Outdated

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CLUSTER_PAR, THREADS_PAR etc are missing

milot-mirdita reviewed Aug 19, 2024

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elpis51613 and others added 8 commits August 25, 2024 18:49

Change createdb.cpp so that it takes in ".txt" file containing paths …

df80f07

…of different fasta files

Merge remote-tracking branch 'refs/remotes/origin/master'

1073ec9

Change filepath format from txt to tsv. Also add explanations of its …

3617ea7

…usage to createdb and easy-search in MMseqsBase.cpp.

createtsv - handle source identifier

3fc7fcd

proteomcluster - change writer / way to select repProteome

0487a1f

easy proteomecluster workflow

3f4fc91

indexreader - handle source identifier

eeabad3

update mmseqsbase and change module name into proteomecluster

9996821

milot-mirdita reviewed Aug 27, 2024

View reviewed changes

Gyuuul2 added 12 commits August 28, 2024 14:16

set alignment mode default

27d9f68

latest

e2ef229

original index

fd1f5d6

use sync_fetch_and_add when increment memcount

0d7db0f

change submat

1fe489e

add timer

86f6b15

Merge branch 'pr-879'

8344e5b

Remove __packed__ to resolve sync_fetch_and_add error

be5a53d

change chmod in createdb

8d3a38f

update proteome-similarity threshold parameter

bfa1911

Sort redundant proteomes by similarity score in proteome_cluster.tsv

7e912d2

delete redundant code - checking proteome is singleton(no redudant me…

618e2bf

…mber proteome is detected)

Gyuuul2 added 11 commits September 9, 2024 11:12

stop

e990773

jaccardindexTrial

e9ffe22

add normalized scoring

d14217f

add proteome relative(normalized) similarity threshold parameter

5e6ee6d

relative similarity threshold

743370d

latest version-bugfix,relativeProteomeSimilarity added, singleton pro…

44a6fca

…teome handling update

Change Relative Score formula

910bb7f

Remove Debug printout

e24b9e3

style change

ad1acdf

Latest Version

e026260

Add cluster count report

d9213ef

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martin-steinegger commented Aug 18, 2024

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