add phylop

[qingl0331]

add readme

[qingl0331]

sure~

2017-09-01 14:49 GMT-06:00 Brent Pedersen notifications@github.com:

@brentp commented on this pull request.

In score-sets/GRCh37/sift/make.sh https://github.com/quinlan-lab/pathoscore/pull/27#discussion_r136662826:

@@ -0,0 +1,11 @@ +mkdir -p sift +cd sift +wget ftp://ftp.jcvi.org/pub/data/sift/Human_db_37_ensembl_63/Humansqlite.gz +gunzip gz +set -euo pipefail +(echo -e "#chrom\tpos\tref\talt\tsiftScore"; +for f in ls -v ./Human_CHR*.sqlite; do

• set -e
• perl query.pl $f | sort --temporary-directory=. -k1,1 -k2,2n +done ) | bgzip -c > sift.txt.gz +tabix -b2 -e2 sift.txt.gz

could you cleanup *.sqlite at the end?

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[jimhavrilla]

for getting phyloP you can use http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates/ to get the chromosome scores for phyloP in Wig format then use wigtoBigWig and bigWigtoBedGraph

[jimhavrilla]

additionally there is a newer, more up-to-date SIFT than the one on craig venter's website at http://sift.bii.a-star.edu.sg/sift4g/public/Homo_sapiens/GRCh37.74/ paper is here: http://sift.bii.a-star.edu.sg/www/nprot2016_vaser.pdf

[qingl0331]

Actually I have contacted the developer and they suggested us to use the latest mammalian scores

2017-09-01 15:20 GMT-06:00 Jim Havrilla notifications@github.com:

for getting phyloP you can use http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/primates/ to get the chromosome scores for phyloP in Wig format then use wigtoBigWig and bigWigtoBedGraph

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[jimhavrilla]

you mean the placentalmammal scores?

[qingl0331]

yep

2017-09-01 15:25 GMT-06:00 Jim Havrilla notifications@github.com:

you mean the placentalmammal scores?

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[jimhavrilla]

then you can use the wigs in http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

Craig Venter's that you use in your make.sh is from ENSEMBL 63. The latest version is updated and is for ENSEMBL 74.

[qingl0331]

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla notifications@github.com:

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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[jimhavrilla]

Really? Odd since they put out a new SIFT software last year...sqlite is way faster no doubt though

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:35 PM, qingl0331 notifications@github.com wrote:

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla notifications@github.com:

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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[jimhavrilla]

Did you push your make.sh for phyloP?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:36 PM, Jim Havrilla semjaavria@gmail.com wrote:

Really? Odd since they put out a new SIFT software last year...sqlite is way faster no doubt though

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:35 PM, qingl0331 notifications@github.com wrote:

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla notifications@github.com:

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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[qingl0331]

Not yet, , trying to figure out how to do it in a separate branch

2017-09-01 15:37 GMT-06:00 Jim Havrilla notifications@github.com:

Did you push your make.sh for phyloP?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:36 PM, Jim Havrilla semjaavria@gmail.com wrote:

Really? Odd since they put out a new SIFT software last year...sqlite is way faster no doubt though

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:35 PM, qingl0331 notifications@github.com wrote:

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla notifications@github.com:

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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[jimhavrilla]

It's pretty hard since you made all those commits in master. Best thing to do is rebase all the commits into one. Then make your new branch. Then hard reset the HEAD to the last commit brent made in master, then checkout to your new branch and it should have all those commits in one commit. Then push that branch and create a pull request on it. I think that should cover you.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:39 PM, qingl0331 notifications@github.com wrote:

Not yet, , trying to figure out how to do it in a separate branch

2017-09-01 15:37 GMT-06:00 Jim Havrilla notifications@github.com:

Did you push your make.sh for phyloP?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:36 PM, Jim Havrilla semjaavria@gmail.com wrote:

Really? Odd since they put out a new SIFT software last year...sqlite is way faster no doubt though

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:35 PM, qingl0331 notifications@github.com wrote:

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla notifications@github.com:

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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[jimhavrilla]

Refer to this: https://stackoverflow.com/questions/5189560/squash-my-last-x-commits-together-using-git And this: https://stackoverflow.com/questions/1628563/move-the-most-recent-commits-to-a-new-branch-with-git

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:42 PM, Jim Havrilla semjaavria@gmail.com wrote:

It's pretty hard since you made all those commits in master. Best thing to do is rebase all the commits into one. Then make your new branch. Then hard reset the HEAD to the last commit brent made in master, then checkout to your new branch and it should have all those commits in one commit. Then push that branch and create a pull request on it. I think that should cover you.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:39 PM, qingl0331 notifications@github.com wrote:

Not yet, , trying to figure out how to do it in a separate branch

2017-09-01 15:37 GMT-06:00 Jim Havrilla notifications@github.com:

Did you push your make.sh for phyloP?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:36 PM, Jim Havrilla semjaavria@gmail.com wrote:

Really? Odd since they put out a new SIFT software last year...sqlite is way faster no doubt though

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:35 PM, qingl0331 notifications@github.com wrote:

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla notifications@github.com:

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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[qingl0331]

cool! thnx! 👍

2017-09-01 15:43 GMT-06:00 Jim Havrilla notifications@github.com:

Refer to this: https://stackoverflow.com/questions/5189560/squash-my- last-x-commits-together-using-git And this: https://stackoverflow.com/questions/1628563/move-the- most-recent-commits-to-a-new-branch-with-git

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:42 PM, Jim Havrilla semjaavria@gmail.com wrote:

It's pretty hard since you made all those commits in master. Best thing to do is rebase all the commits into one. Then make your new branch. Then hard reset the HEAD to the last commit brent made in master, then checkout to your new branch and it should have all those commits in one commit. Then push that branch and create a pull request on it. I think that should cover you.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:39 PM, qingl0331 notifications@github.com wrote:

Not yet, , trying to figure out how to do it in a separate branch

2017-09-01 15:37 GMT-06:00 Jim Havrilla notifications@github.com:

Did you push your make.sh for phyloP?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:36 PM, Jim Havrilla semjaavria@gmail.com wrote:

Really? Odd since they put out a new SIFT software last year...sqlite is way faster no doubt though

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:35 PM, qingl0331 <notifications@github.com

wrote:

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla <notifications@github.com :

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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[jimhavrilla]

Sure, git is a pain

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:44 PM, qingl0331 notifications@github.com wrote:

cool! thnx! 👍

2017-09-01 15:43 GMT-06:00 Jim Havrilla notifications@github.com:

Refer to this: https://stackoverflow.com/questions/5189560/squash-my- last-x-commits-together-using-git And this: https://stackoverflow.com/questions/1628563/move-the- most-recent-commits-to-a-new-branch-with-git

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:42 PM, Jim Havrilla semjaavria@gmail.com wrote:

It's pretty hard since you made all those commits in master. Best thing to do is rebase all the commits into one. Then make your new branch. Then hard reset the HEAD to the last commit brent made in master, then checkout to your new branch and it should have all those commits in one commit. Then push that branch and create a pull request on it. I think that should cover you.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:39 PM, qingl0331 notifications@github.com wrote:

Not yet, , trying to figure out how to do it in a separate branch

2017-09-01 15:37 GMT-06:00 Jim Havrilla notifications@github.com:

Did you push your make.sh for phyloP?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:36 PM, Jim Havrilla semjaavria@gmail.com wrote:

Really? Odd since they put out a new SIFT software last year...sqlite is way faster no doubt though

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Fri, Sep 1, 2017 at 3:35 PM, qingl0331 < notifications@github.com

wrote:

Yep, I am done with the wigs~ thnx! For SIFT, I was also directed by the developer of SIFT to get the link , so I guess they are the same as sqlite3...? I can spot check some to make sure they are the same. Actually sqlite3 is much smaller in size to handle ~ I prefer that one~

2017-09-01 15:30 GMT-06:00 Jim Havrilla < notifications@github.com :

then you can use the wigs in http://hgdownload.cse.ucsc. edu/goldenpath/hg19/phyloP46way/placentalMammals/ instead of primates and do the same thing unless there is a newer than 2009 one. did you see the SIFT 4G link above?

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