Compatibility with FALCON headers

[pb-cdunn]

I was just about to pull Zev's fixes since we cut our release, when I noticed 06f5114:

commit 06f5114ecd107e10b3bdb4059b7f317910eb0692
Author: zeeev <jewbaru@gmail.com>
Date:   Wed Sep 12 14:19:25 2018

    Revert "added compatibility with other FALCON Unzip headers"

    This reverts commit aebec592ae0e24bd063409abf3dc01ea82fdbe94.

diff --git bin/scrub_names.pl bin/scrub_names.pl
index 8dd062a..3782dfc 100755
--- bin/scrub_names.pl
+++ bin/scrub_names.pl
@@ -55,8 +55,8 @@ PRI: while (<$IN>) {
     }
     else{
        chomp;
-       $_ =~ /^>(.*F(?:p\d+)?)/;
-       my $p_name = "$1";
+       $_ =~ /^>(.*)F/;
+       my $p_name = "$1F";
        print $OUT ">$p_name\n";
        $primaries{$p_name} = 1;
     }
@@ -92,7 +92,7 @@ HAP: while (<$INB>) {

 foreach my $k (@haplotigs){
     my @sname = split /_/, $k;
-#    $sname[0] =~ s/p\d+//;
+    $sname[0] =~ s/p\d+//;

@zeeev , why did you revert?

@skingan , were you aware of that revert? Is it ok?

[skingan]

If I recall correctly, that code doesn't handle the formatting of the haplotigs correctly so we should keep the reversion. Sarah

…

On Thu, Dec 13, 2018 at 6:47 AM Christopher Dunn ***@***.***> wrote: I was just about to pull Zev's fixes since we cut our release, when I noticed 06f5114 <06f5114> : commit 06f5114 Author: zeeev ***@***.***> Date: Wed Sep 12 14:19:25 2018 Revert "added compatibility with other FALCON Unzip headers" This reverts commit aebec59. diff --git bin/scrub_names.pl bin/scrub_names.pl index 8dd062a..3782dfc 100755--- bin/scrub_names.pl+++ bin/scrub_names.pl@@ -55,8 +55,8 @@ PRI: while (<$IN>) { } else{ chomp;- $_ =~ /^>(.*F(?:p\d+)?)/;- my $p_name = "$1";+ $_ =~ /^>(.*)F/;+ my $p_name = "$1F"; print $OUT ">$p_name\n"; $primaries{$p_name} = 1; }@@ -92,7 +92,7 @@ HAP: while (<$INB>) { foreach my $k ***@***.***){ my @sname = split /_/, $k;-# $sname[0] =~ s/p\d+//;+ $sname[0] =~ s/p\d+//; @zeeev <https://github.com/zeeev> , why did you revert? @skingan <https://github.com/skingan> , were you aware of that revert? Is it ok? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#59>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIjz7fvbM8jbYGdG8LJy7IujECiGqO6Cks5u4mh1gaJpZM4ZRxlW> .

[pb-cdunn]

Oh? The reversion is not in our "release", so it's not in Bioconda. I thought you added it and reverted something else. Here is the git graph:

*   37fa90d Merge pull request #45 from phasegenomics/development
|\
| * 06f5114 (up/development) Revert "added compatibility with other FALCON Unzip headers"
| | * b25e4c6 (HEAD -> develop, tag: 0.2.0, origin/develop) bioconda expect /usr/bin/env shebangs
| | * 3b026a2 fc_ prefixes
| |/
| * aebec59 added compatibility with other FALCON Unzip headers
| *   513241e Merge pull request #46 from PacificBiosciences/develop
| |\
| | * 5eba263 Re-write emit_haplotigs.pl in Python
| |/
| *   79397e4 (origin/development, development) Merge pull request #44 from phasegenomics/trio_snp_validation
| |\
| | * 2c92cce (up/trio_snp_validation) summary report done
| | * d9d6411 classification script done
| | * d951268 about to build out the validation pipeline
| * |   bf2c5ab Merge pull request #41 from PacificBiosciences/development
| |\ \
| | * | af2b1fc Fix scrub_names.pl
...

% git remote -v
origin  git@github.com:PacificBiosciences/pb-falcon-phase.git (fetch)
up      git@github.com:phasegenomics/FALCON-phase (fetch)

• up is the phasegenomics repo.
• origin is our PacBio repo.
• Note that internally, we merge on develop, per our VP.

I think Sarah's commit fixed my own attempt:

commit af2b1fcdb0571cadbe16d753cd26b7552ee7c6b8
Author: Christopher Dunn <cdunn@pacificbiosciences.com>
Date:   Wed Aug 29 22:09:55 2018

    Fix scrub_names.pl

diff --git bin/scrub_names.pl bin/scrub_names.pl
index b2aa7bb..3782dfc 100755
--- bin/scrub_names.pl
+++ bin/scrub_names.pl
@@ -81,7 +81,7 @@ HAP: while (<$INB>) {
     else{
         chomp;
         # Allow new Unzip naming (which we have reverted).
-        if (not ($_ =~ /^>(.*F(?:p\d+)_[0-9]+)/)) {
+        if (not ($_ =~ /^>(.*F(?:p\d+)?_[0-9]+)/)) {

So by reverting Sarah's, we would be back to mine. Is that really correct?

Let's be 100% sure.

[skingan]

I checked the functionality of the scrub_names.pl scripts in the phase genomics master branch and pb-assembly master and develop. We want to use the version in the phase genomics repo. It properly handles both the standard naming convention (000123F, 000123F_001) AND the one temporarily used earlier this year (000123Fp01, 000123Fp01_00001). I'm having trouble following the git graph but as long as we use the perl sript that is in phase's github repo we should be fine. Sarah

…

On Thu, Dec 13, 2018 at 7:08 AM Christopher Dunn ***@***.***> wrote: Oh? The reversion is not in our "release", so it's not in Bioconda. I thought you added it and reverted something else. Here is the git graph: * 37fa90d Merge pull request #45 from phasegenomics/development |\ | * 06f5114 (up/development) Revert "added compatibility with other FALCON Unzip headers" | | * b25e4c6 (HEAD -> develop, tag: 0.2.0, origin/develop) bioconda expect /usr/bin/env shebangs | | * 3b026a2 fc_ prefixes | |/ | * aebec59 added compatibility with other FALCON Unzip headers | * 513241e Merge pull request #46 from PacificBiosciences/develop | |\ | | * 5eba263 Re-write emit_haplotigs.pl in Python | |/ | * 79397e4 (origin/development, development) Merge pull request #44 from phasegenomics/trio_snp_validation | |\ | | * 2c92cce (up/trio_snp_validation) summary report done | | * d9d6411 classification script done | | * d951268 about to build out the validation pipeline | * | bf2c5ab Merge pull request #41 from PacificBiosciences/development | |\ \ | | * | af2b1fc Fix scrub_names.pl ... % git remote -v origin ***@***.***:PacificBiosciences/pb-falcon-phase.git (fetch) up ***@***.***:phasegenomics/FALCON-phase (fetch) - up is the phasegenomics repo. - origin is our PacBio repo. - Note that internally, we merge on develop, per our VP. I think Sarah's commit fixed my own attempt: commit af2b1fc Author: Christopher Dunn ***@***.***> Date: Wed Aug 29 22:09:55 2018 Fix scrub_names.pl diff --git bin/scrub_names.pl bin/scrub_names.pl index b2aa7bb..3782dfc 100755--- bin/scrub_names.pl+++ bin/scrub_names.pl@@ -81,7 +81,7 @@ HAP: while (<$INB>) { else{ chomp; # Allow new Unzip naming (which we have reverted).- if (not ($_ =~ /^>(.*F(?:p\d+)_[0-9]+)/)) {+ if (not ($_ =~ /^>(.*F(?:p\d+)?_[0-9]+)/)) { So by reverting Sarah's, we would be back to mine. Is that really correct? Let's be 100% sure. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#59 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIjz7bpDLQMgQsYJ93bcGnqjvLRkJ-bQks5u4m1zgaJpZM4ZRxlW> .

[zeeev]

Hi @pb-cdunn,

Sorry for the trouble! Going forward I promise to work on the PB repo. I'm trying to get one last merge into master before we sync the PB codebase.

I think the code is starting to stabilize and should require less attention.

#60

[pb-cdunn]

No! Don't apologize! Progress is good.

I'm about to sync these changes. I'm just trying to be sure that we actually want Sarah's "revert". I'm not certain.

[skingan]

This reversion was done in a burst of activity and I take some of the blame for not fulling understanding all the different versions. Chris, let me know if you want me to do any additional testing. Sarah

…

On Thu, Dec 13, 2018 at 10:24 AM Christopher Dunn ***@***.***> wrote: No! Don't apologize! Progress is good. I'm about to sync these changes. I'm just trying to be sure that we actually want Sarah's "revert". I'm not certain. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#59 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIjz7UE1Zze7dOcJRTs4HmfVGmzBIrcuks5u4ptigaJpZM4ZRxlW> .

[pb-cdunn]

Thanks. We are now up-to-date on the develop branch of pb-falcon-phase.

[zeeev]

Cheers! Thanks @pb-cdunn.