phasegenomics/FALCON-Phase

Compatibility with FALCON headers

pb-cdunn opened this issue · 8 comments

pb-cdunn commented

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 commented
pb-cdunn commented

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 commented
zeeev commented

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 commented

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 commented
pb-cdunn commented

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

zeeev commented

Cheers! Thanks @pb-cdunn.

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