Deep Magic - recover a file

We have hopefully managed to recover a file (or two) today from an existing process in which the files live in /tmp/, but if the process goes on too long, get deleted by the system

Find relevant Process ID
  >ps aux or top
  >pstree -p 

Work out files which have handles but are deleted
  >lsof -p 
  bwa     22039 srpipe    4r   REG      104,7  424718660  67171651 /tmp/iFCyWKyDjR/1.sai (deleted)
  bwa     22039 srpipe    5r   REG      104,7  401682372  67171652 /tmp/iFCyWKyDjR/2.sai (deleted)

Rebuild files
  >mkdir /tmp/iFCyWKyDjR
  >cat /proc/22039/fd/4 > /tmp/iFCyWKyDjR/1.sai
  >cat /proc/22039/fd/5 > /tmp/iFCyWKyDjR/2.sai

Check
  >ls -lh /tmp/iFCyWKyDjR
  total 789M
  -rw-rw-r-- 1 srpipe solexa 406M 2011-09-02 09:30 1.sai
  -rw-rw-r-- 1 srpipe solexa 384M 2011-09-02 09:30 2.sai

To remember

my $last_base_index = ( length $fields[$SEQUENCE_INDEX] ) - 1;

The parenthesis are needed!

Bingo!

Last year, my dad, as the Chairman of the local community association says that what might be a good fund raiser is a bingo evening.

Initially, my thought was, who are they going to get to run that then?

But he continued, and came up to the question of sourcing a bingo machine. This is were I came in and said,

'Oh, that's easy, I could write one in a couple of weekends on the computer, we jsut hook my laptop up to a big screen and that's that.'

Can you see where I'm going with this?

So, time passes, I had a quick stab last November, but stopped as Christmas was coming up, and I was writing a perl course for work...

Until March, when Dad turns round and says

'Are you going to be able to write the bingo machine in time for Annual fundraising week? What day of the week is best for you to run it?'

Eeep.

Still, never one to back down from a request to do something, I set to work. Went back to github, and decided to scrap most of what was there, start a new Catalyst project, and a couple of weekends later, I have a bingo caller, with big ball images, and a pretty simple interface.

It could still do with a pretty looking interface, but it does the job, and should run nicely next week - assuming I can sort out Moose

https://github.com/setitesuk/Bingo-Caller

Interesting bug

I have just discovered an interesting bug, which took a lot of staring at to fathom out exactly what is wrong here:

  if ( $self->is_paired_read() ) {
    my $args = {
      dir => $arg_refs->{dir},
      position => $position,
      read => $self->general_values_conf()->{sanger_read_two},
      job_dependencies => $arg_refs->{job_dependencies},
      control => $is_control,
      is_spiked_phix => $is_spiked_phix,
    };

    if ( $self->is_indexed() ) {
      $args->{read} = $self->general_values_conf()->{illumina_read_two};
    }

    $bsub_command = $self->_calibration_table_bsub_command( {
      dir => $arg_refs->{dir},
      position => $position,
      read => $self->general_values_conf()->{sanger_read_two},
      job_dependencies => $arg_refs->{job_dependencies},
      control => $is_control,
      is_spiked_phix => $is_spiked_phix,
    } );

    if ( $self->verbose() ) {
      $self->log( $bsub_command );
    }

    push @{ $job_ids }, $self->submit_bsub_command($bsub_command);
  }

Some of you may have spotted it straight away, but others may not.

The problem comes from a bit of

1) copy and paste programming (there is a read 1 as well)
2) not paying attention

Had I not had the if ( $self->is_indexed ) block, then Perl::Critic would actually have saved me here, with a unused variable error, but because $args (lexically scoped) , is used in the block, we skip that.

Simply, when you go to the trouble of defining your args outside of the call to the method, then use the args, don't rewrite. (Bangs head against wall to try to remember the fact).

The bug in production is that we always get a calibration table name with read 'sanger_read_two', when it should be read 'illumina_read_two' on an indexed run.
(These are config variables, which actually equate to 2 and 3 respectively)

So a change to:

    $bsub_command = $self->_calibration_table_bsub_command( { $args } );

and all is fixed.

Perl Course help!

I need some help as to whether or not to do include something in a beginners perl course I am writing to run at work.

Courses I went on and textbooks I have read (including the excellent Modern Perl) mention the idiom '0 but true', to have a true 0.

Everyone in my office when I asked either went 'what?', 'why?' or 'just something not needed and is confusing'.

Personally, I agree with the 'why?' and 'confusing', so I'm inclined to leave it out. However, what do the community at large think? One of my colleagues has been programming Perl for 15+years, and has never seen it. Is this generally the case?

Thanks to any responses in advance that support either side of the argument, particularly with good reasoning.

Just to confirm my 4 reasons for leaving it out:

1) Never seen it used
2) Too confusing to explain to people experienced in Perl, let alone Newbies
3) Too confusing to read in code
4) Won't be automatically assigned to a variable when answer is 0 (4-4), so better to use defined

Andy

Talk to Software East - Aglie Analysis Pipeline

Last night I gave a talk to the monthly Software East meeting, held by Mark Dalgarno at RedGate Software.

Big Thanks to Mark for inviting me, and everyone who showed up for an interesting discussion on Agile techniques. Also, thanks to RedGate for hosting.

The slides have been uploaded to Slideshare:

Agile analysis development

View more presentations from setitesuk.

It was a great talk, and the first time I didn't get groans outside of work about having used Perl :)

Looking forward to the next Software East meeting in January, which will be Rachel Davies talking about Agile Retrospectives.
I saw Rachel give the second day's keynote at Agile Cambridge, and she was brilliant. She was also very nice to chat to at lunch that day. She has written the book Agile Coaching (Pragmatic Programmers) so for fear of overloading the session with people, I can thoroughly recommend going to this.

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