2015-01-26 9:01 GMT-03:00 Sven Van Caekenberghe <sven@stfx.eu>:

Hern��n,

> On 26 Jan 2015, at 08:00, Hern��n Morales Durand <hernan.morales@gmail.com> wrote:
>
> It is possible :)
> I work with DNA sequences, there could be millions of common SNPs in a genome.

Still weird for CSV. How many record are there then ?

We genotyped few individuals (24 records) but now we have a genotyping platform (GeneTitan) with array plates allowing up to 96 samples, which is up to 2.6 million of markers. The first run I completed generated CSVs of 1 million of records (see attach). Sadly the high-level analysis of this data (annotation, clustering, discrimination) now is performed with R with packages like SNPolisher.

And this is microarray analysis, NGS platforms produce larger volumes of data in a shorter period of time (several genomes in a day). See http://www.slideshare.net/allenday/renaissance-in-medicine-strata-nosql-and-genomics for the 2014-2020 predictions.

Feel free to contact me if you want to experiment with metrics.

I assume they all have the same number of fields ?

Yes, never seen CSV file with variable number of fields (in this domain)

Anyway, could you point me to the specification of the format you want to read ?

Actually I have no rush for this, I want to avoid awk, sed and shell scripts in the next run. I would like to avoid Python but spreads like a virus.

I will be working mostly with CSV's from Axiom annotation files [1] and genotyping results. Other file formats I use are genotype file formats for programs like PLINK [2] (PED files, column 7 onwards) and HaploView. Is worst than you might think, because you have to transpose the output generated by genotyping platforms (millions of records), and then filter & cut them by chromosome because those Java programs cannot deal with all chromosomes at the same time.

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And to the older the that you used to use ?

http://www.smalltalkhub.com/#!/~hernan/CSV

Cheers,

Hern��n

[1] http://www.affymetrix.com/support/technical/annotationfilesmain.affx
[2] http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped

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Thx,

Sven

> Cheers,
>
> Hern��n
>
>
> 2015-01-26 3:33 GMT-03:00 Sven Van Caekenberghe <sven@stfx.eu>:
>
> > On 26 Jan 2015, at 06:32, Hern��n Morales Durand <hernan.morales@gmail.com> wrote:
> >
> >
> >
> > 2015-01-23 18:00 GMT-03:00 Sven Van Caekenberghe <sven@stfx.eu>:
> >
> > > On 23 Jan 2015, at 20:53, Hern��n Morales Durand <hernan.morales@gmail.com> wrote:
> > >
> > > Hi Sven,
> > >
> > > 2015-01-23 16:06 GMT-03:00 Sven Van Caekenberghe <sven@stfx.eu>:
> > > Hi Hern��n,
> > >
> > > > On 23 Jan 2015, at 19:50, Hern��n Morales Durand <hernan.morales@gmail.com> wrote:
> > > >
> > > > I used to use a CSV parser from Squeak where I could attach conditional iterations:
> > > >
> > > > csvParser rowsSkipFirst: 2 do: [: row | " some action ignoring first 2 fields on each row " ].
> > > > csvParser rowsSkipLast: 2 do: [: row | " some action ignoring last 2 fields on each row " ].
> > >
> > > With NeoCSVParser you can describe how each field is read and converted, using the same mechanism you can ignore fields. Have a look at the senders of #addIgnoredField from the unit tests.
> > >
> > >
> > > I am trying to understand the implementation, I see you included #addIgnoredFields: for consecutive fields in Neo-CSV-Core-SvenVanCaekenberghe.21
> > > A question about usage then, adding ignored field(s) requires adding field types on all other remaining fields?
> >
> > Yes, like this:
> >
> > testReadWithIgnoredField
> >�� | input |
> >�� input := (String crlf join: #( '1,2,a,3' '1,2,b,3' '1,2,c,3' '')).
> >�� self
> >�� assert: ((NeoCSVReader on: input readStream)
> >�� addIntegerField;
> >�� addIntegerField;
> >�� addIgnoredField;
> >�� addIntegerField;
> >�� upToEnd)
> >�� equals: {
> >�� #(1 2 3).
> >�� #(1 2 3).
> >�� #(1 2 3).}
> >
> >
> >
> > May be you like to know if you make a pass to NeoCSV, for some data sets I have 1 million of columns, it would be nice an addFieldsInterval: or such.
>
> 1 million columns ? How is that possible, useful ?
>
> The reader is like a builder. You could try to do this yourself by writing a little loop or two.
>
> But still, 1 million ?
>
> > Thank you.
> >
> > Hern��n
> >
>
>
>