csfasta --> fasta conversion

[doxologist]

I have a fast trivial question:
what's the fastest/easier way to "decode" or convert the csfasta to fasta? I'm just doing this for a handful at a time for code-checking.

thanks in advance.

[lgoff]

Comparing?

Are you looking to benchmark methods or just need to decode a set of sequences? Contact me directly if you would like a python module for SOLiD sequence manipulation(s) including csfasta --> fasta.

[Rao]

You mean converting colorspace seq.. to basespace seq...

[westerman]

The ABI 'corona lite' programs (which are free) include 'encodeFasta.py' which will encode and decode to/from color-space, base-space and that abomination 'double-encoded'-space.

[doxologist]

Are you looking to benchmark methods or just need to decode a set of sequences? Contact me directly if you would like a python module for SOLiD sequence manipulation(s) including csfasta --> fasta.

just for trivial conversion... decode

[jsun529]

The ABI 'corona lite' programs (which are free) include 'encodeFasta.py' which will encode and decode to/from color-space, base-space and that abomination 'double-encoded'-space.

I get an error message run that code with :
ImportError: No module named agapython.util.Dibase

Where do I get the module? I run both code on Linux(ubuntu) and mac terminal, neither work

[westerman]

The module should come with corona lite. I suspect that you do not have your corona lite setup environment set up properly. From the README:

3) Configure your environment *

For csh/tcsh:
% setenv CORONAROOT <INSTALL_DIR>/corona_lite
% source $CORONAROOT/etc/profile.d/corona.csh

For sh/ksh/bash:
%export CORONAROOT=<INSTALL_DIR>/corona_lite
%source $CORONAROOT/etc/profile.d/corona.sh

* Remember to update your shell's init script (.cshrc, .bashrc,
etc.) for future sessions with Corona Lite.

[roedel]

csfasta -&gt; fasta

When I tried to register at ABI to download the CORONA-lite program, I did not receive a confirmation. Then I used the colour scheme given in

https://www.iscb.org/uploaded/css/36/12104.pdf

to write a perl script that does the conversion. As far as I understood, the first base in the csfasta is part of the adaptor sequence and should therefore be omitted in the fasta. This can be triggered by setting the shift parameter to 1 (0 would repeat the first base).

./csfasta2fasta.pl seqence.csfasta 1 > output.fasta

If anyone could tell me if this does approximately the same as the CORONA-lite conversion script, I would be happy.

[chiuchengliu]

When I tried to register at ABI to download the CORONA-lite program, I did not receive a confirmation. Then I used the colour scheme given in

https://www.iscb.org/uploaded/css/36/12104.pdf

to write a perl script that does the conversion. As far as I understood, the first base in the csfasta is part of the adaptor sequence and should therefore be omitted in the fasta. This can be triggered by setting the shift parameter to 1 (0 would repeat the first base).

./csfasta2fasta.pl seqence.csfasta 1 > output.fasta

If anyone could tell me if this does approximately the same as the CORONA-lite conversion script, I would be happy.

Your script works well except for an extra ">\n" in the output file.

ps: the translation of cs to bs loses the independent quality of adjacent color spaces. say, one miscalled colorspace in the middle will spoil the latter half bases.

[yoyoq]

thank you for that tool,

what the hell is double encoded fasta?

[westerman]

'Double-encoded' is where a color-space file is encoded as ACGT. Said ACGT is not base space but a way to encode the 0123 of color-space into something that non color-space aware programs can use.

As an example, given the base-space sequence:

GTGCACCGTGCACG

This encodes into color-space:

G1131103113113

And can be double-encoded into:

GCCTCCATCCTCCT

Double-encoding is simple. 0 goes to 'A', 1 to 'C', etc. As I mention it is simply a way to make color-space into ACGT. I call it an abomination since it means nothing biologically useful yet looks like a biological sequence. It can lead to all sorts of false results if one does not realize what one is dealing with.

[yoyoq]

thanks

thanks,
yes i can confirm that it leads to biological confusion.

[yoyoq]

slight mod to conversion perl script

modified the conversion to avoid making that huge hash.
i was hitting memory limits the old way.

[mbreese]

The included colorspace -> basespace mapping is missing a few entries. Basically anything that includes a '4' or '.' is an N.

(Python format)
__colorspace = {
'A0': 'A',
'A1': 'C',
'A2': 'G',
'A3': 'T',
'A4': 'N',
'A.': 'N',
'C0': 'C',
'C1': 'A',
'C2': 'T',
'C3': 'G',
'C4': 'N',
'C.': 'N',
'G0': 'G',
'G1': 'T',
'G2': 'A',
'G3': 'C',
'G4': 'N',
'G.': 'N',
'T0': 'T',
'T1': 'G',
'T2': 'C',
'T3': 'A'
'T4': 'N',
'T.': 'N',
'N0': 'N',
'N1': 'N',
'N2': 'N',
'N3': 'N',
'N.': 'N',
}

[westerman]

Actually you are also missing '5' and '6'. Also what about base-space that isn't an N (e.g., R, Y, etc.). Using a table like the above -- which is what the ABI-provided encodeFasta.py program uses -- is a poor way of handling the conversion IMHO. Unless you want to force non-1,2,3,4 to being a 4 and non-A,C,G,T to an N.