[Bioperl-l] Repeatmasker scripts
daray
david.ray at mail.wvu.edu
Fri Mar 9 00:41:11 UTC 2007
I'm new here and new to BioPerl. Please let me know if I am breaking any
rules.
Does anyone know of scripts designed to parse repeatmasker output so that
split repetitive elements can be recovered as a single row? I tried a
search but I am either searching for the wrong terms or there isn't anything
to find. Below is an example of what I would like to do but any comparable
system would be useful.
This is the output, single elements are split over two lines.
591 7.1 0 2.4 Mluc_cont1.010442 1392 1478 -967 C Tc2_ML1_coding Unknown 0
1296 1212 1
3825 4.7 0.6 1 Mluc_cont1.010442 1470 1959 -486 C Tc2_ML1_coding Unknown
-808 488 1 1
1816 7 0 7 Mluc_cont1.010866 3614 3890 -836 C Tc2_ML1_coding Unknown -1037
259 1 2
596 3.6 2.4 2.4 Mluc_cont1.011200 1155 1239 -847 C Tc2_ML1_coding Unknown 0
1296 1212 3
3848 5.2 0.8 0.6 Mluc_cont1.011200 1231 1717 -369 C Tc2_ML1_coding Unknown
-808 488 1 3
It would be nice to combine the multiple entries as follows or do something
similar.
591 7.1 0 2.4 Mluc_cont1.010442 1392 1959 -967 C Tc2_ML1_coding Unknown 0
1296 1212 1
1816 7 0 7 Mluc_cont1.010866 3614 3890 -836 C Tc2_ML1_coding Unknown -1037
259 1 2
596 3.6 2.4 2.4 Mluc_cont1.011200 1155 1717 -847 C Tc2_ML1_coding Unknown 0
1296 1212 3
Any help would be appreciated.
--
View this message in context: http://www.nabble.com/Repeatmasker-scripts-tf3372839.html#a9385755
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
More information about the Bioperl-l
mailing list