Hi Burak,
Your file is not FASTA. Comments in a FASTA file are lines that start
with a semi-colon:
http://en.wikipedia.org/wiki/FASTA_format
You need to fix your file first by replacing # by ; and then you should
be able to read it with read.BStringSet().
Cheers,
H.
burak kutlu wrote:
Hi
I am trying to fasta files into my session.
Is there a way to ignore the comment lines ( that start with #) when using
read.BStringSet?
Here's the error I get when there are such lines at the beginning of the fasta
file.
read.BStringSet(file= 'burak.test', format = "fasta")
Error in .read.fasta.in.XStringSet(filepath, set.names, elementType, lkup) :
reading FASTA file : ">" expected at beginning of line 1
And this is how the file looks like
# Cwd: /home/pipeline
# Title: solid0131_20090316_1_H683_
2_21_1117_F3
T00212313200111233020001110130100100
2_21_1543_F3
T01022123123230121000121013333113111
.....
Many thanks
-burak
sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.2 Biostrings_2.14.8
[5] IRanges_1.4.9
loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.10.1 hwriter_1.1 tools_2.10.1
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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