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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
