Hello Gentlepeople,
I am interested in using regular expressions to search the human genome
for occurrences of my favorite motif. I need coordinate values for each
hit. I chose the EMBOSS program "dreg" for this task. I have a set of
of fasta files; I have one fasta file per human chromosome. I wish to
index these files with dbifasta so that I can use the dreg program for
the regex search.
I use the following command:
m...@mycpu$ dbifasta -dbname UCSC_hg19_softmask -idformat simple
-directory /storage/EMBOSS/Emboss_DB -filenames *.fa -release hg19 -date
01/04/11 -outfile /storage/EMBOSS/Emboss_DB/logfile.dbifasta
And receive the following error:
Error: Argument 'seq01' : Too many parameters 2/1
...the file that holds the chromosome sequences are named seq00.fa,
seq01.fa, seq02.fa ... so on.
Any sort of help is greatly appreciated.
Thank you for your time in developing and maintaining this resource!
-Lionel Brooks III
Genetics Grad Student
Dartmouth College
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