Automatization of Sequence Handling (Staden's pregap4 and gap4)
By jeltsch on Sat, 05/19/2007 - 19:41Already a while ago I wrote a script, that tries to automatize most of the work involved in getting sequences from our ABI sequencer into a gap4 database. The script is far from perfect and looks like this:
!/bin/sh rm *.seq *.log Log\ file.txt for i in `ls *.ab1`; do echo "Renaming $i" mv $i `echo $i | sed "s/\(.\{27\}\).*/\1\.ab1/"` done ls *.ab1 *.txt > tracefile.list pregap4 -nowin -config /home/jeltsch/bin/pregap4_gap4.conf -fofn tracefile.list gap4 test.0.aux