# this works as a bash include
#
#COMM diagnosis flag "SrcMulti", attribute to sequence data structure
#COMM - note, we check on a selection of parsing functions. The same (?) code
#COMM   constructs are used elsewhere

# give include precedence to code directory, perl -I would not work!
PERLPATH_SV="$PERLPATH"
export PERLPATH="$dircode"

echo --- single physical, fastA format ---
perl "$dircode"/SeqHandle.pl $dirtest/test_seq_ntsing.fa -OutSeqFmt=struct | grep SrcMulti
perl "$dircode"/SeqHandle.pl $dirtest/test_seq_prot.fa -OutSeqFmt=struct | grep SrcMulti
echo --- single piped, fastA format ---
cat $dirtest/test_seq_ntsing.fa | perl "$dircode"/SeqHandle.pl - -OutSeqFmt=struct | grep SrcMulti
cat $dirtest/test_seq_prot.fa | perl "$dircode"/SeqHandle.pl - -OutSeqFmt=struct | grep SrcMulti
echo --- multi physical, fastA format ---
perl "$dircode"/SeqHandle.pl $dirtest/test_seq_ntmult.fa -OutSeqFmt=struct | grep SrcMulti
echo --- multi piped, fastA format ---
cat $dirtest/test_seq_ntmult.fa | perl "$dircode"/SeqHandle.pl - -OutSeqFmt=struct | grep SrcMulti
echo --- multi physical, Experiment format ---
perl "$dircode"/SeqHandle.pl $dirtest/test_seq_ntmult.exp -OutSeqFmt=struct  \
 | grep SrcMulti  \
 | head -3

export PERLPATH="$PERLPATH_SV"
