Talk:Make

A list of random make/gmake/shell commands:

DSSP

• CPH -> RSCB -> ALIGNAA -> JNET
• Fasta file containing all pdb entries (pdb): ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z
• Non-redundant database of known protein sequences (sp) compiled from files: ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/fasta/*.fas.gz (Swiss-prot)
• PDB entries: ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/

%.cph.fa:       %.cph
        for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq);
                do wget http://www.rcsb.org/pdb/files/$$pdbid.pdb.gz;
        done
        wait
        for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq | gawk '{print $$1".pdb.gz"}');
                do gunzip $$pdbid;
        done
        for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq);
                do gmake $$pdbid.fa;
        done
        #for pdbid in *.fa;
        #       do perl multi_alignaa.pl $(shell basename $< .cph).fa $$pdbid >> $@;
        #done
        for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq | gawk '{print $$1".fa"}');
                do cat $$pdbid >>$@;
        done