Talk:Make - Revision history

Christoph at 01:28, 18 October 2006

2006-10-18T01:28:46Z

Christoph at 23:21, 17 October 2006

2006-10-17T23:21:08Z

Christoph at 23:20, 17 October 2006

2006-10-17T23:20:35Z

Christoph at 22:54, 17 October 2006

2006-10-17T22:54:39Z

Christoph at 21:58, 17 October 2006

2006-10-17T21:58:06Z

New page

A list of random make/gmake/shell commands:

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

@@ Line 12: / Line 12: @@
          done
          wait
-         for pdbid in *.gz; do gunzip $$pdbid; done
+         for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq | gawk '{print $$1".pdb.gz"}');
-         for pdbid in $$(for pdbid in *.pdb; do basename $$pdbid .pdb; done);
+                do gunzip $$pdbid;
                  do gmake $$pdbid.fa;
          done
-         for pdbid in *.fa;
+         #for pdbid in *.fa;
-                do perl multi_alignaa.pl $(shell basename $< .cph).fa $$pdbid >> $@;
+        #       do perl multi_alignaa.pl $(shell basename $< .cph).fa $$pdbid >> $@;
          done
 </pre>

@@ Line 1: / Line 1: @@
 A list of random make/gmake/shell commands:
-== Align ==
+== DSSP ==
 * CPH -> RSCB -> ALIGNAA -> JNET
 * Fasta file containing all pdb entries (pdb): <nowiki>ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z</nowiki>

@@ Line 1: / Line 1: @@
 A list of random make/gmake/shell commands:
 <pre>
 %.cph.fa:       %.cph

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