Difference between revisions of "Talk:Make"
From Christoph's Personal Wiki
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A list of random make/gmake/shell commands: | A list of random make/gmake/shell commands: | ||
| − | == | + | == DSSP == |
* CPH -> RSCB -> ALIGNAA -> JNET | * CPH -> RSCB -> ALIGNAA -> JNET | ||
* Fasta file containing all pdb entries (pdb): <nowiki>ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z</nowiki> | * Fasta file containing all pdb entries (pdb): <nowiki>ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z</nowiki> | ||
| Line 12: | Line 12: | ||
done | done | ||
wait | wait | ||
| − | for pdbid in | + | for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq | gawk '{print $$1".pdb.gz"}'); |
| − | for pdbid in $$( | + | do gunzip $$pdbid; |
| + | done | ||
| + | for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq); | ||
do gmake $$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 >> $@; | |
| + | #done | ||
| + | for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq | gawk '{print $$1".fa"}'); | ||
| + | do cat $$pdbid >>$@; | ||
done | done | ||
</pre> | </pre> | ||
Latest revision as of 01:28, 18 October 2006
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
