Difference between revisions of "Talk:Make"
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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 | ||
| + | * Fasta file containing all pdb entries (pdb): <nowiki>ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z</nowiki> | ||
| + | * Non-redundant database of known protein sequences (sp) compiled from files: <nowiki>ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/fasta/*.fas.gz</nowiki> (Swiss-prot) | ||
| + | * PDB entries: <nowiki>ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/</nowiki> | ||
<pre> | <pre> | ||
| − | for pdbid in $(cat | + | %.cph.fa: %.cph |
| − | + | for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq); | |
| − | done | + | do wget http://www.rcsb.org/pdb/files/$$pdbid.pdb.gz; |
| − | wait | + | done |
| − | for pdbid in | + | wait |
| − | + | for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq | gawk '{print $$1".pdb.gz"}'); | |
| − | done | + | do gunzip $$pdbid; |
| − | for pdbid in $( | + | done |
| − | + | for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq); | |
| − | done | + | do gmake $$pdbid.fa; |
| − | for pdbid in *.fa; | + | done |
| − | do perl multi_alignaa.pl | + | #for pdbid in *.fa; |
| − | done | + | # 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 $$pdbid >>$@; | ||
| + | done | ||
</pre> | </pre> | ||
Latest revision as of 01:28, 18 October 2006
A list of random make/gmake/shell commands:
DSSP
- CPH -> RSCB -> ALIGNAA -> JNET
- Fasta file containing all pdb entries (pdb): ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z
- Non-redundant database of known protein sequences (sp) compiled from files: ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/fasta/*.fas.gz (Swiss-prot)
- PDB entries: ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/
%.cph.fa: %.cph
for pdbid in $$(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
