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mirror.pl

Posted by naveen (naveen), 28 January 2008
can anyone help me out wit downloading or copying a ncbi file using a program.i read about mirror.pl.but cant understand it.

Posted by KevinAD (KevinAD), 28 January 2008
Typically you can use LWP::Simple to get pages/files from the internet. What is an ncbi file?

Posted by admin (Graham Ellis), 29 January 2008
I think an ncbi file is a bioinformatics format - similar to FastA? But, please Naveen, do post a little bit more detail of your question as you've not given us very many pointers.

Please bear in mind that we're very much advisors on helping with programs that you are writing where you come across coding problems, rather than being able to help with what could be larger programs written by others.  Post 10 or 20 lines of code and say "why can't I get this to work - I've tried X and Y" and we're in our element.  But you'll get far better advise about someone else's code by getting in touch with the people who wrote it (which you should find in the code or documentation) or support forums they and their friends have set up for the specific code if it's popular.

Posted by naveen (naveen), 31 January 2008
this is an ncbi file which i was referring to


LOCUS       ZP_01386825              252 aa            linear   BCT 20-JUL-2006
DEFINITION  PAS [Chlorobium ferrooxidans DSM 13031].
ACCESSION   ZP_01386825
VERSION     ZP_01386825.1  GI:110598556
DBSOURCE    REFSEQ: accession NZ_AASE01000022.1
KEYWORDS    .
SOURCE      Chlorobium ferrooxidans DSM 13031
 ORGANISM  Chlorobium ferrooxidans DSM 13031
           Bacteria; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae;
           Chlorobium/Pelodictyon group; Chlorobium.
REFERENCE   1  (residues 1 to 252)
 AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T.,
           Dalin,E., Tice,H., Bruce,D., Pitluck,S. and Richardson,P.
 CONSRTM   US DOE Joint Genome Institute (JGI-PGF)
 TITLE     Sequencing of the draft genome and assembly of Chlorobium
           ferroxidans DSM 13031
 JOURNAL   Unpublished
REFERENCE   2  (residues 1 to 252)
 AUTHORS   Larimer,F., Land,M. and Hauser,L.
 CONSRTM   US DOE Joint Genome Institute (JGI-ORNL)
 TITLE     Annotation of the draft genome assembly of Chlorobium ferroxidans
           DSM 13031
 JOURNAL   Unpublished
REFERENCE   3  (residues 1 to 252)
 AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T.,
           Dalin,E., Tice,H., Bruce,D., Pitluck,S. and Richardson,P.
 CONSRTM   US DOE Joint Genome Institute (JGI-PGF)
 TITLE     Direct Submission
 JOURNAL   Submitted (11-JUL-2006) US DOE Joint Genome Institute, 2800
           Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
COMMENT     PREDICTED REFSEQ: The mRNA record is supported by experimental
           evidence; however, the coding sequence is predicted. The reference
           sequence was derived from EAT58366.
           URL -- http://www.jgi.doe.gov
           JGI Project ID: 4001304
           Source DNA and Bacteria available from Don Bryant (dab14@psu.edu)
           Bacteria also available from DSMZ: DSM 13031
           Contacts: Don Bryant (dab14@psu.edu)
                     Paul Richardson (microbes@cuba.jgi-psf.org)
           Whole genome sequencing and draft assembly at JGI-PGF
           Annotation by JGI-ORNL
           The JGI and collaborators endorse the principles for the
           distribution and use of large scale sequencing data adopted by the
           larger genome sequencing community and urge users of this data to
           follow them. It is our intention to publish the work of this
           project in a timely fashion and we welcome collaborative
           interaction on the project and analysis.
           (http://www.genome.gov/page.cfm?pageID=10506376).
           Method: conceptual translation.
FEATURES             Location/Qualifiers
    source          1..252
                    /organism="Chlorobium ferrooxidans DSM 13031"
                    /strain="DSM 13031"
                    /db_xref="taxon:377431"
    Protein         1..252
                    /product="PAS"
                    /calculated_mol_wt=28517
    Region          23..110
                    /region_name="PAS"
                    /note="PAS domain; PAS motifs appear in archaea,
                    eubacteria and eukarya. Probably the most surprising
                    identification of a PAS domain was that in EAG-like
                    K+-channels; cd00130"
                    /db_xref="CDD:29035"
    Region          <29..>214
                    /region_name="PRK09776"
                    /note="predicted diguanylate cyclase, GGDEF domain
                    signaling protein; PRK09776"
                    /db_xref="CDD:77397"
    Site            order(39,43,49,62..65,90,95)
                    /site_type="other"
                    /note="putative active site"
                    /db_xref="CDD:29035"
    Site            order(59,63,71,74..75,102,104)
                    /site_type="other"
                    /note="heme pocket"
                    /db_xref="CDD:29035"
    Region          152..230
                    /region_name="PAS"
                    /note="PAS domain; PAS motifs appear in archaea,
                    eubacteria and eukarya. Probably the most surprising
                    identification of a PAS domain was that in EAG-like
                    K+-channels; cd00130"
                    /db_xref="CDD:29035"
    Site            order(156,160,166,179..182,207,212)
                    /site_type="other"
                    /note="putative active site"
                    /db_xref="CDD:29035"
    Site            order(176,180,188,190..191,219,221)
                    /site_type="other"
                    /note="heme pocket"
                    /db_xref="CDD:29035"
    CDS             1..252
                    /locus_tag="CferDRAFT_0414"
                    /coded_by="NZ_AASE01000022.1:31939..32697"
                    /note="PFAM: PAS"
                    /transl_table=11
                    /db_xref="InterPro:IPR000014"
ORIGIN      
       1 mitqgkniqq qaeqdpdrff dlipdpvciv ssdgsfrkvn aawelvlgys neellsisff
      61 dlihpedrel tikelepqaa lknrhfinry raksgdyrwl ewnanpadgg vlyatardvt
     121 crieaeeqir lladtftwca hgiaigipst krimtcnhaf aamhgmside vsgqlffdly
     181 pesehaaiqr hltelkqkds lrfetrrlkk dgsvfaaqmd ivniqddqgq galsyhnssg
     241 yhrknkargc tp
//


if i have to use this file, it has to be in my computer so that i can specify the path in the perl program. i m askin how should i get this file directly to my computer without copyin it.
is there any perl code for this.

Posted by KevinAD (KevinAD), 31 January 2008
There is no way to get it into your computer without copying it. For your perl program to be able to use the file you will have to store a copy of it to disk or memory in your computer. How you get the file depends on where it is. Unless we know where it is so we can't really provide specific information about how you can get it.



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