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sh-miR / designer

sh-miR Designer is a software aimed for fast and efficient design of effective RNA interference (RNAi) reagents - sh-miRs, also known as artificial miRNAs.
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mfold - użytkowanie #13

Closed ghost closed 10 years ago

ghost commented 11 years ago

postawienie na serwerze mfolda i ogarnięcie korzystania, tzn. napisanie funkcji korzystającej tzn. bierzemy długiego stringa, wrzucamy w program i odbieramy RNAml.

Nozdi commented 11 years ago

Hahaha ten task to jakiś zabójca, bo póki co nie udało nam się znaleźć kodu mfold'a, ani biblioteki.

Co prawda udostępniane są binarki: http://mfold.rit.albany.edu/?q=mfold/download-mfold To co piszemy jakiś pythonowy interfejs do tych binarek? Można szukać dalej ale research nic nam nie dał... Może teraz wszyscy poszukamy czegoś, może ktoś znajdzie bo jeśli nie to trzeba napisać interfejs komunikujacy się z binarkami.... :-1:

nhlfr commented 11 years ago

Moja próba kompilacji mfolda:

$ make all g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/batgen src/batgen.f src/getseq.f src/batgen.f: In subroutine `efiles': src/batgen.f:615: warning: 50 write(outunit,2) ' Miscloop',miscloop 1 src/batgen.f:666: (continued): go to 50 2 Reference to label at (2) is outside block containing definition at (1) ld: warning: -macosx_version_min not specified, assuming 10.6 g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/distance src/distance.f src/bpin.f src/bpsrch.f ld: warning: -macosx_version_min not specified, assuming 10.6 gcc -O -Wno-deprecated -fomit-frame-pointer -o bin/ct2rnaml src/ct2rnaml.c cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/ct_compare src/ct_compare.f ld: warning: -macosx_version_min not specified, assuming 10.6 gcc -O -Wno-deprecated -fomit-frame-pointer -o bin/ct_boxplot_ng src/ct_boxplot_ng.c -lm cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C In file included from src/ct_boxplot_ng.c:65: src/ct_boxplot_gif.inc: In function ‘finish_making_gif’: src/ct_boxplot_gif.inc:729: warning: format not a string literal and no format arguments src/ct_boxplot_gif.inc:729: warning: format not a string literal and no format arguments g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/efn src/efn.f ld: warning: -macosx_versionmin not specified, assuming 10.6 g++ -O -Wno-deprecated -fomit-frame-pointer -o bin/efn2 c++/efn2.cpp -lm In file included from c++/efn2.cpp:3: c++/algorithm.cpp: In function ‘char* tobase(int)’: c++/algorithm.cpp:4584: warning: deprecated conversion from string constant to ‘char’ c++/algorithm.cpp:4585: warning: deprecated conversion from string constant to ‘char’ c++/algorithm.cpp:4586: warning: deprecated conversion from string constant to ‘char’ c++/algorithm.cpp:4587: warning: deprecated conversion from string constant to ‘char’ c++/algorithm.cpp:4588: warning: deprecated conversion from string constant to ‘char’ c++/algorithm.cpp:4589: warning: deprecated conversion from string constant to ‘char’ c++/algorithm.cpp:4590: warning: deprecated conversion from string constant to ‘char’ g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/newtemp src/ion.f src/dc.f src/newtemp.f ld: warning: -macosx_version_min not specified, assuming 10.6 g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/scorer src/scorer.f ld: warning: -macosx_version_min not specified, assuming 10.6 g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/auxgen src/auxgen.f ld: warning: -macosx_version_min not specified, assuming 10.6 echo " parameter (maxn=8000)" > src/maxn.inc g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/sav2plot src/sav2plot.f ld: warning: -macosx_version_min not specified, assuming 10.6 g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/sav2p-num src/sav2p-num.f ld: warning: -macosx_version_min not specified, assuming 10.6 g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/h-num.exe src/h-num.f ld: warning: -macosx_version_min not specified, assuming 10.6 g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/ss-count src/ss-count.f ld: warning: -macosx_version_min not specified, assuming 10.6 g77 -O3 -C -fno-automatic -ffixed-line-length-none -o bin/add-dHdSTm src/add-dHdSTm.f ld: warning: -macosx_version_min not specified, assuming 10.6 _cat src/main.f | sed 's/^cNODOT/ /' > src/main-nodot.f sed: RE error: illegal byte sequence make: \ [src/main-nodot.f] Error 1

Linijka pogrubiona przeze mnie, tu się wywala.

Niech ktoś z was też spróbuje. Paczka ze źródłami jest tu: http://mfold.rit.albany.edu/download/mfold-3.1.2.tar.gz Potrzebny jest g77 (taki jeden stary kompilator Fortrana).

Nozdi commented 11 years ago

Paczka z nowymi źródłami http://mfold.rna.albany.edu/download/mfold-3.6.tar.gz ,

[sudo] apt-get install gfortran libgd2-xpm-dev gawk texlive-font-utils
./configure --prefix=/usr/local
make all
[sudo] make install
Nozdi commented 11 years ago

Z jakich opcji będziemy korzystać? - Martyna!

Usage is
mfold SEQ='file_name' with optional parameters:
    [ AUX='auxfile_name' ] [ RUN_TYPE=text (default) or html ]
    [ NA=RNA (default) or DNA ] [ LC=sequence type (default = linear) ]
    [ T=temperature (default = 37 deg C) ] [ P=percent (default = 5) ]
    [ NA_CONC=Na+ molar concentration (default = 1.0) ]
    [ MG_CONC=Mg++ molar concentration (default = 0.0) ]
    [ W=window parameter (default - set by sequence length) ]
    [ MAXBP=max base pair distance (default - no limit) ]
    [ MAX=maximum number of foldings to be computed (default 100) ]
    [ MAX_LP=maximum bulge/interior loop size (default 30) ]
    [ MAX_AS=maximum asymmetry of a bulge/interior loop (default 30) ]
    [ ANN=structure annotation type: none (default), p-num or ss-count ]
    [ MODE=structure display mode: auto (default), bases or lines ]
    [ LAB_FR=base numbering frequency ] [ ROT_ANG=structure rotation angle ]
    [ START=5' base # (default = 1)] [ STOP=3' base # (default = end) ]
    [ REUSE=NO/YES (default=NO) reuse existing .sav file ]
ghost commented 11 years ago

Możemy zmniejszyć MAX, ale po za tym to lecimy na defaultach

Nozdi commented 11 years ago

Możecie spróbować zinstalować to na waszych maszynach, u mnie auxgen cały czas wywala, może źle to instaluje... Sprawa wygląda tak jakbym w ogóle nie instalował auxgena (nie ma go w tej paczce?) .

nhlfr commented 11 years ago

Nawet jak nie masz zainstalowanego auxgena, to configure powinno Cię powinno informować o takich faktach, więc tak czy inaczej to ich fail. Sprawdzę u siebie jakoś wieczorem / późnym popołudniem

Nozdi commented 11 years ago

Po zainstalowaniu fortrana (f77)jest auxgen, ale nadal nie ma nafold, dodaje do schematu instalacji fortrana :D

Nozdi commented 11 years ago

gfortran kompiluje.

Nozdi commented 11 years ago

http://mfold.rna.albany.edu/?q=mfold/documentation tutaj opis, ale nic o rnaml, więc napisałem na forum: http://mfold.rna.albany.edu/?q=node/537

Nozdi commented 10 years ago

mfold jest na serwerze?

Nozdi commented 10 years ago

Server nie ma mfolda.