Make movie subset.csh: Difference between revisions

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(Created page with " #!/usr/bin/env csh # if ($# != 3) then echo 'Usage: ' $0 ' run1_data.star particles_movie.star particles_movie_selected.star' echo 'Where run1_data.star is a sel...")
 
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  #
  #
  if ($# != 3) then  
  if ($# != 3) then  
  echo 'Usage:    ' $0 ' run1_data.star particles_movie.star  particles_movie_selected.star'
  echo 'Usage:    ' $0 ' run1_data.star particles_movie.star  particles_movie_subset.star'
  echo 'Where run1_data.star is a selection of an originally larger data set of the averaged particles.'
  echo 'Where run1_data.star is a selection of an originally larger data set of the averaged particles.'
  echo 'The input particles_movie.star contains the movie frames of the entire larger data set.'
  echo 'The input particles_movie.star contains the movie frames of the entire larger data set.'
  echo 'The output particles_movie_selected.star will contain the movie frames only for those particles in run1_data.star.'
  echo 'The output particles_movie_subset.star will contain the movie frames only for those particles in run1_data.star.'
  echo 'Using particles_movie_selected.star in a continuation of run1 will speed up the expansion of the movie frames.'
  echo 'Using particles_movie_subset.star in a continuation of run1 will speed up the expansion of the movie frames.'
  else
  else
   
   
set star_selected_particles=$1
  set star_selected_particles=$1
set star_all_movies_frame=$2
  set star_all_movies_frame=$2
set star_selected_movie_frames=$3
  set star_selected_movie_frames=$3
awk '{if (NF > 3) exit; print }' < ${star_all_movies_frame} > ${star_selected_movie_frames}
  awk '{if (NF > 3) exit; print }' < ${star_all_movies_frame} > ${star_selected_movie_frames}
 
relion_star_printtable ${star_selected_particles} data_ rlnMicrographName | sort | uniq | sed 's|.mrc||' > mics.dat
  relion_star_printtable ${star_selected_particles} data_ rlnMicrographName | sort | uniq | sed 's|.mrc||' > mics.dat
relion_star_printtable ${star_selected_particles} data_ rlnImageName > parts.dat
  relion_star_printtable ${star_selected_particles} data_ rlnImageName > parts.dat
foreach m (`cat mics.dat`)
  foreach m (`cat mics.dat`)
  grep $m ${star_all_movies_frame} > mics_part.dat
  grep $m ${star_all_movies_frame} > mics_part.dat
  grep $m parts.dat > parts_mic.dat
  grep $m parts.dat > parts_mic.dat
  foreach p (`cat parts_mic.dat`)
  foreach p (`cat parts_mic.dat`)
  grep ${p} mics_part.dat  >> ${star_selected_movie_frames}
    grep ${p} mics_part.dat  >> ${star_selected_movie_frames}
  end
  echo -n "."
   end
   end
   echo -n "."
   echo " "
end
  echo "done!"
echo " "
echo "done!"
  endif
  endif

Latest revision as of 20:29, 9 February 2015

#!/usr/bin/env csh
#
if ($# != 3) then 
 echo 'Usage:    ' $0 ' run1_data.star particles_movie.star  particles_movie_subset.star'
 echo 'Where run1_data.star is a selection of an originally larger data set of the averaged particles.'
 echo 'The input particles_movie.star contains the movie frames of the entire larger data set.'
 echo 'The output particles_movie_subset.star will contain the movie frames only for those particles in run1_data.star.'
 echo 'Using particles_movie_subset.star in a continuation of run1 will speed up the expansion of the movie frames.'
else

 set star_selected_particles=$1
 set star_all_movies_frame=$2
 set star_selected_movie_frames=$3
 awk '{if (NF > 3) exit; print }' < ${star_all_movies_frame} > ${star_selected_movie_frames}
 
 relion_star_printtable ${star_selected_particles} data_ rlnMicrographName | sort | uniq | sed 's|.mrc||' > mics.dat
 relion_star_printtable ${star_selected_particles} data_ rlnImageName > parts.dat
 foreach m (`cat mics.dat`)
  grep $m ${star_all_movies_frame} > mics_part.dat
  grep $m parts.dat > parts_mic.dat
  foreach p (`cat parts_mic.dat`)
   grep ${p} mics_part.dat  >> ${star_selected_movie_frames}
  end
  echo -n "."
 end
 echo " "
 echo "done!"
endif