Exemplo n.º 1
0
def archive_file(input_file_name, path):
    """
    This function simply moves one file to another location.
    Its purpose is to move the xml file after it has undergone conversion
      to the archival path.
    """
    mv(input_file_name, path + input_file_name)
Exemplo n.º 2
0
    def save(self):
        if not os.path.exists(self.destination) or not os.path.isdir(self.destination):
            os.mkdir(self.destination)
            logging.info("Created a new directory for your tracked files at %s", self.destination)

        # TODO: Figure out how to copy shit
        os.mv(self.source, self.destination)
        os.symlink(self.source, self.destination)
        os.remove(self.source)

        logging.info("Successfully copied and symlink'd %s to %s", self.source, self.destination)
Exemplo n.º 3
0
 def move(self, new_basedir, path_format):
     formatted_path = path_format.format(**self.tags)
     new_dir = os.join(new_basedir, formatted_path)
     try:
         mkdir_p(new_dir)
     except OSError:
         logging.info("Directory %s already exist" % new_dir)
     #extract the extension
     try:
         ext = self.get_extension()
     except:  # TODO specify error
         logging.error("Moving file %s failed, extension is undefined"
         % self.path)
         return
     formatted_path = path_format.format(self.tags)
     new_filename = os.path.join(new_basedir, formatted_path + ext)
     try:
         os.mv(self.path, new_filename)
     except OSError:
         logging.error("Moving file %s failed, cannot move the file")
Exemplo n.º 4
0
def rename(direc, db, files):
    '''
    This isn't really for bioinformatics, this is more for the pipeline, to
    rename the files generated by cluster.py with a little human interaction.
    '''

    names = []
    seqdb = dict((s.name, s) for s in io.open(db, 'r'))
    nt_dir, aa_dir = direc + 'nt' + sep, direc + 'aa' + sep
    for f in files:
        seq = io.open(nt_dir + f, 'r').next()
        ids = seq.defline.split(', ')
        print("File\033[33;1m", f, \
              "\033[0mis described by the following sequences:")
        try:
            for id in ids:
                seqdb[id]
                print("* " + seqdb[id].name + ': ' +
                      seqdb[id].defline.split('[')[0])
        except KeyError:
            print("* (none)")
            continue
        pre = get_input("\033[33;1mWhat should we call this file " +
                        "(or hit enter to skip)? \033[0m")
        fpre = f[:f.find('.')]

        if pre != "":
            count = 0
            while True:
                rpre = pre + ((" (%d)" % count) if count > 0 else "")
                try:
                    fh = open(nt_dir + rpre + ".fasta", 'r')
                    fh.close()
                    count += 1
                    continue
                except IOError:
                    nt_old, nt_new = nt_dir + fpre, nt_dir + rpre
                    aa_old, aa_new = aa_dir + fpre, aa_dir + rpre
                    print("Renaming " + fpre + ".* to " + rpre + ".*")
                    try:
                        mv(nt_old + ".fasta", nt_new + ".fasta")
                        mv(aa_old + ".fasta", aa_new + ".fasta")
                        mv(nt_old + ".clustalw", nt_new + ".clustalw")
                        mv(aa_old + ".clustalw", aa_new + ".clustalw")
                        names.append(nt_new + '.clustalw')
                        names.append(aa_new + '.clustalw')
                    except OSError:
                        pass
                    break
    return names
Exemplo n.º 5
0

def starAndCap(st):
    ''' idea: read from st into new buf word by word until len of new buf
    >= 77, then add buf into new string with a newline and star attached '''
    buf = ''
    newst = ''
    words = st.split(' ')
    for word in words:
        if len(buf) + len(word) >= 77:
            newst += ' * ' + buf.strip() + '\n'  # kill hanging space
            buf = ''
        while len(
                word
        ) >= 77:  # comes after buf clear because that needs to happen anyway if len(word) too big
            newst += ' * ' + word[:77] + '\n'
            word = word[77:]
        buf += word + ' '
    # clear remainder of buf
    newst += ' * ' + buf.strip() + '\n'
    return newst


if __name__ == '__main__':
    for arg in argv[1:]:
        mv(arg, arg + '.bak')
        with open(arg, 'w') as f:
            cls()
            print 'FILE', arg, '\n\n\n\n'
            f.write(autodoc(arg + '.bak'))
Exemplo n.º 6
0
module = MODULE(board)

fpid = FPID('mine')

module.SetFPID(fpid)

plugin.FootprintSave(lib_path2, module)

# Verify that the same plugin instance can edge trigger on a lib_path change
# for a FootprintSave()
plugin.FootprintSave(lib_path1, module)

# create a disparity between the library's name ("footprint"),
# and the module's internal useless name ("mine").  Module is officially named "footprint" now
# but has (module mine ...) internally:
mv("%s/mine.kicad_mod" % lib_path2, "%s/footprint.kicad_mod" % lib_path2)

footprint = plugin.FootprintLoad(lib_path2, 'footprint')

fpid = footprint.GetFPID()
fpid.SetLibNickname(UTF8('mylib'))
name = fpid.Format().GetChars()  # example to get the UTF8 char buffer

# Always after a FootprintLoad() the internal name should match the one used to load it.
print("Internal name should be 'footprint': '%s'" % name)

# Verify that the same plugin instance can edge trigger on a lib_path change
# for FootprintLoad()
footprint = plugin.FootprintLoad(lib_path1, 'mine')

fpid = footprint.GetFPID()
Exemplo n.º 7
0
def trucate_video(target, start=25, end=600):

    import os
    from moviepy.video.io.ffmpeg_tools import ffmpeg_extract_subclip
    os.mv(target, target + '_original')
    ffmpeg_extract_subclip(target + '_original', start, end, targetname=target)
Exemplo n.º 8
0
from os import rename as mv
from sys import argv

if __name__ == '__main__':
    for arg in argv[1:]:
        mv(arg + '.bak', arg)
Exemplo n.º 9
0
 def move(self):
     mv(self.path, f'{self.destination}/{self.name}')
module = MODULE( board )

fpid = FPID( 'mine' )

module.SetFPID( fpid )

plugin.FootprintSave( lib_path2, module )

# Verify that the same plugin instance can edge trigger on a lib_path change
# for a FootprintSave()
plugin.FootprintSave( lib_path1, module )

# create a disparity between the library's name ("footprint"),
# and the module's internal useless name ("mine").  Module is officially named "footprint" now
# but has (module mine ...) internally:
mv( "%s/mine.kicad_mod" % lib_path2, "%s/footprint.kicad_mod" % lib_path2 )

footprint = plugin.FootprintLoad( lib_path2, 'footprint' )

fpid = footprint.GetFPID()
fpid.SetLibNickname( UTF8( 'mylib' ) )
name = fpid.Format().GetChars() # example to get the UTF8 char buffer

# Always after a FootprintLoad() the internal name should match the one used to load it.
print( "Internal name should be 'footprint': '%s'" % name  )

# Verify that the same plugin instance can edge trigger on a lib_path change
# for FootprintLoad()
footprint = plugin.FootprintLoad( lib_path1, 'mine' )

fpid = footprint.GetFPID()