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)
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)
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")
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
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'))
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()
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)
from os import rename as mv
from sys import argv
if __name__ == '__main__':
for arg in argv[1:]:
mv(arg + '.bak', arg)
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()
