def assemble(options):
# check output directory
out_dir = create_dir(options['--output'])
# check tophat results
tophat_dir = options['--tophat']
# check cufflinks
if which('cufflinks') is None:
sys.exit('Cufflinks is required for CIRCexplorer2 assemble!')
# check genePredToGtf
if which('genePredToGtf') is None:
sys.exit('genePredToGtf is required for CIRCexplorer2 assemble!')
# check gtfToGenePred
if which('gtfToGenePred') is None:
sys.exit('gtfToGenePred is required for CIRCexplorer2 assemble!')
# prepare cufflinks directory
cufflinks_dir = out_dir
create_dir(cufflinks_dir)
# filter ref file
ref_filter(options['--ref'], tophat_dir, cufflinks_dir)
# assemble with cufflinks
cufflinks_assemble(tophat_dir, cufflinks_dir, options['--thread'],
options['--remove-rRNA'], options['--max-bundle-frags'])
# convert assembly results
convert_assembly_gtf(tophat_dir, cufflinks_dir, options['--ref'],
options['--bb'], options['--chrom-size'])
def run(self):
"""Run fastqc and fastqc report"""
fq_files = []
# list fastq files
for x in self.input:
q1 = self.get_fq_files(x)
fq_files.extend(q1)
if not os.path.exists(self.output):
os.makedirs(self.output)
fastqc_exe = which('fastqc')
# check fastqc output
log.info('fastqc')
fq_files = self.check_fastqc(self.output, fq_files, overwrite=False)
# run fastqc
fq_list = ' '.join(fq_files)
cmd1 = '{} -t 8 -o {} {} 2> {}'.format(fastqc_exe, self.output,
fq_list,
self.output + '.fastqc.log')
# cmd1 = 'fastqc -t 8 -o %s %s' % (self.output, fq_list)
if len(fq_files) > 0:
run_shell_cmd(cmd1)
# self.run_shell_cmd(cmd1)
# fastqc report
log.info('fastqc-report')
main_script = os.path.realpath(__file__)
home = os.path.dirname(main_script)
report_r = os.path.join(home, 'qc_report.R')
report_html = os.path.join(self.output, 'fastqc_report.html')
## for update template
if self.template is None:
self.template = ''
elif os.path.exists(self.template):
self.template = os.path.abspath(self.template)
else:
self.template = ''
Rscript_exe = which('Rscript')
cmd2 = ' '.join([Rscript_exe, report_r, self.output, self.template])
if os.path.exists(report_html):
log.info('file exists, fastqc-report skipped')
else:
run_shell_cmd(cmd2)
if not os.path.exists(report_html):
log.error('failed, generating html file')
# finish
log.info('output - %s' % report_html)
def main(hostname, port, ca_file, clientcert_file, server_certificates, proxy, insecure):
print_h1("Überprüfe Systemvorraussetzungen")
if which('openssl')==None:
logger.error('Could not find openssl in the path. Please install openssl and add it to the path. The call this script again. Will exit now.')
exit (1)
if server_certificates is None and proxy is not None:
if ssl.OPENSSL_VERSION_NUMBER < 9999999999: # TODO: ab welcher version von openssl wird --proxy unterstuetz
logger.error('Your version of OpenSSL does not support proxy setting. Please install OpenSSL x.x.x or later or try --servercertificates argument.')
exit(1)
if ca_file is not None:
if os.path.exists(ca_file):
logger.info("Using the following ca certificate file: "+ca_file)
else:
logger.error("ca file not found")
sys.exit()
else:
logger.info("No dedicated ca_file provided. Using system ca.")
if clientcert_file is not None:
if os.path.exists(clientcert_file):
logger.info("Using the following client certificate file: "+clientcert_file)
else:
logger.info("client certificate file not found.")
sys.exit()
if which('sslyze')==None:
logger.error('Could not find sslyze in the path. Please install sslyze and add it to the path. The call this script again. Will exit now.')
exit (1)
svr=Server(hostname,port,ca_file,clientcert_file,server_certificates, split_proxy(proxy), insecure)
svr.test_server_for_protocol()
svr.read_certificates(server_certificates)
if len(svr.certs)<1:
logger.error("Zertifikate konnten nicht gelesen werden.")
exit (1)
svr.certs[0].check_leaf_certificate()
if len(svr.certs)>1:
svr.certs[-1].check_root_certificate()
if len(svr.certs)>2:
for crt in svr.certs[1:-1]:
crt.check_intermediate_certificate()
def tophat_map(gtf, out_dir, prefix, fastq, thread, bw=False, scale=False,
gtf_flag=1):
'''
1. Map reads with TopHat2
2. Extract unmapped reads
3. Create BigWig file if needed
'''
# tophat2 mapping
print('Map reads with TopHat2...')
tophat_cmd = 'tophat2 -g 1 --microexon-search -m 2 '
if gtf_flag:
tophat_cmd += '-G %s ' % gtf
tophat_cmd += '-p %s -o %s ' % (thread, out_dir + '/tophat')
tophat_cmd += '%s/bowtie2_index/%s ' % (out_dir, prefix) + ','.join(fastq)
tophat_cmd += ' 2> %s/tophat.log' % out_dir
print('TopHat2 mapping command:')
print(tophat_cmd)
return_code = os.system(tophat_cmd) >> 8
if return_code:
sys.exit('Error: cannot map reads with TopHat2!')
# extract unmapped reads
print('Extract unmapped reads...')
unmapped_bam = pybedtools.BedTool('%s/tophat/unmapped.bam' % out_dir)
unmapped_bam.bam_to_fastq(fq='%s/tophat/unmapped.fastq' % out_dir)
# create Bigwig file if needed
if bw and which('bedGraphToBigWig') is not None:
print('Create BigWig file...')
map_bam_fname = '%s/tophat/accepted_hits.bam' % out_dir
# index bam if not exist
if not os.path.isfile(map_bam_fname + '.bai'):
pysam.index(map_bam_fname)
map_bam = pysam.AlignmentFile(map_bam_fname, 'rb')
# extract chrom size file
chrom_size_fname = '%s/tophat/chrom.size' % out_dir
with open(chrom_size_fname, 'w') as chrom_size_f:
for seq in map_bam.header['SQ']:
chrom_size_f.write('%s\t%s\n' % (seq['SN'], seq['LN']))
if scale: # scale to HPB
mapped_reads = map_bam.mapped
for read in map_bam:
read_length = read.query_length
break
s = 1000000000.0 / mapped_reads / read_length
else:
s = 1
map_bam = pybedtools.BedTool(map_bam_fname)
bedgraph_fname = '%s/tophat/accepted_hits.bg' % out_dir
with open(bedgraph_fname, 'w') as bedgraph_f:
for line in map_bam.genome_coverage(bg=True, g=chrom_size_fname,
scale=s, split=True):
value = str(int(float(line[3]) + 0.5))
bedgraph_f.write('\t'.join(line[:3]) + '\t%s\n' % value)
bigwig_fname = '%s/tophat/accepted_hits.bw' % out_dir
return_code = os.system('bedGraphToBigWig %s %s %s' %
(bedgraph_fname, chrom_size_fname,
bigwig_fname)) >> 8
if return_code:
sys.exit('Error: cannot convert bedGraph to BigWig!')
else:
print('Could not find bedGraphToBigWig, so skip this step!')
def main(hostname, port, ca_file, server_certificates, proxy):
print_h1("Überprüfe Systemvorraussetzungen")
if which('openssl') == None:
logger.error(
'Could not find openssl in the path. Please install openssl and add it to the path. The call this script again. Will exit now.'
)
exit(1)
if server_certificates is None and proxy is not None:
if ssl.OPENSSL_VERSION_NUMBER < 9999999999: # TODO: ab welcher version von openssl wird --proxy unterstuetz
logger.error(
'Your version of OpenSSL does not support proxy setting. Please install OpenSSL x.x.x or later or try --servercertificates argument.'
)
exit(1)
if ca_file is None:
logger.info("No dedicated ca_file provided. Using default vaule.")
ca_file = ssl.get_default_verify_paths().openssl_cafile
logger.info("Using the follwing ca_file: " + ca_file)
if which('sslyze') == None:
logger.error(
'Could not find sslyze in the path. Please install sslyze and add it to the path. The call this script again. Will exit now.'
)
exit(1)
svr = Server(hostname, port, ca_file, server_certificates,
split_proxy(proxy))
svr.test_server_for_protocol()
svr.read_certificates(server_certificates)
svr.certs[0].check_leaf_certificate()
if len(svr.certs) > 1:
svr.certs[-1].check_root_certificate()
if len(svr.certs) > 2:
for crt in svr.certs[1:-1]:
crt.check_intermediate_certificate()
def align(options):
# check options
if options['--skip-tophat'] and options['--skip-tophat-fusion']:
sys.exit('Cannot set --skip-tophat and --skip-tophat-fusion together!')
if not options['--genome']:
if not options['--bowtie1'] and not options['--skip-tophat-fusion']:
sys.exit('TopHat-Fusion require bowtie1 index files!')
elif not options['--bowtie2'] and not options['--skip-tophat']:
sys.exit('TopHat2 require bowtie2 index files!')
skip_tophat = True if options['--skip-tophat'] else False
skip_tophat_fusion = True if options['--skip-tophat-fusion'] else False
# check output directory
out_dir = check_outdir(options['--output'])
# check tophat
if which('tophat2') is None:
sys.exit('TopHat2 is required for CIRCexplorer2 align!')
# check index files
if options['--genome']: # build index
index_flag = (True, skip_tophat, skip_tophat_fusion)
prefix1, prefix2 = check_index(index_flag, out_dir,
options['--genome'],
options['--thread'])
else: # index exist
index_flag = (False, skip_tophat, skip_tophat_fusion)
prefix1, prefix2 = check_index(
index_flag, out_dir, (options['--bowtie1'], options['--bowtie2']),
options['--thread'])
if not skip_tophat:
# tophat2 mapping
tophat_map(options['--gtf'],
out_dir,
prefix2,
options['<fastq>'],
options['--thread'],
bw=options['--bw'],
scale=options['--scale'])
if not skip_tophat_fusion:
# tophat fusion mapping
if skip_tophat: # skip tophat, so use fastq files directly
tophat_fusion_map(out_dir,
prefix1,
options['--thread'],
fq=options['<fastq>'])
else:
tophat_fusion_map(out_dir, prefix1, options['--thread'])
# parse tophat fusion results
fusion_bam_f = '%s/tophat_fusion/accepted_hits.bam' % out_dir
out = '%s/fusion_junction.bed' % out_dir
tophat_fusion_parse(fusion_bam_f, out)
def convert_assembly_gtf(tophat_dir, cufflinks_dir, ref, bb, chrom_size):
'''
1. Convert Cufflinks GTF to GenePred
2. Add gene symbols
3. Convert to BigBed file if needed
'''
# convert cufflinks gtf to genepred
print('Convert Cufflinks GTF to GenePred...')
gtf_path = '%s/transcripts.gtf' % cufflinks_dir
genePred_path = '%s/transcripts.txt' % cufflinks_dir
return_code = os.system('gtfToGenePred %s %s' %
(gtf_path, genePred_path)) >> 8
if return_code:
sys.exit('Error: cannot convert gtf to GenePred!')
# add gene symbol
print('Add gene symbols...')
with open(ref, 'r') as ref_f:
gene_symbol = {line.split()[1]: line.split()[0] for line in ref_f}
ref_path = '%s/transcripts_ref.txt' % cufflinks_dir
with open(genePred_path, 'r') as genePred_f, open(ref_path, 'w') as ref_f:
for line in genePred_f:
iso = line.split()[0]
symbol = gene_symbol[iso] if iso in gene_symbol else iso
ref_f.write(symbol + '\t' + line)
# convert to bigbed if needed
if bb:
if which('bedToBigBed') is not None:
print('Convert to BigBed file...')
if not chrom_size: # no chromsize file, search it in tophat folder
chrom_size = '%s/tophat/chrom.size' % tophat_dir
if not os.path.isfile(chrom_size):
sys.exit('Please offer the path of chrom.size!')
bed_path = '%s/transcripts_ref.bed' % cufflinks_dir
genepred_to_bed(ref_path, bed_path)
sorted_bed_path = '%s/transcripts_ref_sorted.bed' % cufflinks_dir
bed = pybedtools.BedTool(bed_path)
bed = bed.sort()
bed.saveas(sorted_bed_path)
bb_path = '%s/transcripts_ref_sorted.bb' % cufflinks_dir
return_code = os.system(
'bedToBigBed -type=bed12 %s %s %s' %
(sorted_bed_path, chrom_size, bb_path)) >> 8
if return_code:
sys.exit('Error: cannot convert bed to BigBed!')
else:
print('Could not find bedToBigBed, so skip this step!')
def align(options):
# check output directory
out_dir = check_outdir(options['--output'])
# check tophat
if which('tophat2') is None:
sys.exit('TopHat2 is required for CIRCexplorer2 align!')
# check index files
if options['--genome']: # build index
prefix1, prefix2 = check_index(False, out_dir, options['--genome'])
else: # index exist
prefix1, prefix2 = check_index(True, out_dir, (options['--bowtie1'],
options['--bowtie2']))
# tophat2 mapping
tophat_map(options['--gtf'], out_dir, prefix2, options['<fastq>'],
options['--thread'], bw=options['--bw'],
scale=options['--scale'])
if not options['--no-tophat-fusion']:
# tophat fusion mapping
tophat_fusion_map(out_dir, prefix1, options['--thread'])
def anno_run(fn, fout, flog, genome):
"""Run annotatePeaks.pl from HOMER"""
assert os.path.exists(fn)
assert isinstance(fout, str)
assert isinstance(flog, str)
assert isinstance(genome, str)
annotatePeaks = which('annotatePeaks.pl')
if annotatePeaks is None:
raise ValueError('%10s | command not found: annotatePeaks.pl' %
'failed')
logging.info('running annotatePeaks.pl for %s' % os.path.basename(fn))
c1 = '%s %s %s' % (annotatePeaks, fn, genome)
with open(fout, 'wt') as ffout, open(flog, 'wt') as fflog:
p1 = subprocess.run(shlex.split(c1), stdout=ffout, stderr=fflog)
if os.path.exists(fout):
return fout
else:
return None
def align(options):
# check output directory
out_dir = check_outdir(options['--output'])
# check tophat
if which('tophat2') is None:
sys.exit('TopHat2 is required for CIRCexplorer2 align!')
# check index files
if options['--genome']: # build index
prefix1, prefix2 = check_index(False, out_dir, options['--genome'])
else: # index exist
prefix1, prefix2 = check_index(
True, out_dir, (options['--bowtie1'], options['--bowtie2']))
# tophat2 mapping
tophat_map(options['--gtf'],
out_dir,
prefix2,
options['<fastq>'],
options['--thread'],
bw=options['--bw'],
scale=options['--scale'])
if not options['--no-tophat-fusion']:
# tophat fusion mapping
tophat_fusion_map(out_dir, prefix1, options['--thread'])
def tophat_map(gtf, out_dir, prefix, fastq, thread, bw=False, scale=False,
gtf_flag=1):
'''
1. Map reads with TopHat2
2. Extract unmapped reads
3. Create BigWig file if needed
'''
# tophat2 mapping
print('Map reads with TopHat2...')
tophat_cmd = 'tophat2 -g 1 --microexon-search -m 2 '
if gtf_flag:
tophat_cmd += '-G %s ' % gtf
tophat_cmd += '-p %s -o %s ' % (thread, out_dir + '/tophat')
tophat_cmd += '%s/bowtie2_index/%s ' % (out_dir, prefix) + fastq
tophat_cmd += ' 2> %s/tophat.log' % out_dir
print('TopHat2 mapping command:')
print(tophat_cmd)
return_code = os.system(tophat_cmd) >> 8
if return_code:
sys.exit('Error: cannot map reads with TopHat2!')
# extract unmapped reads
print('Extract unmapped reads...')
unmapped_bam = pybedtools.BedTool('%s/tophat/unmapped.bam' % out_dir)
unmapped_bam.bam_to_fastq(fq='%s/tophat/unmapped.fastq' % out_dir)
# create Bigwig file if needed
if bw:
if which('bedGraphToBigWig') is not None:
print('Create BigWig file...')
map_bam_fname = '%s/tophat/accepted_hits.bam' % out_dir
# index bam if not exist
if not os.path.isfile(map_bam_fname + '.bai'):
pysam.index(map_bam_fname)
map_bam = pysam.AlignmentFile(map_bam_fname, 'rb')
# extract chrom size file
chrom_size_fname = '%s/tophat/chrom.size' % out_dir
with open(chrom_size_fname, 'w') as chrom_size_f:
for seq in map_bam.header['SQ']:
chrom_size_f.write('%s\t%s\n' % (seq['SN'], seq['LN']))
if scale: # scale to HPB
mapped_reads = map_bam.mapped
for read in map_bam:
read_length = read.query_length
break
s = 1000000000.0 / mapped_reads / read_length
else:
s = 1
map_bam = pybedtools.BedTool(map_bam_fname)
bedgraph_fname = '%s/tophat/accepted_hits.bg' % out_dir
with open(bedgraph_fname, 'w') as bedgraph_f:
for line in map_bam.genome_coverage(bg=True,
g=chrom_size_fname,
scale=s, split=True):
value = str(int(float(line[3]) + 0.5))
bedgraph_f.write('\t'.join(line[:3]) + '\t%s\n' % value)
bigwig_fname = '%s/tophat/accepted_hits.bw' % out_dir
return_code = os.system('bedGraphToBigWig %s %s %s' %
(bedgraph_fname, chrom_size_fname,
bigwig_fname)) >> 8
if return_code:
sys.exit('Error: cannot convert bedGraph to BigWig!')
else:
print('Could not find bedGraphToBigWig, so skip this step!')
def __init__(self):
"""
Create the main window.
:return:
"""
super(RF_Qt, self).__init__()
# Define variables
self.fnt_styles = ["Regular", "Italic", "Bold", "Bold Italic"]
self.fnt_sty_combo_list = []
self.fnt_file_name_list = []
self.font_files = None
self.font_info = FontInfo()
# Create a QProcess object, and connect it to appropriate slots
self.cli_process = QProcess(self)
self.cli_process.setProcessChannelMode(QProcess.MergedChannels)
self.cli_process.readyRead.connect(self.read_proc_output)
self.cli_process.started.connect(self.manage_proc)
self.cli_process.finished.connect(self.manage_proc)
self.cli_process.error.connect(self.manage_proc)
# Style for all groupbox labels
gb_style = "QGroupBox { font-weight: bold; }"
# Top level layout manager for the window.
win_layout = QVBoxLayout()
gb_fnt_files = QGroupBox("Font Files")
gb_fnt_files.setStyleSheet(gb_style)
grid_f_f = QGridLayout()
grid_pos = 0
# Font Files and styles #
# Create a grid of font names with their respective font style combo boxes
for i in range(len(self.fnt_styles)):
self.fnt_file_name_list.append(QLabel("Load font file..."))
cmb = QComboBox()
cmb.addItem("")
cmb.addItems(self.fnt_styles)
cmb.setEnabled(False)
cmb.setToolTip(
"<qt/>If not automatically detected when the font is added, allows you to select what font "
"sub-family the font file belongs to"
)
self.fnt_sty_combo_list.append(cmb)
row, col = helper.calc_grid_pos(grid_pos, 2)
grid_f_f.addWidget(self.fnt_file_name_list[i], row, col)
grid_pos += 1
row, col = helper.calc_grid_pos(grid_pos, 2)
grid_f_f.addWidget(self.fnt_sty_combo_list[i], row, col)
grid_pos += 1
grid_f_f.setColumnStretch(0, 1)
gb_fnt_files.setLayout(grid_f_f)
win_layout.addWidget(gb_fnt_files)
# New Font Name #
gb_fnt_name = QGroupBox("Font Family Name")
gb_fnt_name.setStyleSheet(gb_style)
hb_fnt_name = QHBoxLayout()
self.new_fnt_name = QLineEdit()
self.new_fnt_name.setToolTip("Enter a name for the modified font.")
self.new_fnt_name.textEdited[str].connect(self.set_family_name)
hb_fnt_name.addWidget(self.new_fnt_name)
gb_fnt_name.setLayout(hb_fnt_name)
win_layout.addWidget(gb_fnt_name)
# Options #
hb_options = QHBoxLayout()
## Kerning, Panose, Alt. Name ##
gb_basic_opt = QGroupBox("Basic Options")
gb_basic_opt.setStyleSheet(gb_style)
hb_basic_opt = QHBoxLayout()
self.basic_opt_list = []
basic_tooltips = (
"<qt/>Some readers and software require 'legacy', or 'old style' kerning to be "
"present for kerning to work.",
"<qt/>Kobo readers can get confused by PANOSE settings. This option sets all "
"PANOSE information to 0, or 'any'",
"<qt/>Some fonts have issues with renaming. If the generated font does not have "
"the same internal font name as you entered, try enabling this option.",
)
for opt, tip in zip(("Legacy Kerning", "Clear PANOSE", "Alt. Name"), basic_tooltips):
self.basic_opt_list.append(QCheckBox(opt))
self.basic_opt_list[-1].setToolTip(tip)
hb_basic_opt.addWidget(self.basic_opt_list[-1])
gb_basic_opt.setLayout(hb_basic_opt)
hb_options.addWidget(gb_basic_opt)
## Hinting ##
gb_hint_opt = QGroupBox("Hinting Option")
gb_hint_opt.setStyleSheet(gb_style)
hb_hint_opt = QHBoxLayout()
self.hint_opt_list = []
hint_tooltips = (
"<qt/>Keep font hinting as it exists in the orginal font files.<br />"
"In most cases, this will look fine on most ebook reading devices.",
'<qt/>Some fonts are manually, or "hand" hinted for specific display types (such as LCD). '
"These fonts may not look good on other display types such as e-ink, therefore they can be "
"removed.",
"<qt/>If you don't like the original hinting, but you want your font to be hinted, "
"this option will auto hint your font.",
)
for opt, tip in zip(("Keep Existing", "Remove Existing", "AutoHint"), hint_tooltips):
self.hint_opt_list.append(QRadioButton(opt))
self.hint_opt_list[-1].setToolTip(tip)
self.hint_opt_list[-1].toggled.connect(self.set_hint)
hb_hint_opt.addWidget(self.hint_opt_list[-1])
self.hint_opt_list[0].setChecked(Qt.Checked)
gb_hint_opt.setLayout(hb_hint_opt)
hb_options.addWidget(gb_hint_opt)
win_layout.addLayout(hb_options)
## Darken ##
gb_dark_opt = QGroupBox("Darken Options")
gb_dark_opt.setStyleSheet(gb_style)
hb_dark_opt = QHBoxLayout()
self.darken_opt = QCheckBox("Darken Font")
self.darken_opt.setToolTip("<qt/>Darken, or add weight to a font to make it easier to read on e-ink screens.")
self.darken_opt.toggled.connect(self.set_darken_opt)
hb_dark_opt.addWidget(self.darken_opt)
self.mod_bearing_opt = QCheckBox("Modify Bearings")
self.mod_bearing_opt.setToolTip(
"<qt/>By default, adding weight to a font increases glyph width. Enable this "
"option to set the glyph width to be roughly equal to the original.<br/><br/>"
"WARNING: This reduces the spacing between glyphs, and should not be used if "
"you have added too much weight."
)
self.mod_bearing_opt.toggled.connect(self.set_mod_bearing)
self.mod_bearing_opt.setEnabled(False)
hb_dark_opt.addWidget(self.mod_bearing_opt)
self.lbl = QLabel("Darken Amount:")
self.lbl.setEnabled(False)
hb_dark_opt.addWidget(self.lbl)
self.darken_amount_opt = QSlider(Qt.Horizontal)
self.darken_amount_opt.setMinimum(1)
self.darken_amount_opt.setMaximum(50)
self.darken_amount_opt.setValue(12)
self.darken_amount_opt.setEnabled(False)
self.darken_amount_opt.setToolTip(
"<qt/>Set the amount to darken a font by. 50 is considered turning a "
"regular weight font into a bold weight font. It is not recommended to "
"darken a font that much however."
)
self.darken_amount_opt.valueChanged[int].connect(self.set_darken_amount)
hb_dark_opt.addWidget(self.darken_amount_opt)
self.darken_amount_lab = QLabel()
self.darken_amount_lab.setText(str(self.darken_amount_opt.value()))
self.darken_amount_lab.setEnabled(False)
hb_dark_opt.addWidget(self.darken_amount_lab)
gb_dark_opt.setLayout(hb_dark_opt)
win_layout.addWidget(gb_dark_opt)
# Buttons #
hb_buttons = QHBoxLayout()
# hb_buttons.addStretch()
self.gen_ttf_btn = QPushButton("Generate TTF")
self.gen_ttf_btn.setEnabled(False)
self.gen_ttf_btn.setToolTip(
"<qt/>Generate a new TrueType font based on the options chosen in this program. "
"<br /><br />"
"The new fonts are saved in a directory of your choosing."
)
self.gen_ttf_btn.clicked.connect(self.gen_ttf)
hb_buttons.addWidget(self.gen_ttf_btn)
self.load_font_btn = QPushButton("Load Fonts")
self.load_font_btn.setToolTip("<qt/>Load font files to modify.")
self.load_font_btn.clicked.connect(self.load_fonts)
hb_buttons.addWidget(self.load_font_btn)
self.prog_bar = QProgressBar()
self.prog_bar.setRange(0, 100)
hb_buttons.addWidget(self.prog_bar)
win_layout.addLayout(hb_buttons)
# Output Log #
gb_log_win = QGroupBox("Log Window")
gb_log_win.setStyleSheet(gb_style)
vb_log = QVBoxLayout()
out_font = QFont("Courier")
out_font.setStyleHint(QFont.Monospace)
self.log_win = QTextEdit()
self.log_win.setAcceptRichText(False)
self.log_win.setFont(out_font)
vb_log.addWidget(self.log_win)
gb_log_win.setLayout(vb_log)
win_layout.addWidget(gb_log_win)
# Show Window #
self.setCentralWidget(QWidget(self))
self.centralWidget().setLayout(win_layout)
self.setWindowTitle("Readify Font")
self.show()
# Check if fontforge is actually in users PATH. If it isn't, prompt user to provice a location
self.ff_path = helper.which("fontforge")
if not self.ff_path:
self.set_ff_path()
def __init__(self):
"""
Create the main window.
:return:
"""
super(RF_Qt, self).__init__()
# Define variables
self.fnt_styles = ['Regular', 'Italic', 'Bold', 'Bold Italic']
self.fnt_sty_combo_list = []
self.fnt_file_name_list = []
self.font_files = None
self.font_info = FontInfo()
# Create a QProcess object, and connect it to appropriate slots
self.cli_process = QProcess(self)
self.cli_process.setProcessChannelMode(QProcess.MergedChannels)
self.cli_process.readyRead.connect(self.read_proc_output)
self.cli_process.started.connect(self.manage_proc)
self.cli_process.finished.connect(self.manage_proc)
self.cli_process.error.connect(self.manage_proc)
# Style for all groupbox labels
gb_style = 'QGroupBox { font-weight: bold; }'
# Top level layout manager for the window.
win_layout = QVBoxLayout()
gb_fnt_files = QGroupBox('Font Files')
gb_fnt_files.setStyleSheet(gb_style)
grid_f_f = QGridLayout()
grid_pos = 0
# Font Files and styles #
# Create a grid of font names with their respective font style combo boxes
for i in range(len(self.fnt_styles)):
self.fnt_file_name_list.append(QLabel('Load font file...'))
cmb = QComboBox()
cmb.addItem('')
cmb.addItems(self.fnt_styles)
cmb.setEnabled(False)
cmb.setToolTip(
'<qt/>If not automatically detected when the font is added, allows you to select what font '
'sub-family the font file belongs to')
self.fnt_sty_combo_list.append(cmb)
row, col = helper.calc_grid_pos(grid_pos, 2)
grid_f_f.addWidget(self.fnt_file_name_list[i], row, col)
grid_pos += 1
row, col = helper.calc_grid_pos(grid_pos, 2)
grid_f_f.addWidget(self.fnt_sty_combo_list[i], row, col)
grid_pos += 1
grid_f_f.setColumnStretch(0, 1)
gb_fnt_files.setLayout(grid_f_f)
win_layout.addWidget(gb_fnt_files)
# New Font Name #
gb_fnt_name = QGroupBox('Font Family Name')
gb_fnt_name.setStyleSheet(gb_style)
hb_fnt_name = QHBoxLayout()
self.new_fnt_name = QLineEdit()
self.new_fnt_name.setToolTip('Enter a name for the modified font.')
self.new_fnt_name.textEdited[str].connect(self.set_family_name)
hb_fnt_name.addWidget(self.new_fnt_name)
gb_fnt_name.setLayout(hb_fnt_name)
win_layout.addWidget(gb_fnt_name)
# Options #
hb_options = QHBoxLayout()
## Kerning, Panose, Alt. Name ##
gb_basic_opt = QGroupBox('Basic Options')
gb_basic_opt.setStyleSheet(gb_style)
hb_basic_opt = QHBoxLayout()
self.basic_opt_list = []
basic_tooltips = (
'<qt/>Some readers and software require \'legacy\', or \'old style\' kerning to be '
'present for kerning to work.',
'<qt/>Kobo readers can get confused by PANOSE settings. This option sets all '
'PANOSE information to 0, or \'any\'',
'<qt/>Some fonts have issues with renaming. If the generated font does not have '
'the same internal font name as you entered, try enabling this option.'
)
for opt, tip in zip(('Legacy Kerning', 'Clear PANOSE', 'Alt. Name'),
basic_tooltips):
self.basic_opt_list.append(QCheckBox(opt))
self.basic_opt_list[-1].setToolTip(tip)
hb_basic_opt.addWidget(self.basic_opt_list[-1])
gb_basic_opt.setLayout(hb_basic_opt)
hb_options.addWidget(gb_basic_opt)
## Hinting ##
gb_hint_opt = QGroupBox('Hinting Option')
gb_hint_opt.setStyleSheet(gb_style)
hb_hint_opt = QHBoxLayout()
self.hint_opt_list = []
hint_tooltips = (
'<qt/>Keep font hinting as it exists in the orginal font files.<br />'
'In most cases, this will look fine on most ebook reading devices.',
'<qt/>Some fonts are manually, or "hand" hinted for specific display types (such as LCD). '
'These fonts may not look good on other display types such as e-ink, therefore they can be '
'removed.',
'<qt/>If you don\'t like the original hinting, but you want your font to be hinted, '
'this option will auto hint your font.')
for opt, tip in zip(('Keep Existing', 'Remove Existing', 'AutoHint'),
hint_tooltips):
self.hint_opt_list.append(QRadioButton(opt))
self.hint_opt_list[-1].setToolTip(tip)
self.hint_opt_list[-1].toggled.connect(self.set_hint)
hb_hint_opt.addWidget(self.hint_opt_list[-1])
self.hint_opt_list[0].setChecked(Qt.Checked)
gb_hint_opt.setLayout(hb_hint_opt)
hb_options.addWidget(gb_hint_opt)
win_layout.addLayout(hb_options)
## Darken ##
gb_dark_opt = QGroupBox('Darken Options')
gb_dark_opt.setStyleSheet(gb_style)
hb_dark_opt = QHBoxLayout()
self.darken_opt = QCheckBox('Darken Font')
self.darken_opt.setToolTip(
'<qt/>Darken, or add weight to a font to make it easier to read on e-ink screens.'
)
self.darken_opt.toggled.connect(self.set_darken_opt)
hb_dark_opt.addWidget(self.darken_opt)
self.mod_bearing_opt = QCheckBox('Modify Bearings')
self.mod_bearing_opt.setToolTip(
'<qt/>By default, adding weight to a font increases glyph width. Enable this '
'option to set the glyph width to be roughly equal to the original.<br/><br/>'
'WARNING: This reduces the spacing between glyphs, and should not be used if '
'you have added too much weight.')
self.mod_bearing_opt.toggled.connect(self.set_mod_bearing)
self.mod_bearing_opt.setEnabled(False)
hb_dark_opt.addWidget(self.mod_bearing_opt)
self.lbl = QLabel('Darken Amount:')
self.lbl.setEnabled(False)
hb_dark_opt.addWidget(self.lbl)
self.darken_amount_opt = QSlider(Qt.Horizontal)
self.darken_amount_opt.setMinimum(1)
self.darken_amount_opt.setMaximum(50)
self.darken_amount_opt.setValue(12)
self.darken_amount_opt.setEnabled(False)
self.darken_amount_opt.setToolTip(
'<qt/>Set the amount to darken a font by. 50 is considered turning a '
'regular weight font into a bold weight font. It is not recommended to '
'darken a font that much however.')
self.darken_amount_opt.valueChanged[int].connect(
self.set_darken_amount)
hb_dark_opt.addWidget(self.darken_amount_opt)
self.darken_amount_lab = QLabel()
self.darken_amount_lab.setText(str(self.darken_amount_opt.value()))
self.darken_amount_lab.setEnabled(False)
hb_dark_opt.addWidget(self.darken_amount_lab)
gb_dark_opt.setLayout(hb_dark_opt)
win_layout.addWidget(gb_dark_opt)
# Buttons #
hb_buttons = QHBoxLayout()
#hb_buttons.addStretch()
self.gen_ttf_btn = QPushButton('Generate TTF')
self.gen_ttf_btn.setEnabled(False)
self.gen_ttf_btn.setToolTip(
'<qt/>Generate a new TrueType font based on the options chosen in this program. '
'<br /><br />'
'The new fonts are saved in a directory of your choosing.')
self.gen_ttf_btn.clicked.connect(self.gen_ttf)
hb_buttons.addWidget(self.gen_ttf_btn)
self.load_font_btn = QPushButton('Load Fonts')
self.load_font_btn.setToolTip('<qt/>Load font files to modify.')
self.load_font_btn.clicked.connect(self.load_fonts)
hb_buttons.addWidget(self.load_font_btn)
self.prog_bar = QProgressBar()
self.prog_bar.setRange(0, 100)
hb_buttons.addWidget(self.prog_bar)
win_layout.addLayout(hb_buttons)
# Output Log #
gb_log_win = QGroupBox('Log Window')
gb_log_win.setStyleSheet(gb_style)
vb_log = QVBoxLayout()
out_font = QFont('Courier')
out_font.setStyleHint(QFont.Monospace)
self.log_win = QTextEdit()
self.log_win.setAcceptRichText(False)
self.log_win.setFont(out_font)
vb_log.addWidget(self.log_win)
gb_log_win.setLayout(vb_log)
win_layout.addWidget(gb_log_win)
# Show Window #
self.setCentralWidget(QWidget(self))
self.centralWidget().setLayout(win_layout)
self.setWindowTitle('Readify Font')
self.show()
# Check if fontforge is actually in users PATH. If it isn't, prompt user to provice a location
self.ff_path = helper.which('fontforge')
if not self.ff_path:
self.set_ff_path()