def main(fasta_file, root_page):
# Remove extension.
root = os.path.splitext(root_page)[0]
# Make sure there is a folder to the root.
make_dir(root)
# Define organism tag by reading the root name.
organism = os.path.basename(root)
# Parse FASTA file.
loci = SeqIO.parse(fasta_file, 'fasta')
# Create loci page and directory.
loci_file = os.path.join(root, 'Loci.txt')
loci_page = open(loci_file, 'w')
loci_page.write(make_header('Loci'))
loci_page.close()
# Define Loci directory.
loci_dir = os.path.join(root, 'Loci')
make_dir(loci_dir)
# Iterate over each locus.
for locus in loci:
# Sanitize locus.id.
locus_id = locus.id.replace('/', '-')
# Define locus file.
locus_file = os.path.join(loci_dir, '%s.txt' % locus_id)
# Verify if page already exists.
try:
locus_page = open(locus_file, 'r')
locus_page.close()
# If it does, skip page.
continue
except:
# If not, create page.
pass
# Identify the frame and the strand by parsing the description.
# Example: >Lrub_5432 | frame: +1 | candidates: Six3-6, Optix
frame = int(locus.description.split('|')[-2][-2])
frame_step = frame - 1
strand = locus.description.split('|')[-2][-3]
# Always garantee that the sequence is a plus strand.
if strand == '-':
locus.seq = locus.seq.reverse_complement()
locus.description = locus.description.replace('frame: %s%d' % (strand, frame), 'frame: +%d' % frame)
# Translate using the correct frame.
translated_seq = locus.seq[frame_step:].translate()
# Create SeqRecord for protein.
protein = SeqRecord(translated_seq, id=locus.id, name=locus.name, description=locus.description)
# Create locus_page and write header.
locus_page = open(locus_file, 'w')
locus_page.write(make_header(locus_id))
# Write organism name.
locus_page.write('@%s ' % organism)
locus_page.write('\n\n')
# Write sequence in FASTA format.
locus_page.write('@locus %d bp \n' % len(locus.seq))
locus_page.write("'''\n")
locus_page.write(locus.format('fasta'))
locus_page.write("\n'''\n")
# Write protein sequence.
locus_page.write('@protein \n')
locus_page.write("'''\n")
locus_page.write(protein.format('fasta'))
locus_page.write("\n'''\n")
# Close locus file.
locus_page.close()
# Exit program.
sys.exit(0)
absroot = os.path.abspath(root_page)
# Remove extension.
root = os.path.splitext(root_page)[0]
# Make sure there is a folder to the root.
make_dir(root)
# Define organism and initials by reading the root name.
organism = os.path.basename(root).replace('_', ' ')
initials = organism.split()[0][0] + organism.split()[1][:3]
# Create page for genes and directory.
genes_file = os.path.join(root, 'Genes.txt')
genes_page = open(genes_file, 'w')
genes_page.write(make_header('Genes'))
genes_page.close()
# Define genes directory.
genes_dir = os.path.join(root, 'Genes')
make_dir(genes_dir)
# Open BLASTer file.
genes = open(absblaster)
# Create variables for parsing.
plain = ''
space_count = 0
reciprocal = False
contig_id = ''
gene_names = []
# Remove extension.
root = os.path.splitext(absroot)[0]
# Make sure there is a folder to the root.
make_dir(root)
# Define organism tag by reading the root name.
organism = os.path.basename(root)
# Parse FASTA file.
loci = SeqIO.parse(absfasta, 'fasta')
# Create loci page and directory.
loci_file = os.path.join(root, 'Loci.txt')
loci_page = open(loci_file, 'w')
loci_page.write(make_header('Loci'))
loci_page.close()
# Define Loci directory.
loci_dir = os.path.join(root, 'Loci')
make_dir(loci_dir)
# Iterate over each locus.
for locus in loci:
# Sanitize locus.id.
locus_id = locus.id.replace('/', '-')
# Define locus file.
locus_file = os.path.join(loci_dir, '{}.txt'.format(locus_id))