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check_introns_for_stopps.py
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check_introns_for_stopps.py
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### Boas Pucker ###
### [email protected] ###
### v0.2 ###
__usage__ = """
python check_introns_for_stopps.py
--in <FULL_PATH_TO_INPUT_FOLDER>
--out <FULL_PATH_TO_OUTPUT_FOLDER>
bug reports and feature requests: [email protected]
"""
import glob, os, sys, re
from operator import itemgetter
# --- end of imports --- #
def load_sequences( fasta_file ):
"""! @brief load candidate gene IDs from file """
sequences = {}
with open( fasta_file ) as f:
header = f.readline()[1:].strip().split(" ")[0]
seq = ""
line = f.readline()
while line:
if line[0] == '>':
sequences.update( { header: seq } )
header = line.strip()[1:].split(" ")[0]
seq = ""
else:
seq += line.strip()
line = f.readline()
sequences.update( { header: seq } )
return sequences
def run_intron_size_analysis( filename ):
"""! @brief fun intron size analysis """
# --- loading data --- #
css = []
gcag = []
atac = []
other = []
total_css_counter = 0
total_gcag_counter = 0
total_atac_counter = 0
total_other_counter = 0
with open( filename, "r" ) as f:
line = f.readline()
while line:
parts = line.strip().split('\t')
if len( parts ) > 3:
status = True
for each in parts[1] + parts[2]:
if each not in "ACGT":
status = False
if status:
control_length = int( parts[-1] )
intron_blocks = parts[4].split(',')
left_values = map( int, intron_blocks[1].split('_') )
right_values = map( int, intron_blocks[2].split('_') )
if left_values[0] < right_values[0]: #gene on forward strand
start = left_values[0] - 1
end = right_values[1] - 1
orientation = True
else: #gene on reverse strand
start = right_values[0] - 1
end = left_values[1] -1
orientation = False
if end-start != control_length:
print "ERROR: " + str( control_length ) + "\t" + str( start ) + "\t" + str( end )
if parts[1] + parts[2] == "GTAG":
total_css_counter += 1
if control_length % 3 == 0:
css.append( { 'ID': parts[0], 'start': start, 'end': end, 'orientation': orientation } )
elif parts[1] + parts[2] == "GCAG":
total_gcag_counter += 1
if control_length % 3 == 0:
gcag.append( { 'ID': parts[0], 'start': start, 'end': end, 'orientation': orientation } )
elif parts[1] + parts[2] == "ATAC":
total_atac_counter += 1
if control_length % 3 == 0:
atac.append( { 'ID': parts[0], 'start': start, 'end': end, 'orientation': orientation } )
else:
total_other_counter += 1
if control_length % 3 == 0:
other.append( { 'ID': parts[0], 'start': start, 'end': end, 'orientation': orientation } )
line = f.readline()
return css, gcag, atac, other, total_css_counter, total_gcag_counter, total_atac_counter, total_other_counter
def load_pos_from_gff( gff_file ):
"""! @brief load positions from GFF3 file """
pos = {}
with open( gff_file, "r" ) as f:
line = f.readline()
while line:
if line[0] != '#':
parts = line.strip().split('\t')
if parts[2] in [ "gene", "mRNA" ]:
try:
ID = re.findall( "rna\d+", parts[-1] )[0]
parent = re.findall( "gene\d+", parts[-1] )[0]
except IndexError:
ID = re.findall( "gene\d+", parts[-1] )[0]
parent = re.findall( "gene\d+", parts[-1] )[0]
if parts[6] == "+":
orientation = True
else:
orientation = False
try:
pos.update( { ID: { 'id': ID, 'parent': parent, 'chr': parts[0], 'orientation': orientation } } )
except:
pass
line = f.readline()
return pos
def analyze_introns( data, rna_info, seqs ):
"""! @brief screen introns of length 3x for in frame stopp codons """
clean_counter = 0
stopp_counter = 0
for each in data:
chromosome = rna_info[ each['ID'] ]['chr']
seq = seqs[ chromosome ][ each['start']: each['end'] ].upper()
if seq.count( "A" ) + seq.count( "C" ) + seq.count( "G" ) + seq.count( "T" ) == len( seq ):
# ---- count stopp codons --- #
codons = [ seq[ i : i+3 ] for i in range( 0, len( seq ), 3 ) ]
if each['orientation']:
stopps = codons.count( "TAA" ) + codons.count( "TGA" ) + codons.count( "TAG" )
else:
stopps = codons.count( "TTA" ) + codons.count( "TCA" ) + codons.count( "CTA" )
# --- count introns with stopp / without stopp codons --- #
if stopps == 0:
clean_counter += 1
else:
stopp_counter += 1
else:
pass #print "ERROR: ambiguity character detected - skipping sequence"
return clean_counter, stopp_counter
def main( arguments ):
"""! @brief runs all parts """
data_dir = arguments[ arguments.index('--in')+1 ] #NCBI splice site check result folder
output_dir = arguments[ arguments.index('--out')+1 ] #output folder
if not os.path.exists( output_dir ):
os.makedirs( output_dir )
cutoff = 5000
small_intron_ncss = {}
large_intron_ncss = {}
filenames = sorted( glob.glob( data_dir + "*.txt" ) )
data = []
report_file = output_dir + "report.txt"
global_css_counter = 0
global_gcag_counter = 0
global_atac_counter = 0
global_other_counter = 0
d3_global_css_counter = 0
d3_global_gcag_counter = 0
d3_global_atac_counter = 0
d3_global_other_counter = 0
d3_global_css_clean_counter = 0
d3_global_gcag_clean_counter = 0
d3_global_atac_clean_counter = 0
d3_global_other_clean_counter = 0
with open( report_file, "w" ) as out:
out.write( "\t".join( [ "SpeciesID",
"Number_GTAG_3D", "Number_GTAG", "GTAG_CLEAN", "GTAG_STOPP",
"Number_GCAG_3D", "Number_GCAG", "GCAG_CLEAN", "GCAG_STOPP",
"Number_ATAC_3D", "Number_ATAC", "ATAC_CLEAN", "ATAC_STOPP",
"Number_OTHER_3D", "Number_OTHER", "OTHER_CLEAN", "OTHER_STOPP"
] ) + '\n' )
for filename in filenames:
ID = filename.split('/')[-1].split('.')[0]
print ID
gff_file = data_dir + ID + ".gff"
fasta_file = data_dir + ID + ".fna"
css, gcag, atac, other, total_css_counter, total_gcag_counter, total_atac_counter, total_other_counter = run_intron_size_analysis( filename )
global_css_counter += total_css_counter
global_gcag_counter += total_gcag_counter
global_atac_counter += total_atac_counter
global_other_counter += total_other_counter
d3_global_css_counter += len( css )
d3_global_gcag_counter += len( gcag )
d3_global_atac_counter += len( atac )
d3_global_other_counter += len( other )
rna_info = load_pos_from_gff( gff_file )
seqs = load_sequences( fasta_file )
css_info = analyze_introns( css, rna_info, seqs )
gcag_info = analyze_introns( gcag, rna_info, seqs )
atac_info = analyze_introns( atac, rna_info, seqs )
other_info = analyze_introns( other, rna_info, seqs )
d3_global_css_clean_counter += css_info[0]
d3_global_gcag_clean_counter += gcag_info[0]
d3_global_atac_clean_counter += atac_info[0]
d3_global_other_clean_counter += other_info[0]
out.write( "\t".join( map( str, [ ID,
len( css ), total_css_counter, css_info[0], css_info[1],
len( gcag ), total_gcag_counter, gcag_info[0], gcag_info[1],
len( atac ), total_atac_counter, atac_info[0], atac_info[1],
len( other ), total_other_counter, other_info[0], other_info[1]
] ) ) + "\n" )
print "GT-AG introns divisible by 3: " + str( d3_global_css_counter / float( global_css_counter ) )
print "GC-AG introns divisible by 3: " + str( d3_global_gcag_counter / float( global_gcag_counter ) )
print "AT-AC introns divisible by 3: " + str( d3_global_atac_counter / float( global_atac_counter ) )
print "OTHER introns divisible by 3: " + str( d3_global_other_counter / float( global_other_counter ) )
print "GT-AG introns divisible by 3: " + str( d3_global_css_clean_counter / float( global_css_counter ) ) + "\tn=" + str( d3_global_css_clean_counter )
print "GC-AG introns divisible by 3: " + str( d3_global_gcag_clean_counter / float( global_gcag_counter ) ) + "\tn=" + str( d3_global_gcag_clean_counter )
print "AT-AC introns divisible by 3: " + str( d3_global_atac_clean_counter / float( global_atac_counter ) ) + "\tn=" + str( d3_global_atac_clean_counter )
print "OTHER introns divisible by 3: " + str( d3_global_other_clean_counter / float( global_other_counter ) ) + "\tn=" + str( d3_global_other_clean_counter )
if __name__ == '__main__':
if '--in' in sys.argv and '--out' in sys.argv:
main( sys.argv )
else:
sys.exit( __usage__ )