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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
'''
Creation of a FA file from a compacted fact int file.
'''
__author__ = "Pierre Peterlongo"
__email__ = "pierre.peterlongo@inria.fr"
import sys
import K3000_common as kc
def generate_sequence_paths(sequences, compacted_fact_file_name, int_facts_format):
'''
Given a set of indexed sequences, the k value and some compacted facts, prints the corresponding fasta seequences
Enables also to validate the compacted facts.
'''
mfile = open(compacted_fact_file_name)
nb_non_writen=0
for line in mfile:
if line[0] == "#": continue
# * int_facts_format:
# 38772_0;-21479_1;27388_3;-494_28;-45551_36;-11894_10;-50927_7;-66981_10;29405_22;34837_1;20095_5;
# * not int_facts_format:
# -1000l_0;-136l_-24;-254h_-18;493l_-16; -577h_0;-977h_-26;1354h_-25; => 1
line = line.split("=")[0].strip() # in case a line contains an abundance, it is indicated by " => 1"
# from "-1000l_0;-136l_-24;-254h_-18;493l_-16; -577h_0;-977h_-26;1354h_-25; => 1"
# to "-1000l_0;-136l_-24;-254h_-18;493l_-16; -577h_0;-977h_-26;1354h_-25;"
# if the input fact contains a space it means that this is a paired fact, each part is treated
for fact_as_ids in line.split():
# print(fact_as_ids)
toprint, header, bubble_facts_position_start_stops, full_seq = kc.line2seq(fact_as_ids, sequences, int_facts_format, 0)
if toprint:
print(f">{header}\t{bubble_facts_position_start_stops}\n{full_seq}")
else: nb_non_writen+=1
if nb_non_writen>0:
sys.stderr.write("Warning, "+str(nb_non_writen)+" facts were removed as their sequence concatenation were not coherent or because they contained non coherent predictions\n")
mfile.close()
def is_int_fact(file_name):
'''
Determines if a given file is under the format
2468_0;-2708_6;1954_-25;1154_-26; (called 'int_facts')
or
-577h_0;-977h_-26;1354h_-25; => 1
'''
with open(file_name) as my_file:
while True:
line = my_file.readline()
if not line:
raise RuntimeError (f'input file {file_name} does not contain correctly formated facts')
if line[0] == "#" : continue # comment
if ';' not in line:
raise RuntimeError (f'input file {file_name} does not contain correctly formated facts. The line {line} should contain at least a \';\'')
# here we are check the kind of file:
line = line.split()[0]
if 'h' in line or 'l' in line:
return False
return True
def main():
'''
Creation of a FA file from a compacted fact int file.
'''
sequences=kc.index_sequences(sys.argv[1]) #for each snp id: sequences[snp_id]=[left_unitig_len, right_unitig_len, upperseq, lowerseq]
sequences=kc.index_sequences(sys.argv[2], sequences) #for each snp id: sequences[snp_id]=[left_unitig_len, right_unitig_len, upperseq, lowerseq]
int_facts_format = is_int_fact(sys.argv[3])
generate_sequence_paths(sequences, sys.argv[3], int_facts_format)
if __name__ == "__main__":
main()
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