<reponame>bhagesh-codebeast/nextflowdualrnaseq
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 16 11:26:46 2019

@author: <NAME> and <NAME>

Input files: Fasta and GFF
Output file: Fasta
Description: Used to create a transcriptome fasta from user specified fields within a GFF file. 

-----
For example, from the host, you can extract genes and gene IDs:
-----
python gff_to_fasta_transcriptome.py -fasta chr1.fa -gff chr1.gff -f gene -a gene_id -o chr1_genes.fa

-----
Or, transcripts and associated IDs:  
-----
python gff_to_fasta_transcriptome.py -fasta chr1.fa -gff chr1.gff -f transcript -a ID -o chr1_transcripts.fa

"""

import argparse
from Bio import SeqIO

def create_transcriptome(fasta_records_dict, gff_files,feature, gene_attribute, output_file_name):
    with open(output_file_name, 'a') as out_name: #Open output file
        for gff_file in gff_files: 
            for line in open(gff_file):
                 if len(line.split()) == 0: #ignore blank lines
                    continue
                 d = line.rstrip()  #remove '\n'
                 if ((d[0] != '#') and (d != '') and (d != ' ')): #Ignore comments
                    d_list = d.split('\t') #Split based on tabs
                    if d_list[2] in feature: 
                        reference_name = d_list[0]
                        split_8 = d_list[8].split(';') #Further split based on ;
                        #find index of id of interest
                        index_feature = [split_8.index(el) for el in split_8 if gene_attribute in el]
                        description = [s.split("=")[1] for s in split_8]
                        #re-order ids from column 8
                        if not index_feature:
                            print('lack of ' + gene_attribute + ' attribute for record:' + split_8[0].split('=')[1] )
                        else: 
                            out_name.write('>' + description[index_feature[0]] + '\n')
                            #Determine sequence based on direction
                            if d_list[6] == '+' :
                                out_name.write(str(fasta_records_dict[reference_name].seq[int(d_list[3])-1:int(d_list[4])]) + '\n') 
                            elif d_list[6] == '-' :
                                out_name.write(str(fasta_records_dict[reference_name].seq[int(d_list[3])-1:int(d_list[4])].reverse_complement()) + '\n') 
                        

#Script arguments and descriptions                         
parser = argparse.ArgumentParser()
parser.add_argument("-fasta",nargs='+',help="genome fasta file")
parser.add_argument("-gff", nargs='+', help="gff file")
parser.add_argument("-f", "--gene_feature", nargs='+', help="gene feature defined in the 3rd column of the gff file")
parser.add_argument("-a", "--gene_attribute", help="gene attribute")
parser.add_argument("-o", help="output file name")

#Parse params
args = parser.parse_args()

#Format features when multiple options are parsed 
gene_features = [feature.replace('[' , '').replace(']','').replace(',','') for feature in args.gene_feature ]
#Create empty dict.
fasta_records_dict = dict()
#Add fasta into dict.
for fasta_file in  args.fasta:
        fasta_records_dict.update(SeqIO.to_dict(SeqIO.parse(fasta_file, 'fasta')))
#pass fasta, features and attributes to function
create_transcriptome(fasta_records_dict, args.gff, gene_features, args.gene_attribute, args.o)
    


#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 16 11:26:46 2019

@author: <NAME> and <NAME>

Input files: Fasta and GFF
Output file: Fasta
Description: Used to create a transcriptome fasta from user specified fields within a GFF file. 

-----
For example, from the host, you can extract genes and gene IDs:
-----
python gff_to_fasta_transcriptome.py -fasta chr1.fa -gff chr1.gff -f gene -a gene_id -o chr1_genes.fa

-----
Or, transcripts and associated IDs:  
-----
python gff_to_fasta_transcriptome.py -fasta chr1.fa -gff chr1.gff -f transcript -a ID -o chr1_transcripts.fa

"""

import argparse
from Bio import SeqIO

def create_transcriptome(fasta_records_dict, gff_files,feature, gene_attribute, output_file_name):
    with open(output_file_name, 'a') as out_name: #Open output file
        for gff_file in gff_files: 
            for line in open(gff_file):
                 if len(line.split()) == 0: #ignore blank lines
                    continue
                 d = line.rstrip()  #remove '\n'
                 if ((d[0] != '#') and (d != '') and (d != ' ')): #Ignore comments
                    d_list = d.split('\t') #Split based on tabs
                    if d_list[2] in feature: 
                        reference_name = d_list[0]
                        split_8 = d_list[8].split(';') #Further split based on ;
                        #find index of id of interest
                        index_feature = [split_8.index(el) for el in split_8 if gene_attribute in el]
                        description = [s.split("=")[1] for s in split_8]
                        #re-order ids from column 8
                        if not index_feature:
                            print('lack of ' + gene_attribute + ' attribute for record:' + split_8[0].split('=')[1] )
                        else: 
                            out_name.write('>' + description[index_feature[0]] + '\n')
                            #Determine sequence based on direction
                            if d_list[6] == '+' :
                                out_name.write(str(fasta_records_dict[reference_name].seq[int(d_list[3])-1:int(d_list[4])]) + '\n') 
                            elif d_list[6] == '-' :
                                out_name.write(str(fasta_records_dict[reference_name].seq[int(d_list[3])-1:int(d_list[4])].reverse_complement()) + '\n') 
                        

#Script arguments and descriptions                         
parser = argparse.ArgumentParser()
parser.add_argument("-fasta",nargs='+',help="genome fasta file")
parser.add_argument("-gff", nargs='+', help="gff file")
parser.add_argument("-f", "--gene_feature", nargs='+', help="gene feature defined in the 3rd column of the gff file")
parser.add_argument("-a", "--gene_attribute", help="gene attribute")
parser.add_argument("-o", help="output file name")

#Parse params
args = parser.parse_args()

#Format features when multiple options are parsed 
gene_features = [feature.replace('[' , '').replace(']','').replace(',','') for feature in args.gene_feature ]
#Create empty dict.
fasta_records_dict = dict()
#Add fasta into dict.
for fasta_file in  args.fasta:
        fasta_records_dict.update(SeqIO.to_dict(SeqIO.parse(fasta_file, 'fasta')))
#pass fasta, features and attributes to function
create_transcriptome(fasta_records_dict, args.gff, gene_features, args.gene_attribute, args.o)
#!/usr/bin/env python3 # -*- coding: utf-8 -*- Created on Tue Apr 16 11:26:46 2019  @author: <NAME> and <NAME>  Input files: Fasta and GFF Output file: Fasta Description: Used to create a transcriptome fasta from user specified fields within a GFF file.   ----- For example, from the host, you can extract genes and gene IDs: ----- python gff_to_fasta_transcriptome.py -fasta chr1.fa -gff chr1.gff -f gene -a gene_id -o chr1_genes.fa  ----- Or, transcripts and associated IDs:   ----- python gff_to_fasta_transcriptome.py -fasta chr1.fa -gff chr1.gff -f transcript -a ID -o chr1_transcripts.fa #Open output file #ignore blank lines #remove '\n' #Ignore comments #Split based on tabs #Further split based on ; #find index of id of interest #re-order ids from column 8 #Determine sequence based on direction #Script arguments and descriptions #Parse params #Format features when multiple options are parsed #Create empty dict. #Add fasta into dict. #pass fasta, features and attributes to function