Hw14

Bio_Files_Processor.py

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+import os
+from typing import List
+
+def convert_multiline_fasta_to_oneline(input_fasta: str, output_fasta: str = None) -> str:
+    """
+    Function conver multiline fasta file into fasta with name line marked by '>' and the other line with sequence.
+    Results save into new folder "Converted_data". If the folder already exists, new data is written to it.
+
+    :param input_fasta: Path to fasta-file with your seqs with. 
+     !! It is necessary to indicate the name along with extensions (.fasta) !!
+    :type input_fasta: str
+    :param output_fasta: Name of new fasta-file with your seqs in one line, default value = None
+    It is necessary to indicate the name along with extensions (.fasta)
+    :type output_fasta: str
+    :rtype: str
+    :return: Script completion message 
+    """
+    if input_fasta.find('.fasta') == 0:
+        raise ValueError(f'Wrong file format in input!')
+    if os.path.exists(os.path.join('.', 'Converted_data')) == False:
+        os.mkdir(os.path.join('.', 'Converted_data'))
+    if output_fasta == None:
+        out_name = 'one_line_' + input_fasta.strip("/")[-1]
+    else:
+        out_name = output_fasta
+    gene = 0
+    seq = 0
+    gene_name = ''
+    prot_seq = ''
+    gene_and_seq = dict()
+    with open (input_fasta) as seq_fasta:
+        for line in seq_fasta:
+            if gene == 1:
+                if line.startswith('>') == False:
+                    gene_and_seq[gene_name] += line.strip('\n')
+                else:
+                    gene_name = line.strip('\n')
+                    gene_and_seq[gene_name] = ''
+            if gene == 0 and line.startswith('>'):
+                gene_name = line.strip('\n')
+                gene_and_seq[gene_name] = ''
+                gene = 1
+    with open (os.path.join('.', 'Converted_data', out_name), mode = 'w') as new_seq_fasta:
+        for key, item in gene_and_seq.items():
+            new_seq_fasta.write(key + '\n')
+            new_seq_fasta.write(item + '\n')
+    return 'All sequences processed!'
+
+
+def select_genes_from_gbk_to_fasta(input_gbk: str, genes: List[str], n_before: int = 1, n_after: int = 1, 
+                                   output_fasta: str = None) -> str:
+    '''
+    Function help to search neighbours of GOI (gene of interest). Function writes neighbours of GOI in new FASTA-file 
+    as: name of gene, protein sequence. Results save into new folder "Analyzed_data". If the folder already exists, 
+    new data is written to it.
+
+    :input_gbk: Path to gbk-file with your seqs with.
+    !! It is necessary to indicate the name along with extensions (.gbk) !!
+    :type input_gbk: str
+    :param genes: Gene of interest names
+    :type genes: List[str]
+    :param n_before: number of genes before GOI (>0), default value = 1
+    :type n_before: int
+    :param n_after: number of genes after GOI (>0), default value = 1
+    :type n_after: int
+    :output_fasta: Name of FASTA-file with neighbours of GOI (names and seqs), default value = None
+    :type output_fasta: str
+    :rtype: str
+    :return: Script completion message
+
+    '''
+    if input_gbk.find('.gbk') == 0:
+        raise ValueError(f'Wrong file format in input!')
+    if os.path.exists(os.path.join('.', 'Analyzed_data')) == False:
+        os.mkdir(os.path.join('.', 'Analyzed_data'))
+    genes_for_search = genes
+    genes_gbk = []
+    genes_for_search_in_gbk = []
+    neighbour_genes = dict()
+    if output_fasta == None:
+        output_fasta = 'output_for_gbk.fasta'
+    with open (input_gbk) as gbk:
+        for line in gbk:
+            if '/gene' in line:
+                genes_gbk += [line.strip().split('=')[1]]
+    for el in genes_for_search:
+        genes_for_search_in_gbk += [gn for gn in genes_gbk if el in gn]
+    for gene in genes_for_search_in_gbk:
+        gene_index = genes_gbk.index(gene)
+        if gene_index >= 0 and gene_index < (len(genes_gbk) - 1):
+            for i in range(1, n_before + 1):
+                neighbour_genes[(genes_gbk[gene_index - i])] = 0
+            for i in range(1, n_after + 1):
+                neighbour_genes[(genes_gbk[gene_index + i])] = 0
+        else:
+            for i in range(1, n_before + 1):
+                neighbour_genes[(genes_gbk[gene_index - i])] = 0
+            for i in range(1, n_after):
+                neighbour_genes[(genes_gbk[0 + i])] = 0
+    with open (input_gbk) as gbk:
+        gene_name_read = 0
+        protein_read = 0
+        gene_name = ''
+        protein = ''
+        for line in gbk:
+            if '/gene' in line:
+                gene_name = line.strip().split('=')[1]
+                if gene_name in neighbour_genes:
+                    gene_name_read = 1
+            if protein_read == 1:
+                protein += line.strip('\n').strip(' ')
+                if '"' in line:
+                    protein_read = 0
+                    gene_name_read = 0
+                    neighbour_genes[gene_name] = protein
+                    protein = ''
+            if gene_name_read == 1 and '/translation' in line:
+                protein_read = 1
+                protein += line.strip().split('=')[1]
+    with open (os.path.join('.', 'Analyzed_data', output_fasta), mode = 'w') as fasta:
+        for name, seq in neighbour_genes.items():
+            name = '>'+name.replace('\"','')
+            fasta.write(name + '\n')
+            fasta.write(seq.replace('\"','') + '\n')
+    return 'All sequences processed!'
+