Add file input argparse feature for different file formats

file_input_argparse.py

@@ -0,0 +1,102 @@
+# ===================================================== DEPENDENCIES ==============================================================
+import argparse
+from Bio import SeqIO
+from Bio import Align
+from Bio.SeqUtils import gc_fraction
+from matplotlib import pyplot as plt
+plt.style.use('seaborn-v0_8')
+
+# ===================================================== ARGPARSE SETUP =============================================================
+# Create parser instance
+parser = argparse.ArgumentParser(description = 'Calculate GC content of DNA/RNA sequences from files.')
+
+# ----------------------------- Single sequence file formats as optional arguments ------------------------------
+# FASTA nucleic acid files
+parser.add_argument('-fna', nargs='+', type = argparse.FileType('r', encoding = 'UTF-8'), help = 'Provide .fna file')
+
+# FASTA files
+parser.add_argument('-fasta', nargs = '+', type = argparse.FileType('r', encoding = 'UTF-8'), help = 'Provide .fasta file')
+
+# GenBank files
+parser.add_argument('-gb', nargs = '+', type = argparse.FileType('r', encoding = 'UTF-8'), help = 'Provide .gb file')
+
+
+# ------------------------------ Sequence alignment file formats as optional arguments ------------------------------
+# Aligned FASTA files
+parser.add_argument('-fa', type = argparse.FileType('r', encoding = 'UTF-8'), help = 'Provide .fa file')
+
+# ClustalW files
+parser.add_argument('-aln', type = argparse.FileType('r', encoding = 'UTF-8'), help = 'Provide .aln file')
+
+
+# Parse command-line arguments that were passed to the script and store them as attributes to args object
+args = parser.parse_args()
+
+if args.fna is not None:
+    record_list =[SeqIO.read(file, "fasta") for file in args.fna]
+    sequence_list = [record.seq for record in record_list]
+    accession_num_list = [record.id.split('|')[3] for record in record_list]
+
+elif args.fasta is not None:
+    record_list =[SeqIO.read(file, "fasta") for file in args.fasta]
+    sequence_list = [record.seq for record in record_list]
+    accession_num_list = [record.id for record in record_list]
+
+elif args.gb is not None:
+    record_list =[SeqIO.read(file, "genbank") for file in args.gb]
+    sequence_list = [record.seq for record in record_list]
+    accession_num_list = [record.id for record in record_list]
+
+elif args.fa is not None:
+    alignment = Align.read(args.fa, 'fasta')
+    record_list = alignment.sequences
+    sequence_list = [record.seq for record in record_list]
+    accession_num_list = [record.id for record in record_list]
+
+elif args.aln is not None:
+    alignment = Align.read(args.aln, 'clustal')
+    record_list = alignment.sequences
+    sequence_list = [record.seq for record in record_list]
+    accession_num_list = [record.id.split('|')[3] for record in record_list]
+
+# ===================================================== FUNCTIONS ==================================================================
+def calc_gc(sequence_list):
+    ''' Calculates GC content of sequences and returns list of GC content of each sequence.
+    '''
+    gc_list = []
+    for i in sequence_list:
+        gc_list.append(round(gc_fraction(i), 2))
+    return gc_list
+
+def create_GC_barplot(accession_num_list, gc_list):
+    '''Function that creates barplot of the GC value calculated (not with SWAN) of multiple sequences.
+    '''
+    fig, ax = plt.subplots()
+
+    # Create the bar plot
+    bar_container = ax.bar(accession_num_list, gc_list, width = 0.3, color = '#3937b3')
+
+    # Set plot titles and labels
+    ax.set_title("Sequence GC Content Analysis")
+    ax.set_xlabel("Sequences")
+    ax.set_ylabel("GC content")
+
+    # Add labels on the bars
+    ax.bar_label(bar_container)
+
+    # Set axis limits if only one sequence is present
+    if len(accession_num_list) == 1:
+        ax.set_xlim(-0.5, 0.5)
+
+    # Style the spines (borders) of the plot
+    ax.spines['top'].set_color('0.5')
+    ax.spines['right'].set_color('0.5')
+    ax.spines['bottom'].set_color('0.5')
+    ax.spines['left'].set_color('0.5')
+
+    # Display the plot
+    plt.show()
+
+
+gc_content_list = calc_gc(sequence_list)
+create_GC_barplot(accession_num_list, gc_content_list)