update

_log

@@ -0,0 +1,33 @@
+.
+├── alg
+│   ├── ampf.py
+│   ├── analysis.py
+│   ├── blast.py
+│   ├── _log
+│   ├── out
+│   └── startery.py
+├── cmd
+│   ├── gen.py
+│   └── seq2fasta.py
+├── data
+│   ├── 217314860.fasta
+│   ├── 2187833333.fasta
+│   ├── 2813891763.fasta
+│   ├── 2813891767.fasta
+│   ├── 599088294.fasta
+│   ├── ITS1.fasta
+│   ├── ITS4.fasta
+│   └── sequence.fasta
+├── doc
+│   ├── main.pdf
+│   ├── main.tex
+│   └── references.bib
+├── _l
+├── _log
+├── log
+│   ├── amplification_analysis_log.txt
+│   └── __log.txt
+└── out
+    └── blast_results.xml
+
+9 directories, 22 files

_log/amplification_analysis_log.txt

@@ -1,2 +0,0 @@
-Amplified Regions:
-No amplification regions found.

alg/ampf.py

@@ -1,13 +1,16 @@
-from Bio import SeqIO
 import os
+from Bio import SeqIO
 
-# Ścieżki do plików FASTA w katalogu ../data
+# Ścieżki do katalogów i plików FASTA
 data_dir = "../data"
-genome_file = os.path.join(data_dir, "genome.fasta")  # Nazwa pliku FASTA dla genomu Fusarium solani
+output_dir = "../out"
+os.makedirs(output_dir, exist_ok=True)
+
+# Pliki primerów
 primer_ITS1_file = os.path.join(data_dir, "ITS1.fasta")
 primer_ITS4_file = os.path.join(data_dir, "ITS4.fasta")
 
-# Wczytywanie sekwencji primerów z plików FASTA
+# Funkcja do wczytywania sekwencji primerów z plików FASTA
 def load_primer(primer_file):
     record = SeqIO.read(primer_file, "fasta")
     return str(record.seq)
@@ -39,25 +42,33 @@ def find_amplified_regions(genome_seq, primer_its1, primer_its4):
                 break  # Przerwij po znalezieniu pierwszego pasującego ITS4 po ITS1
     return amplified_regions
 
-# Wczytywanie primerów
+# Wczytywanie primerów ITS1 i ITS4
 primer_ITS1 = load_primer(primer_ITS1_file)
 primer_ITS4 = load_primer(primer_ITS4_file)
 
-# Wczytywanie genomu z pliku FASTA
+# Lista plików genomów do analizy
-with open(genome_file) as f:
+genome_files = [
-    genome_record = SeqIO.read(f, "fasta")
+    os.path.join(data_dir, filename)
-    genome_seq = str(genome_record.seq)
+    for filename in ["217314860.fasta", "2187833333.fasta", "2813891763.fasta", "2813891767.fasta", "599088294.fasta"]
+]
 
-# Znajdowanie amplifikowanych regionów
+# Analiza amplifikacji dla każdego pliku genomu
-amplified_regions = find_amplified_regions(genome_seq, primer_ITS1, primer_ITS4)
+for genome_file in genome_files:
+    with open(genome_file) as f:
+        genome_record = SeqIO.read(f, "fasta")
+        genome_seq = str(genome_record.seq)
 
-# Zapis wyników
+    # Znajdowanie amplifikowanych regionów
-output_path = os.path.join(data_dir, "amplified_regions.txt")
+    amplified_regions = find_amplified_regions(genome_seq, primer_ITS1, primer_ITS4)
-with open(output_path, "w") as output_file:
-    output_file.write("Amplified Regions:\n")
-    for start, end, region in amplified_regions:
-        output_file.write(f"Start: {start}, End: {end}, Length: {len(region)}\n")
-        output_file.write(f"Region sequence: {region}\n\n")
 
-print(f"Amplified regions saved to {output_path}")
+    # Zapis wyników dla każdego pliku genomu do ../out
+    output_filename = f"amplified_regions_{os.path.basename(genome_file)}.txt"
+    output_path = os.path.join(output_dir, output_filename)
+    with open(output_path, "w") as output_file:
+        output_file.write(f"Amplified Regions for {os.path.basename(genome_file)}:\n")
+        for start, end, region in amplified_regions:
+            output_file.write(f"Start: {start}, End: {end}, Length: {len(region)}\n")
+            output_file.write(f"Region sequence: {region}\n\n")
+    
+    print(f"Amplified regions for {os.path.basename(genome_file)} saved to {output_path}")
 

out/amplified_regions_217314860.fasta.txt

@@ -0,0 +1 @@
+Amplified Regions for 217314860.fasta:

out/amplified_regions_2187833333.fasta.txt

@@ -0,0 +1 @@
+Amplified Regions for 2187833333.fasta:

out/amplified_regions_2813891763.fasta.txt

@@ -0,0 +1 @@
+Amplified Regions for 2813891763.fasta:

out/amplified_regions_2813891767.fasta.txt

@@ -0,0 +1 @@
+Amplified Regions for 2813891767.fasta:

out/amplified_regions_599088294.fasta.txt

@@ -0,0 +1 @@
+Amplified Regions for 599088294.fasta: