u

_l

@@ -0,0 +1,34 @@
+.
+├── 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
+│   └── amplification_analysis_log.txt
+├── log
+│   ├── amplification_analysis_log.txt
+│   └── __log.txt
+└── out
+    └── blast_results.xml
+
+10 directories, 22 files

_log/amplification_analysis_log.txt

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

alg/ampf.py

@@ -0,0 +1,63 @@
+from Bio import SeqIO
+import os
+
+# Ścieżki do plików FASTA w katalogu ../data
+data_dir = "../data"
+genome_file = os.path.join(data_dir, "genome.fasta")  # Nazwa pliku FASTA dla genomu Fusarium solani
+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
+def load_primer(primer_file):
+    record = SeqIO.read(primer_file, "fasta")
+    return str(record.seq)
+
+# Funkcja do znajdowania pozycji amplifikowanych regionów
+def find_amplified_regions(genome_seq, primer_its1, primer_its4):
+    its1_positions = []
+    its4_positions = []
+    
+    # Szukanie dopasowań dla ITS1
+    pos = genome_seq.find(primer_its1)
+    while pos != -1:
+        its1_positions.append(pos)
+        pos = genome_seq.find(primer_its1, pos + 1)
+        
+    # Szukanie dopasowań dla ITS4
+    pos = genome_seq.find(primer_its4)
+    while pos != -1:
+        its4_positions.append(pos)
+        pos = genome_seq.find(primer_its4, pos + 1)
+        
+    # Znajdowanie regionów amplifikowanych między primerami ITS1 i ITS4
+    amplified_regions = []
+    for start in its1_positions:
+        for end in its4_positions:
+            if end > start:
+                amplified_region = genome_seq[start:end + len(primer_its4)]
+                amplified_regions.append((start, end + len(primer_its4), amplified_region))
+                break  # Przerwij po znalezieniu pierwszego pasującego ITS4 po ITS1
+    return amplified_regions
+
+# Wczytywanie primerów
+primer_ITS1 = load_primer(primer_ITS1_file)
+primer_ITS4 = load_primer(primer_ITS4_file)
+
+# Wczytywanie genomu z pliku FASTA
+with open(genome_file) as f:
+    genome_record = SeqIO.read(f, "fasta")
+    genome_seq = str(genome_record.seq)
+
+# Znajdowanie amplifikowanych regionów
+amplified_regions = find_amplified_regions(genome_seq, primer_ITS1, primer_ITS4)
+
+# Zapis wyników
+output_path = os.path.join(data_dir, "amplified_regions.txt")
+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}")
+

alg/analysis.py

@@ -8,9 +8,9 @@ import time
 Entrez.email = "baiobelfer@gmail.com"
 
 # Ścieżki do plików
-data_dir = "data"
+data_dir = "../data"
-log_dir = "_log"
+log_dir = "../_log"
-out_dir = "out"
+out_dir = "../out"
 os.makedirs(log_dir, exist_ok=True)
 os.makedirs(out_dir, exist_ok=True)
 

cmd/gen.py

@@ -0,0 +1,38 @@
+from Bio import Entrez, SeqIO
+import os
+
+# Konfiguracja email dla Entrez (wymagane przez NCBI)
+Entrez.email = "baiobelfer@gmail.com"
+
+# Identyfikatory GenBank dla wybranych izolatów Fusarium solani
+genbank_ids = [
+    "217314860",  # Fusarium solani isolate T03
+    "2813891763", # Fusarium solani isolate Fso2
+    "599088294",  # Uncultured Fusarium clone TTRK-10
+    "2813891767", # Fusarium solani isolate Fso6
+    "2187833333"  # Fusarium solani isolate CBG103
+]
+
+# Katalog do zapisu plików FASTA
+data_dir = "../data"
+os.makedirs(data_dir, exist_ok=True)
+
+# Funkcja do pobierania genomów i zapisywania ich w plikach FASTA
+def download_genome(genbank_id):
+    try:
+        # Pobieranie rekordu z NCBI w formacie FASTA
+        with Entrez.efetch(db="nucleotide", id=genbank_id, rettype="fasta", retmode="text") as handle:
+            record = SeqIO.read(handle, "fasta")
+            # Zapis rekordu do pliku FASTA w katalogu ../data
+            fasta_path = os.path.join(data_dir, f"{genbank_id}.fasta")
+            SeqIO.write(record, fasta_path, "fasta")
+            print(f"Pobrano i zapisano {genbank_id} do {fasta_path}")
+    except Exception as e:
+        print(f"Nie udało się pobrać {genbank_id}: {e}")
+
+# Pobieranie i zapisywanie genomów dla każdego ID
+for genbank_id in genbank_ids:
+    download_genome(genbank_id)
+
+print("Pobieranie zakończone.")
+

data/217314860.fasta

@@ -0,0 +1,11 @@
+>FJ459973.1 Fusarium solani isolate T03 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
+TCCGTAGGTGAACCTGCGGAGGGATCATTACCGAGTTATACAACTCATCAACCCTGTGAA
+CATACCTAAACGTTGCCTCGGCGGGAACAGACGGCCCCGTGAAACGGGCCGCCCCCGCCA
+GAGGACCCCCTAACTCTGTTTCTATAATGTTTCTTCTGAGTAAAACAAGCAAATAAATTA
+AAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGAT
+AAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCG
+CCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTACAACCCTCAGGCCCCCGGGCCT
+GGCGTTGGGGATCGGCGGAGCCCCCCGTGGGCACACGCCGTCCCCCAAATACAGTGGCGG
+TCCCGCCGCAGCTTCCATCGCGTAGTAGCTAACACCTCGCGACTGGAGAGCGGCGCGGCC
+ACGCCGTAAAACACCCCAACTCTTCTGAAGTTGACCTCGAATCAGGTAGGAATACCCGCT
+GAACTTAAGCATATCAATAAGCGGAGGA

data/2187833333.fasta

@@ -0,0 +1,11 @@
+>OM502955.1 Fusarium solani isolate CBG103 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
+CCGTAGGTGAACCTGCGGAGGGATCATTACCGAGTTATACAACTCATCAACCCTGTGAAC
+ATACCTAAACGTTGCTTCGGCGGGAACAGACGGCCCCGTGAAACGGGCCGCCCCCGCCAG
+AGGACCCCTAACTCTGTTTCTATAATGTTTCTTCTGAGTAAAACAAGCAAATAAATTAAA
+ACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAA
+GTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCC
+AGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTACAACCCTCAGGCCCCCGGGCCTGG
+CGTTGGGGATCGGCGGAGCCCCCCGTGGGCACACGCCGTCCCCCAAATACAGTGGCGGTC
+CCGCCGCAGCTTCCATCGCGTAGTAGCTAACACCTCGCGACTGGAGAGCGGCGCGGCCAC
+GCCGTAAAACACCCAACTCTTCTGAAGTTGACCTCGAATCAGGTAGGAATACCCGCTGAA
+CTTAAGCATATCAATAAGCGGAG

data/2813891763.fasta

@@ -0,0 +1,11 @@
+>PQ432857.1 Fusarium solani isolate Fso2 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
+CGTAGGTGAACCTGCGGAGGGATCATTACCGAGTTATACAACTCATCAACCCTGTGAACA
+TACCTAAACGTTGCCTCGGCGGGAACAGACGGCCCCGTGAAACGGGCCGCCCCCGCCAGA
+GGACCCTTAACTCTGTTTCTATAATGTTTCTTCTGAGTAAAACAAGCAAATAAATTAAAA
+CTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAG
+TAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCA
+GTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTACAACCCTCAGGCCCCCGGGCCTGGC
+GTTGGGGATCGGCGGAGCCCCTCCGTGGGCACACGCCGTCCCCCAAATACAGTGGCGGTC
+CCGCCGCAGCTTCCATCGCGTAGTAGCTAACACCTCGCGACTGGAGAGCGGCGCGGCCAC
+GCCGTAAAACACCCAACTCTTCTGAAGTTGACCTCGAATCAGGTAGGAATACCCGCTGAA
+CTTAAGCATATCAATAAGCGG

data/2813891767.fasta

@@ -0,0 +1,11 @@
+>PQ432861.1 Fusarium solani isolate Fso6 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
+TCCGTAGGTGAACCTGCGGAGGGATCATTACCGAGTTATACAACTCATCAACCCTGTGAA
+CATACCTAAACGTTGCCTCGGCGGGAACAGACGGCCCCGTGAAACGGGCCGCCCCCGCCA
+GAGGACCCTTAACTCTGTTTCTATAATGTTTCTTCTGAGTAAAACAAGCAAATAAATTAA
+AACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATA
+AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGC
+CAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTACAACCCTCAGGCCCCCGGGCCTG
+GCGTTGGGGATCGGCGGAGCCCCTCCGTGGGCACACGCCGTCCCCCAAATACAGTGGCGG
+TCCCGCCGCAGCTTCCATCGCGTAGTAGCTAACACCTCGCGACTGGAGAGCGGCGCGGCC
+ACGCCGTAAAACACCCAACTCTTCTGAAGTTGACCTCGAATCAGGTAGGAATACCCGCTG
+AACTTAAGCATATCAATAAGCGGAGGA

data/599088294.fasta

@@ -0,0 +1,11 @@
+>KJ400965.1 Uncultured Fusarium clone TTRK-10 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
+TCCGTAGGTGAACCTGCGGAGGGATCATTACCGAGTTATACAACTCATCAACCCTGTGAA
+CATACCTAAACGTTGCCTCGGCGGGAACAGACGGCCCCGTGAAACGGGCCGCCCCCGCCA
+GAGGACCCCCTAACTCTGTTTCTATAATGTTTCTTCTGAGTAAAACAAGCAAATAAATTA
+AAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGAT
+AAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCG
+CCAGTATTCTGGCGGGCATGCCTGTTCGAGCGTCATTACAACCCTCAGGCCCCCGGGCCT
+GGCGTTGGGGATCGGCGGAGCCCCCCGTGGGCACACGCCGTCCCCCAAATACAGTGGCGG
+TCCCGCCGCAGCTTCCATCGCGTAGTAGCTAACACCTCGCGACTGGAGAGCGGCGCGGCC
+ACGCCGTAAAACACCCAACTCTTCTGAAGTTGACCTCGAATCAGGTAGGAATACCCGCTG
+AACTTAAGCATATCAATAAGCGGAGGA