Merge branch 'tanya2' into 'main'

frag-changes

See merge request !25

frag_package/fragmentation_v2.py

@@ -21,12 +21,13 @@ def fasta_process(fasta_file):
                 genes[seq_id] = (seq_pattern.search(line)).group(1)
     return genes
 
-def fragmentation(fasta_file, counts_file, mean_length, std):
+def fragmentation(fasta_file, counts_file, mean_length, std, a_prob, t_prob, g_prob, c_prob):
     fasta = fasta_process(fasta_file)
     seq_counts = pd.read_csv(counts_file, names = ["seqID", "count"])
 
-    nucs = ['A','T','G','C']
-    mononuc_freqs = [0.22, 0.25, 0.23, 0.30]
+    # nucs = ['A','T','G','C']
+    # mononuc_freqs = [0.22, 0.25, 0.23, 0.30]
+    nuc_probs = {'A':a_prob, 'T':t_prob, 'G':g_prob, 'C':c_prob} # calculated using https://www.nature.com/articles/srep04532#MOESM1
 
     term_frags = [] 
     for seq_id, seq in fasta.items():
@@ -37,7 +38,7 @@ def fragmentation(fasta_file, counts_file, mean_length, std):
             # non-uniformly random DNA fragmentation implementation based on https://www.nature.com/articles/srep04532#Sec1
             # assume fragmentation by sonication for NGS workflow
             cuts = []
-            cut_nucs = np.random.choice(nucs, n_cuts, p=mononuc_freqs) 
+            cut_nucs = np.random.choice(list(nuc_probs.keys()), n_cuts, p=list(nuc_probs.values())) 
             for nuc in cut_nucs:
                 nuc_pos = [x.start() for x in re.finditer(nuc, seq)]
                 pos = np.random.choice(nuc_pos)

frag_package/main.py

 import argparse
 
 from fragmentation_v2 import fragmentation
-from utils import check_positive, extant_file
+from utils import check_positive, extant_file, check_prob
 
 
 def main(args):   
-    fasta, seq_counts, mean_length, std = args
+    fasta, seq_counts, mean_length, std, a_prob, t_prob, g_prob, c_prob = args
 
-    term_frags = fragmentation(fasta, seq_counts, mean_length, std)
+    term_frags = fragmentation(fasta, seq_counts, mean_length, std, a_prob, t_prob, g_prob, c_prob)
     with open('terminal_frags.txt', 'w') as f:
         for line in term_frags:
             f.write(line)
@@ -15,15 +15,19 @@ def main(args):
 
 # Parse command-line arguments
 def parse_arguments():
-    parser = argparse.ArgumentParser(description="Takes as input FASTA file of cDNA sequences, a CSV with sequence counts, and mean and std. dev. of fragment lengths. Outputs most terminal fragment (within desired length range) for each sequence.")
+    parser = argparse.ArgumentParser(description="Takes as input FASTA file of cDNA sequences, a CSV with sequence counts, and mean and std. dev. of fragment lengths and 4 nucleotide probabilities for the cuts. Outputs most terminal fragment (within desired length range) for each sequence.")
 
     parser.add_argument('--fasta', required=True, type=extant_file, help="FASTA file with cDNA sequences")
     parser.add_argument('--counts', required=True, type=extant_file, help="CSV file with sequence counts")
-    parser.add_argument('--mean', required = False, default = 10, type = check_positive, help="Mean fragment length (default: 10)")
-    parser.add_argument('--std', required = False, default = 1, type = check_positive, help="Standard deviation fragment length (defafult: 1)")
+    parser.add_argument('--mean', required = False, default = 300, type = check_positive, help="Mean fragment length (default: 10)")
+    parser.add_argument('--std', required = False, default = 60, type = check_positive, help="Standard deviation fragment length (defafult: 1)")
+    parser.add_argument('--A_prob', required=False, default = 0.22, type=check_prob, help="Probability cut happens after nucleotide A")
+    parser.add_argument('--T_prob', required=False, default = 0.25, type=check_prob, help="Probability cut happens after nucleotide T")
+    parser.add_argument('--G_prob', required=False, default = 0.25, type=check_prob, help="Probability cut happens after nucleotide G")
+    parser.add_argument('--C_prob', required=False, default = 0.28, type=check_prob, help="Probability cut happens after nucleotide C")
     args = parser.parse_args()
     
-    return args.fasta, args.counts, args.mean, args.std
+    return args
 
 
 if __name__ == '__main__':

frag_package/utils.py

@@ -22,3 +22,8 @@ def check_positive(value):
         raise argparse.ArgumentTypeError("%s is an invalid positive int value" % value)
     return ivalue
 
+def check_prob(value):
+    pvalue = float(value)
+    if pvalue <= 0 or pvalue>1:
+        raise argparse.ArgumentTypeError("%s is an invalid positive int value" % value)
+    return pvalue 
\ No newline at end of file