linting + small fixes

.gitignore

@@ -52,6 +52,7 @@ Temporary Items
 # Ignore all local history of files
 .history
 .ionide
+.vscode
 
 # End of https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode
 

terminal-fragment-selector/fragmentation.py

+"""Fragment sequences."""
 import re
 
 import numpy as np
@@ -5,9 +6,19 @@ import pandas as pd
 
 
 def fasta_process(fasta_file):
+    """
+    Pre-process FASTA file.
+
+    Args:
+        fasta_file (fasta): FASTA file with cDNA sequences
+
+    Returns:
+        dict: Dictionary of gene sequence IDs and their sequence
+    """
     with open(fasta_file, "r") as f:
         lines = f.readlines()
 
+        # Tanya, try \\S instead of \S and see if that works
         ident_pattern = re.compile('>(\S+)')
         seq_pattern = re.compile('^(\S+)$')
 
@@ -21,24 +32,44 @@ 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, a_prob, t_prob, g_prob, c_prob):
+
+def fragmentation(fasta_file, counts_file, mean_length, std,
+                  a_prob, t_prob, g_prob, c_prob):
+    """
+    Fragment cDNA sequences and select terminal fragment.
+
+    Args:
+        fasta_file (fasta): FASTA file with cDNA sequences
+        counts_file (text): CSV or TSV file woth sequence counts
+        mean_length (int): mean length of desired fragments
+        std (int): standard deviation of desired fragment lengths
+        a_prob (float): probability of nucleotide A
+        t_prob (float): probability of nucleotide T
+        g_prob (float): probability of nucleotide G
+        c_prob (float): probability of nucleotide C
+
+    Returns:
+        list: list of selected terminal fragments
+    """
     fasta = fasta_process(fasta_file)
-    seq_counts = pd.read_csv(counts_file, names = ["seqID", "count"])
+    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]
-    nuc_probs = {'A':a_prob, 'T':t_prob, 'G':g_prob, 'C':c_prob} # calculated using https://www.nature.com/articles/srep04532#MOESM1
+    # calculated using https://www.nature.com/articles/srep04532#MOESM1
+    nuc_probs = {'A': a_prob, 'T': t_prob, 'G': g_prob, 'C': c_prob}
 
-    term_frags = [] 
+    term_frags = []
     for seq_id, seq in fasta.items():
         counts = seq_counts[seq_counts["seqID"] == seq_id]["count"]
-        for _ in range(counts): 
+        for _ in range(counts):
             n_cuts = int(len(seq)/mean_length)
-            
-            # non-uniformly random DNA fragmentation implementation based on https://www.nature.com/articles/srep04532#Sec1
+
+            # 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(list(nuc_probs.keys()), n_cuts, p=list(nuc_probs.values())) 
+            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)
@@ -46,8 +77,8 @@ def fragmentation(fasta_file, counts_file, mean_length, std, a_prob, t_prob, g_p
                     pos = np.random.choice(nuc_pos)
                 cuts.append(pos)
 
-            cuts.sort() 
-            cuts.insert(0,0)
+            cuts.sort()
+            cuts.insert(0, 0)
             term_frag = ""
             for i, val in enumerate(cuts):
                 if i == len(cuts)-1:
@@ -61,4 +92,3 @@ def fragmentation(fasta_file, counts_file, mean_length, std, a_prob, t_prob, g_p
             else:
                 term_frags.append(term_frag)
     return term_frags
-

terminal-fragment-selector/main.py

+"""Receive command line arguments, fragment, and output fragments."""
 import argparse
 
-from fragmentation_v2 import fragmentation
+from fragmentation import fragmentation
 from utils import check_positive, extant_file, check_prob
 
 
-def main(args):   
+def main(args):
+    """
+    Use CLI arguments to fragment sequences and output text file \
+    with selected terminal fragments.
+
+    Args:
+        args (parser): list of arguments from CLI.
+    """
     fasta, seq_counts, mean_length, std, a_prob, t_prob, g_prob, c_prob = args
 
-    term_frags = fragmentation(fasta, seq_counts, mean_length, std, a_prob, t_prob, g_prob, c_prob)
+    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)
-            f.write('\n')
+            f.write(f"{line}\n")
+
 
-# 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 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 = 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")
+    """
+    Request parameters from user on CLI.
+
+    Returns:
+        parser: list of arguments from CLI.
+    """
+    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=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
 
 
 if __name__ == '__main__':
     arguments = parse_arguments()
-    main(arguments)
\ No newline at end of file
+    main(arguments)

terminal-fragment-selector/utils.py

+"""Utility functions for command line arguments."""
 import argparse
 import os.path
 
 
-# found on https://stackoverflow.com/questions/11540854/file-as-command-line-argument-for-argparse-error-message-if-argument-is-not-va
+# found on shorturl.at/vzAX4
 def extant_file(x):
-    """
-    'Type' for argparse - checks that file exists but does not open.
-    """
     if not os.path.exists(x):
         # Argparse uses the ArgumentTypeError to give a rejection message like:
         # error: argument input: x does not exist
         raise argparse.ArgumentTypeError("{0} does not exist".format(x))
     elif not x.endswith((".fasta", ".fa", ".csv")):
-        raise argparse.ArgumentTypeError("{0} is not the correct file format".format(x))
+        raise argparse.ArgumentTypeError("""{0} is not the correct
+                                         file format""".format(x))
     return x
 
-# found on https://stackoverflow.com/questions/14117415/in-python-using-argparse-allow-only-positive-integers
+
 def check_positive(value):
-    ivalue = int(value)
-    if ivalue <= 0:
-        raise argparse.ArgumentTypeError("%s is an invalid positive int value" % value)
-    return ivalue
+    """Check input value is a positive integer.
+
+    Args:
+        value (string): command line parameter
+
+    Raises:
+        argparse.ArgumentTypeError: received a negative integer
+        argparse.ArgumentTypeError: received a non-integer value
+
+    Returns:
+        integer: integer version of input value
+    """
+    try:
+        ivalue = round(float(value))
+        if ivalue <= 0:
+            raise argparse.ArgumentTypeError(f"""Expected positive integer,
+                                             got negative integer: {value}""")
+    except ValueError as exc:
+        raise argparse.ArgumentTypeError(f"""Expected positive integer,
+                                         got: {value}""") from exc
+    else:
+        return ivalue
+
 
 def check_prob(value):
+    """
+    Check probability value is within ]0,1] range.
+
+    Args:
+        value (string): command line parameter
+
+    Raises:
+        argparse.ArgumentTypeError: received a value outside valid range
+
+    Returns:
+        float: float version of input 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
+    if pvalue <= 0 or pvalue > 1:
+        raise argparse.ArgumentTypeError("""%s is an invalid positive int
+                                         value""" % value)
+    return pvalue