adding sequence checks

Author: maxibor

README.md

@@ -31,7 +31,7 @@ adrsm -d ./data/genomes ./data/short_genome_list.csv
 ```
 maxime@gph:~$ adrsm --help
 usage: ADRSM [-h] [-d DIRECTORY] [-r READLENGTH] [-l LENSTDEV] [-fwd FWDADAPT]
-             [-rev REVADAPT] [-e ERROR] [-o OUTPUT] [-s STATS]
+             [-rev REVADAPT] [-e ERROR] [-o OUTPUT] [-q QUALITY] [-s STATS]
              confFile
 
 Ancient DNA Read Simulator for Metagenomics
@@ -50,6 +50,7 @@ optional arguments:
                  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
   -e ERROR       Illumina sequecing error. Default = 0.01
   -o OUTPUT      Output file basename. Default = ./metagenome.*
+  -q QUALITY     Base quality encoding. Default = d (PHRED+64)
   -s STATS       Statistic file. Default = stats.csv
 
 ```

adrsm

@@ -47,6 +47,11 @@ def _get_args():
     default="metagenome",
     help="Output file basename. Default = ./metagenome.*")
     parser.add_argument(
+    '-q',
+    dest="quality",
+    default="d",
+    help="Base quality encoding. Default = d (PHRED+64)")
+    parser.add_argument(
     '-s',
     dest="stats",
     default="stats.csv",
@@ -62,9 +67,10 @@ def _get_args():
     a2 = args.revAdapt
     err = float(args.error)
     outfile= args.output
+    quality = args.quality
     stats = args.stats
 
-    return(infile, gendir, readlen, lendev, a1, a2, err, outfile, stats)
+    return(infile, gendir, readlen, lendev, a1, a2, err, outfile, quality, stats)
 
 def read_config(infile, gendir):
     """
@@ -83,7 +89,7 @@ def read_config(infile, gendir):
     return(genomes)
 
 if __name__ == "__main__":
-    INFILE, GENDIR, READLEN, LENDEV, A1, A2, ERR, OUTFILE, STATS = _get_args()
+    INFILE, GENDIR, READLEN, LENDEV, A1, A2, ERR, OUTFILE, QUALITY, STATS = _get_args()
     MINLENGTH = 20
 
     genome_dict = {}
@@ -100,7 +106,8 @@ if __name__ == "__main__":
                                   A2 = A2,
                                   MINLENGTH = MINLENGTH,
                                   ERR = ERR,
-                                  fastq_dict = genome_dict)
+                                  fastq_dict = genome_dict,
+                                  QUALITY=QUALITY)
         stat_dict[ad.get_basename(agenome)] = stat_and_run
 
     ad.write_fastq_multi(fastq_dict=genome_dict, outputfile=OUTFILE)

adrsm_single

@@ -2,7 +2,7 @@
 
 from numpy import random as npr
 
-QUALITY = "G"
+
 
 def get_basename(file_name):
     if ("/") in file_name:
@@ -18,7 +18,7 @@ def reverse_complement(dna) :
     '''
     dna = dna[::-1]
     revcom = []
-    complement = {"A" : "T", "T" : "A" , "G" : "C" , "C" : "G"}
+    complement = {"A" : "T", "T" : "A" , "G" : "C" , "C" : "G", "N": "N"}
     for letter in dna :
         for key in complement.keys() :
             if letter == key :
@@ -66,25 +66,37 @@ def complement_read(all_inserts, adaptor, read_length):
             read = insert
         elif inlen > read_length:
             read = insert[0:read_length]
-        result.append(read)
+        if len(read) == read_length:
+            read = read.upper()
+            read = list(read)
+            for j in range(0, len(read)):
+                if read[j] not in ["A","T","G","C","N"]:
+                    read[j] = "N"
+            result.append("".join(read))
     return(result)
 
 def add_error(all_reads, error_rate):
     for i in range(0, len(all_reads)):
         read = list(all_reads[i])
         for j in range(0, len(read)):
+            if read[j].upper() not in ["A","T","G","C","N"]:
+                read[j] = "N"
             if npr.random() < error_rate:
                 read[j] = npr.choice(["A","T","G","C"])
                 all_reads[i] = "".join(read)
     return(all_reads)
 
-def prepare_fastq(fastq_dict, fwd_reads, rev_reads, basename, read_length):
+def prepare_fastq(fastq_dict, fwd_reads, rev_reads, basename, read_length, quality):
     fastq_dict[basename] = [[] for i in range(2)]
     cnt = 1
     for read1, read2 in zip(fwd_reads, rev_reads):
-        towrite_fwd = "@"+basename+"_"+str(cnt)+"/1"+"\n"+read1+"\n+\n"+QUALITY*read_length+"\n"
+        read1 = read1.rstrip()
+        read2 = read2.rstrip()
+        readlen1 = len(read1)
+        readlen2 = len(read2)
+        towrite_fwd = "@"+basename+"_"+str(cnt)+"/1"+"\n"+read1+"\n+\n"+quality*readlen1+"\n"
         fastq_dict[basename][0].append(towrite_fwd)
-        towrite_rev = "@"+basename+"_"+str(cnt)+"/2"+"\n"+read2+"\n+\n"+QUALITY*read_length+"\n"
+        towrite_rev = "@"+basename+"_"+str(cnt)+"/2"+"\n"+read2+"\n+\n"+quality*readlen2+"\n"
         fastq_dict[basename][1].append(towrite_rev)
         cnt += 1
     return(fastq_dict)
@@ -98,64 +110,8 @@ def write_fastq_multi(fastq_dict, outputfile):
                 for reads2 in fastq_dict[akey][1]:
                     f2.write(reads2)
 
-def write_fastq(all_reads, basename, orientation, read_length, outfile):
-    if not outfile:
-        with open(basename+"."+str(orientation)+".fastq", "w") as fw:
-            for read in all_reads:
-                fw.write("@"+basename+"\n")
-                fw.write(read+"\n")
-                fw.write("+\n")
-                fw.write(QUALITY*read_length+"\n")
-    else:
-        with open(outfile+"."+str(orientation)+".fastq", "w") as fw:
-            for read in all_reads:
-                fw.write("@"+basename+"\n")
-                fw.write(read+"\n")
-                fw.write("+\n")
-                fw.write(QUALITY*read_length+"\n")
-
-
-
-def run_read_simulation(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1, A2, OUTFILE, MINLENGTH, ERR):
-    print("INFILE: ", INFILE)
-    if COV:
-        print("COV: ", COV)
-    else:
-        print("NREAD: ", NREAD)
-    print("READLEN: ", READLEN)
-    print("INSERLEN: ", INSERLEN)
-    print("LENDEV: ", LENDEV)
-    print("A1: ", A1)
-    print("A2: ", A2)
-    print("OUTFILE: ", OUTFILE)
-
-    nread = None
-
-
-    basename = get_basename(INFILE)
-    fasta = read_fasta(INFILE)
-
-    if COV:
-        nread = int(fasta[1]/INSERLEN)
-        print("nread: ", nread)
-
-    insert_lengths = [int(n) for n in npr.normal(INSERLEN, LENDEV, nread)]
-
-
-
-
-    all_inserts = random_insert(fasta, insert_lengths, READLEN, MINLENGTH)
-    fwd_inserts = all_inserts
-    rev_inserts = [reverse_complement(i) for i in all_inserts]
-    fwd_reads = complement_read(fwd_inserts, A1, READLEN)
-    fwd_reads = add_error(fwd_reads, ERR)
-    rev_reads = complement_read(rev_inserts, A2, READLEN)
-    rev_reads = add_error(rev_reads, ERR)
-
-    write_fastq(fwd_reads, basename, 1, READLEN, OUTFILE)
-    write_fastq(rev_reads, basename, 2, READLEN, OUTFILE)
 
-def run_read_simulation_multi(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1, A2, MINLENGTH, ERR, fastq_dict):
+def run_read_simulation_multi(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1, A2, MINLENGTH, ERR, fastq_dict, QUALITY):
     print("INFILE: ", INFILE)
     if COV:
         print("COV: ", COV)
@@ -166,6 +122,7 @@ def run_read_simulation_multi(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1,
     print("LENDEV: ", LENDEV)
     print("A1: ", A1)
     print("A2: ", A2)
+    print("QUALITY", QUALITY)
     nread = None
 
 
@@ -189,7 +146,12 @@ def run_read_simulation_multi(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1,
     rev_reads = complement_read(rev_inserts, A2, READLEN)
     rev_reads = add_error(rev_reads, ERR)
 
-    prepare_fastq(fastq_dict = fastq_dict, fwd_reads = fwd_reads, rev_reads = rev_reads, basename = basename, read_length = READLEN)
+    prepare_fastq(fastq_dict = fastq_dict,
+                  fwd_reads = fwd_reads,
+                  rev_reads = rev_reads,
+                  basename = basename,
+                  read_length = READLEN,
+                  quality = QUALITY)
     return(nread * INSERLEN)
 
 def write_stat(stat_dict, stat_out):