Add files via upload (bit-genbank-to-gene-seqs.py)

bit-genbank-to-gene-seqs.py

@@ -0,0 +1,149 @@
+#!/usr/bin/env python
+
+from Bio import SeqIO
+import argparse
+import re
+import sys
+import os
+from collections import defaultdict
+
+
+def Capilize(seq):
+    outSeq = ""
+    for i in seq:
+        if i == "a":
+            outSeq += "A"
+
+        elif i == "g":
+            outSeq += "G"
+
+        elif i == "c":
+            outSeq += "C"
+
+        elif i == "t":
+            outSeq += "T"
+    return outSeq
+
+
+def remove(stringOrlist, list):
+    emptyList = []
+    for i in stringOrlist:
+        if i not in list:
+            emptyList.append(i)
+        else:
+            pass
+    outString = "".join(emptyList)
+    return outString
+
+
+def customfilter(list, items):
+    outLS = []
+    for i in list:
+        if i not in items:
+            outLS.append(i)
+    return outLS
+
+
+def delim(line):
+    ls = []
+    string = ''
+    for i in line:
+        if i != " ":
+            string += i
+        else:
+            ls.append(string)
+            string = ''
+    ls.append(string)
+    ls = customfilter(ls, [""])
+    return ls
+
+
+def reverseComplement(seq):
+    out = []
+    for i in range(len(seq)-1, -1, -1):
+        nucleotide = seq[i]
+        if nucleotide == "C":
+            nucleotide = "G"
+        elif nucleotide == "G":
+            nucleotide = "C"
+        elif nucleotide == "T":
+            nucleotide = "A"
+        elif nucleotide == "A":
+            nucleotide = "T"
+        out.append(nucleotide)
+    outString = "".join(out)
+    return outString
+
+
+
+
+
+parser = argparse.ArgumentParser(description="This script takes a genbank file and returns nucelotide sequences for all genes. Genbank file needs to be Genbank/ENA/DDJB compliant (that is, with genes included [--addgenes]). For version info, run `bit-version`.")
+
+required = parser.add_argument_group('required arguments')
+
+required.add_argument("-i", "--input_gb", help='input Genbank file (e.g. "*.gbk", "*.gb", "*.gbff"). Needs to be Genbank/ENA/DDJB compliant.', action="store", dest="input_gb", required=True)
+parser.add_argument("-f", "--output_fasta", help='Output fasta file (default: "clean.faa")', action="store", dest="output_fasta", default="clean.faa")
+
+if len(sys.argv)==1:
+  parser.print_help(sys.stderr)
+  sys.exit(0)
+
+args = parser.parse_args()
+
+input_gb = open(args.input_gb, "r")
+
+output_fasta = open(args.output_fasta, "w")
+
+
+contigsDict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
+count = 0
+seq = ""
+locus = ""
+for i in input_gb:
+    if re.match(r'LOCUS', i):
+        locus = (i.rstrip().split(" ")[7])
+        seq = ''
+    if re.match(r'ORIGIN', i.rstrip()):
+        count += 1
+    if count > 0:
+        pass
+        ls = delim(i.rstrip())
+        if len(ls) > 0:
+            seq += ("".join(ls[1:len(ls)]))
+    if re.match(r'//', i.rstrip()):
+        count = 0
+        seq = Capilize(seq)
+        contigsDict[locus] = seq
+
+
+input_gb = open(args.input_gb, "r")
+redundantList = []
+coords = ""
+for i in input_gb:
+    if re.match(r'LOCUS', i):
+        locus = (i.rstrip().split(" ")[7])
+    if re.match(r'     gene', i.rstrip()):
+        coords = (delim(i.rstrip())[1])
+        if re.findall(r'complement', coords):
+            start = (coords.split("(")[1].split(")")[0].split("..")[0])
+            start = remove(start, ["<"])
+            end = (coords.split("(")[1].split(")")[0].split("..")[1])
+            end = remove(end, [">"])
+            seq = (reverseComplement(contigsDict[locus][int(start)-1:int(end)]))
+
+        else:
+            start = (coords.split("..")[0])
+            start = remove(start, ["<"])
+            end = (coords.split("..")[1])
+            end = remove(end, [">"])
+            seq = contigsDict[locus][int(start)-1:int(end)]
+
+    if re.findall(r'/locus_tag=', i.rstrip()):
+        locusTag = (i.rstrip().split("/locus_tag=")[1])
+        locusTag = remove(locusTag, ["\""])
+        if locusTag not in redundantList:
+            redundantList.append(locusTag)
+            output_fasta.write(">" + locusTag + " " + locus + " " + coords + "\n")
+            output_fasta.write(seq + "\n")
+output_fasta.close()

bit/bit-dl-ncbi-assemblies

@@ -23,7 +23,7 @@ if [ "$#" == 0 ] || [ $1 == "-h" ] || [ $1 == "help" ]; then
 
     printf "        - [-f <str>] default: genbank\n"
     printf "                  Specify the desired format. Available options currently\n"
-    printf "                  include: genbank, fasta, protein, nt_cds, gff, feature_tab, report, stats.\n\n"
+    printf "                  include: genbank, fasta, protein, nt_cds, nt_rna, gff, feature_tab, report, stats.\n\n"
 
     printf "        - [-j <int> ] default: 1\n"
     printf "                  The number of downloads you'd like to run in parallel. Write speeds\n"
@@ -68,7 +68,7 @@ fi
 ## making sure format specified is interpretable
 if [[ "$format" != "genbank" && $format != "fasta" && $format != "protein" && $format != "nt_cds" && $format != "gff" && $format != "feature_tab" && $format != "report" && $format != "stats" ]]; then
     printf "\n  ${RED}Invalid argument passed to \'-f' option: $format\n\n${NC}"
-    printf "  Valid options are genbank, fasta, protein, gff, nt_cds, feature_tab, report, or stats.\n"
+    printf "  Valid options are genbank, fasta, protein, gff, nt_cds, nt_rna, feature_tab, report, or stats.\n"
     printf "Exiting for now.\n\n"
     exit
 fi