diff yac.py @ 0:1dde0b3d5f6a draft default tip

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/yac.py	Wed Mar 17 22:08:17 2021 +0000
@@ -0,0 +1,156 @@
+#!/usr/bin/python
+# yac = yet another clipper
+# v 1.2.1 - 23-08-2014 - Support FastQ output
+# v 1.1.0 - 23-08-2014 - argparse implementation
+# Christophe Antoniewski <[e-mail]>
+
+import argparse
+from itertools import islice
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument(
+        '--input', action="store", nargs='+', help="input fastq files")
+    the_parser.add_argument(
+        '--output', action="store", type=str,
+        help="output, clipped fasta file")
+    the_parser.add_argument(
+        '--output_format', action="store", type=str,
+        help="output format, fasta or fastq")
+    the_parser.add_argument(
+        '--adapter_to_clip', action="store", type=str,
+        help="adapter sequence to clip")
+    the_parser.add_argument(
+        '--min', action="store", type=int,
+        help="minimal size of clipped sequence to keep")
+    the_parser.add_argument(
+        '--max', action="store", type=int,
+        help="maximal size of clipped sequence to keep")
+    the_parser.add_argument('--Nmode', action="store", type=str, choices=[
+                            "accept", "reject"],
+                            help="accept or reject Ns in clipped sequences")
+    args = the_parser.parse_args()
+    args.adapter_to_clip = args.adapter_to_clip.upper()
+    return args
+
+
+class Clip:
+
+    def __init__(self, inputfile, outputfile, output_format,
+                 adapter, minsize, maxsize, Nmode):
+        self.inputfile = inputfile
+        self.outputfile = outputfile
+        self.output_format = output_format
+        self.adapter = adapter
+        self.minsize = int(minsize)
+        self.maxsize = int(maxsize)
+        self.Nmode = Nmode
+        for line in open(inputfile):
+            if line[0] == "@":
+                self.inputformat = "fastq"
+                break
+            elif line[0] == ">":
+                self.inputformat = "fasta"
+
+        def motives(sequence):
+            '''
+            return a list of motives for perfect (6nt) or
+            imperfect (7nt with one mismatch) search on import string module
+            '''
+            sequencevariants = [
+                sequence[0:6]]  # initializes list with 6mer perfect match
+            dicsubst = {"A": "TGCN", "T": "AGCN", "G": "TACN", "C": "GATN"}
+            for pos in enumerate(sequence[:6]):
+                for subst in dicsubst[pos[1]]:
+                    sequencevariants.append(
+                        sequence[:pos[0]] + subst + sequence[pos[0] + 1:7])
+            return sequencevariants
+        self.adaptmotifs = motives(self.adapter)
+
+    def scanadapt(self, adaptmotives=[], sequence="", qscore=""):
+        '''scans sequence for adapter motives'''
+        match_position = sequence.rfind(adaptmotives[0])
+        if qscore:
+            if match_position != -1:
+                return sequence[:match_position], qscore[:match_position]
+            for motif in adaptmotives[1:]:
+                match_position = sequence.rfind(motif)
+                if match_position != -1:
+                    return sequence[:match_position], qscore[:match_position]
+            return sequence, qscore
+        else:
+            if match_position != -1:
+                return sequence[:match_position]
+            for motif in adaptmotives[1:]:
+                match_position = sequence.rfind(motif)
+                if match_position != -1:
+                    return sequence[:match_position]
+            return sequence
+
+    def write_output(self, id, read, qscore, output):
+        if self.output_format == "fasta":
+            block = ">{0}\n{1}\n".format(id, read)
+        else:
+            block = "@HWI-{0}\n{1}\n+\n{2}\n".format(id, read, qscore)
+        output.write(block)
+
+    def fasta_in_write_output(self, id, read, output):
+        output.write(">{0}\n{1}\n".format(id, read))
+
+    def handle_io_fastq(self):
+        '''Open input fastq file, pass read sequence and read qscore to
+        scanadapt function. Pass clipped read and qscore to output function.'''
+        id = 0
+        output = open(self.outputfile, "a")
+        with open(self.inputfile, "r") as input:
+            block_gen = islice(input, 1, None, 2)
+            for i, line in enumerate(block_gen):
+                if i % 2:
+                    qscore = line.rstrip()
+                else:
+                    read = line.rstrip()
+                    continue
+                try:
+                    trimmed_read, trimmed_qscore = self.scanadapt(
+                        self.adaptmotifs, read, qscore)
+                except ValueError:
+                    continue
+                if self.minsize <= len(trimmed_read) <= self.maxsize:
+                    if (self.Nmode == "reject") and ("N" in trimmed_read):
+                        continue
+                    id += 1
+                    self.write_output(id, trimmed_read, trimmed_qscore, output)
+        output.close()
+
+    def handle_io_fasta(self):
+        '''Open input fasta file, pass header and read sequence to scanadapt
+        function. Pass clipped read and qscore to output function.'''
+        id = 0
+        output = open(self.outputfile, "a")
+        with open(self.inputfile, "r") as input:
+            block_gen = islice(input, 1, None, 2)
+            for i, line in enumerate(block_gen):
+                read = line.rstrip()
+                trimmed_read = self.scanadapt(self.adaptmotifs, read)
+                if self.minsize <= len(trimmed_read) <= self.maxsize:
+                    if (self.Nmode == "reject") and ("N" in trimmed_read):
+                        continue
+                    id += 1
+                    self.fasta_in_write_output(id, trimmed_read, output)
+        output.close()
+
+
+def main(*argv):
+    instanceClip = Clip(*argv)
+    if instanceClip.inputformat == "fasta":
+        instanceClip.handle_io_fasta()
+    else:
+        instanceClip.handle_io_fastq()
+
+
+if __name__ == "__main__":
+    args = Parser()
+    for inputfile in args.input:
+        main(inputfile, args.output, args.output_format,
+             args.adapter_to_clip, args.min, args.max, args.Nmode)