diff trimal_repo/scripts/get_sequences_gaps_ratio.py @ 0:b15a3147e604 draft

"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/scripts/get_sequences_gaps_ratio.py	Fri Mar 25 17:10:43 2022 +0000
@@ -0,0 +1,78 @@
+#!/usr/bin/python3
+
+#
+# 'get_sequneces_gaps.py'
+#
+#   Script implemented to obtain the sequences index for those seuqneces 
+#   exceding a minimum gaps' ratio threshold.
+#
+#   [2020] S. Capella-Gutierrez - [e-mail]
+#
+#   this script is free software: you can redistribute it and/or modify it under
+#   the terms of the GNU General Public License as published by the Free
+#   Software Foundation, the last available version.
+#
+#   this script is distributed in the hope that it will be useful, but WITHOUT
+#   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+#   more details on <http://www.gnu.org/licenses/>
+#
+from Bio import AlignIO
+import argparse
+import sys
+import os
+
+if __name__ == "__main__":
+
+  parser = argparse.ArgumentParser()
+
+  parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
+    str, help = "Input alignment")
+
+  parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
+    str, help = "Set output file. It will be generated into FASTA format")
+
+  parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \
+    type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \
+    "phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")
+
+  parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
+    type = str, help = "Define the gap symbol used in the input alignment")
+
+  parser.add_argument("--show_only_index", dest = "showIndexes", default = False, \
+    action = "store_true", help = "Show only the indexes of sequences with a "
+    + "gaps' ratio equal or higher than the established threshold")
+    
+  parser.add_argument("--threshold", dest = "gapsThreshold", default = 0.0, \
+    type = float, help = "Identify sequences with a minimum of gaps' ratio")
+
+  parser.add_argument("--keep_header", dest = "keepHeader", default = False,
+    action = "store_true", help = "Keep original alignment sequence IDs indepen"
+    + "dently of blank spaces on it")
+
+  args = parser.parse_args()
+
+  if not os.path.isfile(args.inFile):
+    sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
+
+  index = 0
+  indexes = []
+  ofile = open(args.outFile, "w") if args.outFile else sys.stdout
+  for record in AlignIO.read(args.inFile, format = args.inFormat):
+    sequence_id = record.id if not args.keepHeader else record.description
+    sequence = str(record.seq)
+
+    length = len(sequence)
+    valid = len([ps for ps in range(length) if sequence[ps] != args.gapSymbol])
+    gaps_ratio = 1 - (valid/length)
+
+    if gaps_ratio >= args.gapsThreshold:
+      if not args.showIndexes:
+        print(f'{index:4d}\t{sequence_id:30}\t{gaps_ratio:.4f}', file = ofile)
+      indexes.append(index)
+    index += 1
+
+  if args.showIndexes:
+    print (','.join(map(str, indexes)), file = ofile)
+
+  ofile.close()