--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_length/seq_length.py	Tue May 08 09:35:45 2018 -0400
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+"""Compute length of FASTA, QUAL, FASTQ or SSF sequences.
+
+Takes three command line options: input sequence filename, input type
+(e.g. FASTA or SFF) and the output filename (tabular).
+
+This tool is a short Python script which requires Biopython 1.54 or later
+for SFF file support. If you use this tool in scientific work leading to a
+publication, please cite the Biopython application note:
+
+Cock et al 2009. Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+This script is copyright 2018 by Peter Cock, The James Hutton Institute UK.
+All rights reserved. See accompanying text file for licence details (MIT
+license).
+"""
+
+from __future__ import print_function
+
+import sys
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    print("v0.0.1")
+    sys.exit(0)
+
+try:
+    from Bio import SeqIO
+except ImportError:
+    sys.exit("Missing required Python library Biopython.")
+
+
+# Parse Command Line
+try:
+    in_file, seq_format, out_file = sys.argv[1:]
+except ValueError:
+    sys.exit("Expected three arguments (input file, format, output file), "
+             "got %i:\n%s" % (len(sys.argv) - 1, " ".join(sys.argv)))
+
+
+if seq_format.startswith("fastq"):
+    # We don't care about the quality score encoding, just
+    # need to translate Galaxy format name into something
+    # Biopython will accept:
+    format = "fastq"
+elif seq_format.lower() == "csfasta":
+    # I have not tested with colour space FASTA
+    format = "fasta"
+elif seq_format.lower == "sff":
+    # The masked/trimmed numbers are more interesting
+    format = "sff-trim"
+elif seq_format.lower() in ["fasta", "qual"]:
+    format = seq_format.lower()
+else:
+    # TODO: Does Galaxy understand GenBank, EMBL, etc yet?
+    sys.exit("Unexpected format argument: %r" % seq_format)
+
+
+count = 0
+total = 0
+with open(out_file, "w") as out_handle:
+    out_handle.write("#Identifier\tLength\n")
+    for record in SeqIO.parse(in_file, format):
+        count += 1
+        length = len(record)
+        total += length
+        out_handle.write("%s\t%i\n" % (record.id, length))
+print("%i sequences, total length %i" % (count, total))