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1 #!/usr/bin/env python
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2 """Compute length of FASTA, QUAL, FASTQ or SSF sequences.
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3
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4 Takes three command line options: input sequence filename, input type
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5 (e.g. FASTA or SFF) and the output filename (tabular).
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6
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7 This tool is a short Python script which requires Biopython 1.54 or later
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8 for SFF file support. If you use this tool in scientific work leading to a
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9 publication, please cite the Biopython application note:
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10
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11 Cock et al 2009. Biopython: freely available Python tools for computational
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12 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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13 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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14
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15 This script is copyright 2018 by Peter Cock, The James Hutton Institute UK.
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16 All rights reserved. See accompanying text file for licence details (MIT
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17 license).
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18 """
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19
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20 from __future__ import print_function
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21
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22 import sys
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23
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24 if "-v" in sys.argv or "--version" in sys.argv:
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25 print("v0.0.1")
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26 sys.exit(0)
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27
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28 try:
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29 from Bio import SeqIO
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30 except ImportError:
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31 sys.exit("Missing required Python library Biopython.")
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32
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33
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34 # Parse Command Line
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35 try:
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36 in_file, seq_format, out_file = sys.argv[1:]
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37 except ValueError:
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38 sys.exit("Expected three arguments (input file, format, output file), "
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39 "got %i:\n%s" % (len(sys.argv) - 1, " ".join(sys.argv)))
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40
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41
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42 if seq_format.startswith("fastq"):
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43 # We don't care about the quality score encoding, just
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44 # need to translate Galaxy format name into something
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45 # Biopython will accept:
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46 format = "fastq"
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47 elif seq_format.lower() == "csfasta":
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48 # I have not tested with colour space FASTA
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49 format = "fasta"
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50 elif seq_format.lower == "sff":
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51 # The masked/trimmed numbers are more interesting
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52 format = "sff-trim"
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53 elif seq_format.lower() in ["fasta", "qual"]:
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54 format = seq_format.lower()
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55 else:
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56 # TODO: Does Galaxy understand GenBank, EMBL, etc yet?
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57 sys.exit("Unexpected format argument: %r" % seq_format)
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58
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59
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60 count = 0
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61 total = 0
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62 with open(out_file, "w") as out_handle:
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63 out_handle.write("#Identifier\tLength\n")
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64 for record in SeqIO.parse(in_file, format):
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65 count += 1
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66 length = len(record)
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67 total += length
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68 out_handle.write("%s\t%i\n" % (record.id, length))
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69 print("%i sequences, total length %i" % (count, total))
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