diff tools/fastq/fastq_filter_by_id.py @ 3:e0041942a12d draft default tip

v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license

--- a/tools/fastq/fastq_filter_by_id.py	Tue Jun 07 17:24:08 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-#!/usr/bin/env python
-"""Filter a FASTQ file with IDs from a tabular file, e.g. from BLAST.
-
-NOTE - This script is now OBSOLETE, having been replaced by a new verion
-which handles FASTA, FASTQ and SFF all in one.
-
-Takes five command line options, tabular filename, ID column numbers
-(comma separated list using one based counting), input FASTA filename, and
-two output FASTA filenames (for records with and without the given IDs).
-
-If either output filename is just a minus sign, that file is not created.
-This is intended to allow output for just the matched (or just the non-matched)
-records.
-
-Note in the default NCBI BLAST+ tabular output, the query sequence ID is
-in column one, and the ID of the match from the database is in column two.
-Here sensible values for the column numbers would therefore be "1" or "2".
-
-This script is copyright 2010-2011 by Peter Cock, SCRI, UK. All rights reserved.
-See accompanying text file for licence details (MIT/BSD style).
-
-This is version 0.0.4 of the script.
-"""
-import sys
-from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
-
-def stop_err( msg ):
-    sys.stderr.write( msg )
-    sys.exit()
-
-#Parse Command Line
-try:
-    tabular_file, cols_arg, in_file, out_positive_file, out_negative_file = sys.argv[1:]
-except ValueError:
-    stop_err("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
-try:
-    columns = [int(arg)-1 for arg in cols_arg.split(",")]
-except ValueError:
-    stop_err("Expected list of columns (comma separated integers), got %s" % cols_arg)
-
-#Read tabular file and record all specified identifiers
-ids = set()
-handle = open(tabular_file, "rU")
-if len(columns)>1:
-    #General case of many columns
-    for line in handle:
-        if line.startswith("#"):
-            #Ignore comments
-            continue
-        parts = line.rstrip("\n").split("\t")
-        for col in columns:
-            ids.add(parts[col])
-    print "Using %i IDs from %i columns of tabular file" % (len(ids), len(columns))
-else:
-    #Single column, special case speed up
-    col = columns[0]
-    for line in handle:
-        if not line.startswith("#"):
-            ids.add(line.rstrip("\n").split("\t")[col])
-    print "Using %i IDs from tabular file" % (len(ids))
-handle.close()
-
-#Write filtered FASTQ file based on IDs from tabular file
-reader = fastqReader(open(in_file, "rU"))
-if out_positive_file != "-" and out_negative_file != "-":
-    print "Generating two FASTQ files"
-    positive_writer = fastqWriter(open(out_positive_file, "w"))
-    negative_writer = fastqWriter(open(out_negative_file, "w"))
-    for record in reader:
-        #The [1:] is because the fastaReader leaves the @ on the identifer.
-        if record.identifier and record.identifier.split()[0][1:] in ids:
-            positive_writer.write(record)
-        else:
-            negative_writer.write(record)
-    positive_writer.close()
-    negative_writer.close()
-elif out_positive_file != "-":
-    print "Generating matching FASTQ file"
-    positive_writer = fastqWriter(open(out_positive_file, "w"))
-    for record in reader:
-        #The [1:] is because the fastaReader leaves the @ on the identifer.
-        if record.identifier and record.identifier.split()[0][1:] in ids:
-            positive_writer.write(record)
-    positive_writer.close()
-elif out_negative_file != "-":
-    print "Generating non-matching FASTQ file"
-    negative_writer = fastqWriter(open(out_negative_file, "w"))
-    for record in reader:
-        #The [1:] is because the fastaReader leaves the @ on the identifer.
-        if not record.identifier or record.identifier.split()[0][1:] not in ids:
-            negative_writer.write(record)
-    negative_writer.close()
-else:
-    stop_err("Neither output file requested")
-reader.close()