diff tools/filters/seq_filter_by_id.py @ 0:5844f6a450ed

Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/seq_filter_by_id.py	Tue Jun 07 17:24:30 2011 -0400
@@ -0,0 +1,182 @@
+#!/usr/bin/env python
+"""Filter a FASTA, FASTQ or SSF file with IDs from a tabular file.
+
+Takes six command line options, tabular filename, ID column numbers (comma
+separated list using one based counting), input filename, input type (e.g.
+FASTA or SFF) and two output filenames (for records with and without the
+given IDs, same format as input sequence file).
+
+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.
+
+When filtering an SFF file, any Roche XML manifest in the input file is
+preserved in both output files.
+
+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 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 2010 by Peter Cock, SCRI, UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.1 of the script.
+"""
+import sys
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg.rstrip() + "\n")
+    sys.exit(err)
+
+#Parse Command Line
+try:
+    tabular_file, cols_arg, in_file, seq_format, out_positive_file, out_negative_file = sys.argv[1:]
+except ValueError:
+    stop_err("Expected six 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)
+
+if out_positive_file == "-" and out_negative_file == "-":
+    stop_err("Neither output file requested")
+
+
+#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()
+
+
+if seq_format.lower()=="sff":
+    #Now write filtered SFF file based on IDs from BLAST file
+    try:
+        from Bio.SeqIO.SffIO import SffIterator, SffWriter
+    except ImportError:
+        stop_err("Requires Biopython 1.54 or later")
+
+    try:
+        from Bio.SeqIO.SffIO import ReadRocheXmlManifest
+    except ImportError:
+        #Prior to Biopython 1.56 this was a private function
+        from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
+    in_handle = open(in_file, "rb") #must be binary mode!
+    try:
+        manifest = ReadRocheXmlManifest(in_handle)
+    except ValueError:
+        manifest = None
+    #This makes two passes though the SFF file with isn't so efficient,
+    #but this makes the code simple.
+    if out_positive_file != "-":
+        out_handle = open(out_positive_file, "wb")
+        writer = SffWriter(out_handle, xml=manifest)
+        in_handle.seek(0) #start again after getting manifest
+        pos_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id in ids)
+        out_handle.close()
+    if out_negative_file != "-":
+        out_handle = open(out_negative_file, "wb")
+        writer = SffWriter(out_handle, xml=manifest)
+        in_handle.seek(0) #start again
+        neg_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id not in ids)
+        out_handle.close()
+    #And we're done
+    in_handle.close()
+    #At the time of writing, Galaxy doesn't show SFF file read counts,
+    #so it is useful to put them in stdout and thus shown in job info.
+    if out_positive_file != "-" and out_negative_file != "-":
+        print "%i with and %i without specified IDs" % (pos_count, neg_count)
+    elif out_positive_file != "-":
+        print "%i with specified IDs" % pos_count
+    elif out_negative_file != "-":
+        print "%i without specified IDs" % neg_count
+elif seq_format.lower()=="fasta":
+    #Write filtered FASTA file based on IDs from tabular file
+    from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
+    reader = fastaReader(open(in_file, "rU"))
+    if out_positive_file != "-" and out_negative_file != "-":
+        print "Generating two FASTA files"
+        positive_writer = fastaWriter(open(out_positive_file, "w"))
+        negative_writer = fastaWriter(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 FASTA file"
+        positive_writer = fastaWriter(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 FASTA file"
+        negative_writer = fastaWriter(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()
+elif seq_format.lower().startswith("fastq"):
+    #Write filtered FASTQ file based on IDs from tabular file
+    from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+    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("Unsupported file type %r" % seq_format)