annotate tools/extract/extract_genomic_dna.py @ 1:cdcb0ce84a1b

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#!/usr/bin/env python
"""
usage: %prog $input $out_file1
    -1, --cols=N,N,N,N: Columns for start, end, strand in input file
    -d, --dbkey=N: Genome build of input file
    -o, --output_format=N: the data type of the output file
    -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc
    -I, --interpret_features: if true, complete features are interpreted when input is GFF 
    -F, --fasta=<genomic_sequences>: genomic sequences to use for extraction
    -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format.
"""
from galaxy import eggs
import pkg_resources
pkg_resources.require( "bx-python" )
import sys, string, os, re, tempfile, subprocess
from bx.cookbook import doc_optparse
from bx.intervals.io import Header, Comment
import bx.seq.nib
import bx.seq.twobit
from galaxy.tools.util.galaxyops import *
from galaxy.datatypes.util import gff_util

assert sys.version_info[:2] >= ( 2, 4 )
    
def stop_err( msg ):
    sys.stderr.write( msg )
    sys.exit()

def reverse_complement( s ):
    complement_dna = {"A":"T", "T":"A", "C":"G", "G":"C", "a":"t", "t":"a", "c":"g", "g":"c", "N":"N", "n":"n" }
    reversed_s = []
    for i in s:
        reversed_s.append( complement_dna[i] )
    reversed_s.reverse()
    return "".join( reversed_s )

def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
    seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR
    seq_path = ''
    for line in open( seq_file ):
        line = line.rstrip( '\r\n' )
        if line and not line.startswith( "#" ) and line.startswith( 'seq' ):
            fields = line.split( '\t' )
            if len( fields ) < 3:
                continue
            if fields[1] == dbkey:
                seq_path = fields[2].strip()
                break
    return seq_path
        
def __main__():
    #
    # Parse options, args.
    #
    options, args = doc_optparse.parse( __doc__ )
    try:
        chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
        dbkey = options.dbkey
        output_format = options.output_format
        gff_format = options.gff
        interpret_features = options.interpret_features
        GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
        fasta_file = options.fasta
        input_filename, output_filename = args
    except:
        doc_optparse.exception()

    includes_strand_col = strand_col >= 0
    strand = None
    nibs = {}
    twobits = {}
        
    #
    # Set path to sequence data.
    #
    if fasta_file:
        # Need to create 2bit file from fasta file.
        try:
            seq_path = tempfile.NamedTemporaryFile( dir="." ).name
            cmd = "faToTwoBit %s %s" % ( fasta_file, seq_path )
        
            tmp_name = tempfile.NamedTemporaryFile( dir="." ).name
            tmp_stderr = open( tmp_name, 'wb' )
            proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
            returncode = proc.wait()
            tmp_stderr.close()

            # Get stderr, allowing for case where it's very large.
            tmp_stderr = open( tmp_name, 'rb' )
            stderr = ''
            buffsize = 1048576
            try:
                while True:
                    stderr += tmp_stderr.read( buffsize )
                    if not stderr or len( stderr ) % buffsize != 0:
                        break
            except OverflowError:
                pass
            tmp_stderr.close()

            # Error checking.
            if returncode != 0:
                raise Exception, stderr
        except Exception, e:
            stop_err( 'Error running faToTwoBit. ' + str( e ) )
    else:
        seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR )
        if not os.path.exists( seq_path ):
            # If this occurs, we need to fix the metadata validator.
            stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey )
    
    #
    # Fetch sequences.
    #
    
    # Get feature's line(s).
    def get_lines( feature ):
        if isinstance( feature, gff_util.GFFFeature ):
            return feature.lines()
        else:
            return [ feature.rstrip( '\r\n' ) ]
    
    skipped_lines = 0
    first_invalid_line = 0
    invalid_lines = []
    fout = open( output_filename, "w" )
    warnings = []
    warning = ''
    twobitfile = None
    file_iterator = open( input_filename )
    if gff_format and interpret_features:
        file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False )
    line_count = 1
    for feature in file_iterator:
        # Ignore comments, headers.
        if isinstance( feature, ( Header, Comment ) ):
            line_count += 1
            continue
            
        if gff_format and interpret_features:
            # Processing features.
            gff_util.convert_gff_coords_to_bed( feature )
            chrom = feature.chrom
            start = feature.start
            end = feature.end
            strand = feature.strand
        else:
            # Processing lines, either interval or GFF format.
            line = feature.rstrip( '\r\n' )
            if line and not line.startswith( "#" ):
                fields = line.split( '\t' )
                try:
                    chrom = fields[chrom_col]
                    start = int( fields[start_col] )
                    end = int( fields[end_col] )
                    if gff_format:
                        start, end = gff_util.convert_gff_coords_to_bed( [start, end] )
                    if includes_strand_col:
                        strand = fields[strand_col]
                except:
                    warning = "Invalid chrom, start or end column values. "
                    warnings.append( warning )
                    if not invalid_lines:
                        invalid_lines = get_lines( feature )
                        first_invalid_line = line_count
                    skipped_lines += len( invalid_lines )
                    continue
                if start > end:
                    warning = "Invalid interval, start '%d' > end '%d'.  " % ( start, end )
                    warnings.append( warning )
                    if not invalid_lines:
                        invalid_lines = get_lines( feature )
                        first_invalid_line = line_count
                    skipped_lines += len( invalid_lines )
                    continue

                if strand not in ['+', '-']:
                    strand = '+'
                sequence = ''
            else:
                continue

        # Open sequence file and get sequence for feature/interval. 
        if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ):
            # TODO: improve support for GFF-nib interaction.
            if chrom in nibs:
                nib = nibs[chrom]
            else:
                nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) )
            try:
                sequence = nib.get( start, end-start )
            except Exception, e:
                warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
                warnings.append( warning )
                if not invalid_lines:
                    invalid_lines = get_lines( feature )
                    first_invalid_line = line_count
                skipped_lines += len( invalid_lines )
                continue
        elif seq_path and os.path.isfile( seq_path ):
            if not(twobitfile):
                twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) )
            try:
                if options.gff and interpret_features:
                    # Create sequence from intervals within a feature.
                    sequence = ''
                    for interval in feature.intervals:
                        sequence += twobitfile[interval.chrom][interval.start:interval.end]
                else:
                    sequence = twobitfile[chrom][start:end]
            except:
                warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " %( start, end-start, chrom )
                warnings.append( warning )
                if not invalid_lines:
                    invalid_lines = get_lines( feature )
                    first_invalid_line = line_count
                skipped_lines += len( invalid_lines )
                continue
        else:
            warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey )
            warnings.append( warning )
            if not invalid_lines:
                invalid_lines = get_lines( feature )
                first_invalid_line = line_count
            skipped_lines += len( invalid_lines )
            continue
        if sequence == '':
            warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " \
                        % ( chrom, start, end, dbkey )
            warnings.append( warning )
            if not invalid_lines:
                invalid_lines = get_lines( feature )
                first_invalid_line = line_count
            skipped_lines += len( invalid_lines )
            continue
        if includes_strand_col and strand == "-":
            sequence = reverse_complement( sequence )

        if output_format == "fasta" :
            l = len( sequence )        
            c = 0
            if gff_format:
                start, end = gff_util.convert_bed_coords_to_gff( [ start, end ] )
            fields = [dbkey, str( chrom ), str( start ), str( end ), strand]
            meta_data = "_".join( fields )
            fout.write( ">%s\n" % meta_data )
            while c < l:
                b = min( c + 50, l )
                fout.write( "%s\n" % str( sequence[c:b] ) )
                c = b
        else: # output_format == "interval"
            if gff_format and interpret_features:
                # TODO: need better GFF Reader to capture all information needed
                # to produce this line.
                meta_data = "\t".join( 
                                [feature.chrom, "galaxy_extract_genomic_dna", "interval", \
                                 str( feature.start ), str( feature.end ), feature.score, feature.strand,
                                 ".", gff_util.gff_attributes_to_str( feature.attributes, "GTF" ) ] )
            else:
                meta_data = "\t".join( fields )
            if gff_format:
                format_str = "%s seq \"%s\";\n"
            else:
                format_str = "%s\t%s\n"
            fout.write( format_str % ( meta_data, str( sequence ) ) )
            
        # Update line count.
        if isinstance( feature, gff_util.GFFFeature ):
            line_count += len( feature.intervals )
        else:
            line_count += 1

    fout.close()

    if warnings:
        warn_msg = "%d warnings, 1st is: " % len( warnings )
        warn_msg += warnings[0]
        print warn_msg
    if skipped_lines:
        # Error message includes up to the first 10 skipped lines.
        print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) )

if __name__ == "__main__": __main__()