From 78a71d31e36d40ded490eac713614b44fe7f3bda Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 2 Jul 2007 15:28:46 +0000 Subject: [PATCH] Fix for random_intervals and other tools using bx.intervals.io.GenomicIntervalReader. Header lines are no longer requested. --- tools/encode/random_intervals_no_bits.py | 2 +- tools/extract/interval2maf.py | 2 +- tools/extract/interval2maf_pairwise.py | 2 +- tools/extract/interval_maf_to_merged_fasta.py | 2 +- tools/extract/interval_maf_to_merged_fasta_user.py | 2 +- tools/extract/user_interval2maf.py | 2 +- tools/filters/maf/maf_stats.py | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tools/encode/random_intervals_no_bits.py b/tools/encode/random_intervals_no_bits.py index 77c65445df8..fc9687be6a3 100644 --- a/tools/encode/random_intervals_no_bits.py +++ b/tools/encode/random_intervals_no_bits.py @@ -109,7 +109,7 @@ def main(): #set up length and number of regions to mimic regions = [ [] for i in range(len(bounds)) ] - for region in bx.intervals.io.GenomicIntervalReader( open(intervals_fname, 'r' ), chrom_col=interval_chr, start_col=interval_start, end_col=interval_end, strand_col=interval_strand, fix_strand=True): + for region in bx.intervals.io.GenomicIntervalReader( open(intervals_fname, 'r' ), chrom_col=interval_chr, start_col=interval_start, end_col=interval_end, strand_col=interval_strand, fix_strand=True, return_header=False): #loop through bounds, find first proper bounds then add #if an interval crosses bounds, it will be added to the first bound for i in range(len(bounds)): diff --git a/tools/extract/interval2maf.py b/tools/extract/interval2maf.py index d48cc170b3d..143b947aee5 100755 --- a/tools/extract/interval2maf.py +++ b/tools/extract/interval2maf.py @@ -151,7 +151,7 @@ def __main__(): # Iterate over input ranges num_blocks=0 num_lines = 0 - for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True): + for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False): try: num_lines += 1 src = "%s.%s" % (dbkey,region.chrom) diff --git a/tools/extract/interval2maf_pairwise.py b/tools/extract/interval2maf_pairwise.py index ddc5605a7a1..fdc2353c3ff 100644 --- a/tools/extract/interval2maf_pairwise.py +++ b/tools/extract/interval2maf_pairwise.py @@ -149,7 +149,7 @@ def __main__(): # Iterate over input ranges num_blocks=0 num_lines = 0 - for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True): + for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False): try: num_lines += 1 src = "%s.%s" % (dbkey,region.chrom) diff --git a/tools/extract/interval_maf_to_merged_fasta.py b/tools/extract/interval_maf_to_merged_fasta.py index eb410fb5bbc..783dfe30ef5 100644 --- a/tools/extract/interval_maf_to_merged_fasta.py +++ b/tools/extract/interval_maf_to_merged_fasta.py @@ -146,7 +146,7 @@ def __main__(): sys.exit() #Step through interval file - for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chr_col, start_col=start_col, end_col=end_col, strand_col=strand_col, fix_strand=True): + for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chr_col, start_col=start_col, end_col=end_col, strand_col=strand_col, fix_strand=True, return_header=False): target_sequences = {} alignment = Genomic_Region() for i in range(region.end-region.start): alignment.append(Genomic_Position(dbkey, target_dbkey)) diff --git a/tools/extract/interval_maf_to_merged_fasta_user.py b/tools/extract/interval_maf_to_merged_fasta_user.py index b1c232e3297..ab1a423dabd 100644 --- a/tools/extract/interval_maf_to_merged_fasta_user.py +++ b/tools/extract/interval_maf_to_merged_fasta_user.py @@ -121,7 +121,7 @@ def __main__(): #Step through interval file - for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chr_col, start_col=start_col, end_col=end_col, strand_col=strand_col, fix_strand=True): + for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chr_col, start_col=start_col, end_col=end_col, strand_col=strand_col, fix_strand=True, return_header=False): target_sequences = {} alignment = Genomic_Region() for i in range(region.end-region.start): alignment.append(Genomic_Position(dbkey, target_dbkey)) diff --git a/tools/extract/user_interval2maf.py b/tools/extract/user_interval2maf.py index 9a1d1735aa8..0cec69bbb3d 100644 --- a/tools/extract/user_interval2maf.py +++ b/tools/extract/user_interval2maf.py @@ -111,7 +111,7 @@ def __main__(): # Iterate over input ranges num_blocks=0 num_lines = 0 - for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True): + for region in bx.intervals.io.GenomicIntervalReader( open(interval_file, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False): try: num_lines += 1 src = "%s.%s" % (dbkey,region.chrom) diff --git a/tools/filters/maf/maf_stats.py b/tools/filters/maf/maf_stats.py index 7dc43b8e1f9..19e8485c9ac 100644 --- a/tools/filters/maf/maf_stats.py +++ b/tools/filters/maf/maf_stats.py @@ -46,7 +46,7 @@ def __main__(): num_region = 0 #loop through interval file - for region in bx.intervals.io.GenomicIntervalReader( open(input_interval_filename, 'r' ), chrom_col=chr_col, start_col=start_col, end_col=end_col, fix_strand=True): + for region in bx.intervals.io.GenomicIntervalReader( open(input_interval_filename, 'r' ), chrom_col=chr_col, start_col=start_col, end_col=end_col, fix_strand=True, return_header=False): sequences = {dbkey: [ False for i in range( region.end - region.start)]} src = dbkey + "." + region.chrom