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

@@ -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)):

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)

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)

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))

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))

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)

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