diff bed12.py @ 0:d1d0ee366702 draft default tip

Uploaded first version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed12.py	Wed May 11 04:53:30 2016 -0400
@@ -0,0 +1,170 @@
+"""
+.. module:: bed12
+   :platform: Unix
+   :synopsis: Defines a set a generic function to parse and process bed12 files.
+
+.. moduleauthor:: Mickael Mendez <[e-mail]>
+
+.. source: https://github.com/mmendez12/umicount
+
+"""
+
+__author__ = 'mickael'
+
+
+import operator
+import itertools
+
+def get_chrom(read):
+    """Get chromosome from a bed12 line.
+
+    Args:
+        read: A list of twelve elements where each element refers to a field in the BED format.
+
+    Returns:
+        The chromosome name
+
+    >>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
+    >>> get_chrom(read)
+    'chrX'
+    """
+    return read[0]
+
+
+def get_start(read):
+    """Get start position from a bed12 line.
+
+    Args:
+        read: A list of twelve elements where each element refers to a field in the BED format.
+
+    Returns:
+        An integer representing the start position of the read.
+
+    >>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
+    >>> get_start(read)
+    100
+    """
+    return int(read[1])
+
+
+def get_end(read):
+    """Get end position from a bed12 line.
+
+    Args:
+        read: A list of twelve elements where each element refers to a field in the BED format.
+
+    Returns:
+        An integer representing the end position of the read.
+
+    >>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
+    >>> get_end(read)
+    200
+    """
+    return int(read[2])
+
+
+def get_strand(read):
+    """Get strand from a bed12 line.
+
+    Args:
+        read: A list of twelve elements where each element refers to a field in the BED format.
+
+    Returns:
+        A single char representing the strand of a read
+
+    >>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
+    >>> get_strand(read)
+    '+'
+    """
+    return read[5]
+
+def get_tss(read):
+    """Get Transcription Start Site (TSS) from a bed12 line.
+
+    Args:
+        read: A list of twelve elements where each element refers to a field in the BED format.
+
+    Returns:
+        The start position as an integer if the read is on the plus strand.
+        The end position as an integer if the read is on the minus strand.
+
+    >>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
+    >>> get_tss(read)
+    100
+    >>> read = ['chrX', '100', '200', 'toto', '12', '-', '100', '110', '255,0,0', '2', '21,25', '0,75']
+    >>> get_tss(read)
+    200
+    """
+    strand = get_strand(read)
+
+    if strand == '+':
+        return get_start(read)
+    else:
+        return get_end(read)
+
+
+def blocks_to_absolute_start_end(read):
+    """Calculate the absolute start and end of the blocks from a bed12 line.
+
+    Args:
+        read: A list of twelve elements where each element refers to a field in the BED format.
+
+    Returns:
+        A list of tuple where each tuple contains the absolute start and end coordinates of a block.
+
+    >>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
+    >>> blocks_to_absolute_start_end(read)
+    [(100, 121), (175, 200)]
+    """
+    read_start = get_start(read)
+
+    block_starts = [read_start + int(start) for start in read[11].split(',') if start]
+    block_sizes = [int(size) for size in read[10].split(',') if size]
+
+    block_starts_sizes = zip(block_starts, block_sizes)
+
+    return [(bstart, bstart + bsize) for bstart, bsize in block_starts_sizes]
+
+
+def merge_overlapping_blocks(reads):
+    """Merge blocks if they overlap.
+
+    Args:
+        reads: A list of read in the BED12 format.
+
+    Returns:
+        Two lists where the first list contains the blocks sizes and the second the blocks starts.
+        Values in the lists are integer.
+
+    >>> reads = []
+    >>> reads.append(['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '20,25', '0,75'])
+    >>> reads.append(['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '3', '10,10,25', '0,15,75'])
+    >>> merge_overlapping_blocks(reads)
+    ([25, 25], [0, 75])
+    """
+
+    blocks_list = [blocks_to_absolute_start_end(read) for read in reads]
+
+    #flatten
+    blocks = itertools.chain.from_iterable(blocks_list)
+
+    final_blocks = []
+
+    blocks = sorted(blocks, key = operator.itemgetter(0, 1))
+    known_block_start, known_block_end = blocks[0]
+
+    for block_start, block_end in blocks[1:]:
+        if block_start <= known_block_end:
+            known_block_end = max(block_end, known_block_end)
+        else:
+            final_blocks.append((known_block_start, known_block_end))
+            known_block_start, known_block_end = (block_start, block_end)
+
+    final_blocks.append((known_block_start, known_block_end))
+
+    absolute_block_start = final_blocks[0][0]
+
+    bsizes = [end - start for start, end in final_blocks]
+    bstarts = [start - absolute_block_start for start, end in final_blocks]
+
+    return bsizes, bstarts