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Thursday, October 29, 2015

merge the sub-cytobands to major cytoband and get the coordinates

In my pervious blog post, I wrote How to get the cooridnates of the cytobands
Now, how about I want to get coordinates of the bigger band merging all the sub-bands.
ex. chr1 p36.33 p36.32, p36.31, p36.23, p36.22, p36.13, p36.12, p36.11....p31.1 to p3 chr1 0 84900000
This is a task that requires some efforts for text processing. First look at what the data look like:
head -30 cytoBand.txt  
chr1    0   2300000 p36.33  gneg
chr1    2300000 5400000 p36.32  gpos25
chr1    5400000 7200000 p36.31  gneg
chr1    7200000 9200000 p36.23  gpos25
chr1    9200000 12700000    p36.22  gneg
chr1    12700000    16200000    p36.21  gpos50
chr1    16200000    20400000    p36.13  gneg
chr1    20400000    23900000    p36.12  gpos25
chr1    23900000    28000000    p36.11  gneg
chr1    28000000    30200000    p35.3   gpos25
chr1    30200000    32400000    p35.2   gneg
chr1    32400000    34600000    p35.1   gpos25
chr1    34600000    40100000    p34.3   gneg
chr1    40100000    44100000    p34.2   gpos25
chr1    44100000    46800000    p34.1   gneg
chr1    46800000    50700000    p33 gpos75
chr1    50700000    56100000    p32.3   gneg
chr1    56100000    59000000    p32.2   gpos50
chr1    59000000    61300000    p32.1   gneg
chr1    61300000    68900000    p31.3   gpos50
chr1    68900000    69700000    p31.2   gneg
chr1    69700000    84900000    p31.1   gpos100
chr1    84900000    88400000    p22.3   gneg
chr1    88400000    92000000    p22.2   gpos75
chr1    92000000    94700000    p22.1   gneg
chr1    94700000    99700000    p21.3   gpos75
chr1    99700000    102200000   p21.2   gneg
chr1    102200000   107200000   p21.1   gpos100
chr1    107200000   111800000   p13.3   gneg
chr1    111800000   116100000   p13.2   gpos50

The coordinates are sorted in a way that larger cytoband is also sorted: p3, p2, p1, q1, q2... so we only need to keep the major chromosome band, and keep expanding the end coordinates until it hits a new major band. At the same time, track which chromosome is processed and which major band is processed.
A python script using a list of lists data structure can serve this purpose:
import re
with open("/Users/Tammy/annotations/human/hg19_UCSC_genome/cytoBand.txt", "r") as f:
    # A list of lists
    # { ['chr1', 'p1','107200000', '125000000'], ['chr1',  'p2','84900000', '107200000'] ... ['chr2', 'p1' , '47800000', '93300000'],...} }
    genome_list = []
    # a set of chromosomes seen so far
    chrSet = set()
    # a set of chromosome arms seen so far
    armSet = set()
    # loop over each line
    for line in f:
        # split each line to a list
        lineSplit = line.strip().split()
        chr = lineSplit[0]
        start = lineSplit[1]
        end = lineSplit[2]
        band = lineSplit[3]
        ## this regex capture the p1 of p11, p11.1 or p12...
        arm = re.search('([pq]\d).+', band).group(1)

        # if this is the first time see this chr,
        # empty the armSet
        if chr not in chrSet:
            chrSet.add(chr)
            armSet = set()
            armSet.add(arm)
            arm_list = [chr, start, end, arm]
            genome_list.append(arm_list)
        else:
            if arm not in armSet:
                armSet.add(arm)
                arm_list = [chr, start, end, arm]
                ## append this to the genome_list
                genome_list.append(arm_list)
            else:
                ## keep the start of the arm as previous 
                new_start = genome_list[-1][1]
                ## change the previous end of the arm to current end
                new_end = end
                arm_list = [chr, new_start, new_end, arm]
                # mutate the last entry of arm_list
                genome_list[-1] = arm_list

ofile = open("/Users/Tammy/annotations/human/hg19_UCSC_genome/chrom_arm_list.txt", "w")
for arm_list in genome_list:
    ofile.write(arm_list[0] +"\t" + arm_list[1] + "\t" + arm_list[2] + "\t" + arm_list[3] + "\n")
    ## always remember to close the file!
ofile.close()
Let's look at the results.
$ head chrom_arm_list.txt 
chr1    0   84900000    p3
chr1    84900000    107200000   p2
chr1    107200000   125000000   p1
chr1    125000000   142600000   q1
chr1    142600000   185800000   q2
chr1    185800000   214500000   q3
chr1    214500000   249250621   q4
chr10   0   40200000    p1
chr10   40200000    52900000    q1
chr10   52900000    135534747   q2
There are many ways to achieve the same purpose. Just for some advanture, I used dictionary of dictionaries to record the data
import re
with open("/Users/Tammy/annotations/human/hg19_UCSC_genome/cytoBand.txt", "r") as f:
    # A dictionary of dictionaries
    # { chr1: {'p1': ['107200000', '125000000'], 'p2': ['84900000', '107200000'] ...}, chr2:{ 'p1': ['47800000', '93300000'],...} }
    genome_dict = {}
    # a set of chromosomes seen so far
    chrSet = set()
    for line in f:
        lineSplit = line.strip().split()
        chr = lineSplit[0]
        start = lineSplit[1]
        end = lineSplit[2]
        band = lineSplit[3]
        ## this regex capture the p1 of p11, p11.1 or p12
        arm = re.search('([pq]\d).+', band).group(1)

        ## if it is the first time see this chromosome
        if chr not in chrSet:
            chrSet.add(chr)
            # initiate an empty dictionary
            arm_dict = dict()
            arm_dict[arm] = [start, end]
            genome_dict[chr] = arm_dict
        else:
            # if this chromosome arm seen the first time
            if not arm_dict.get(arm):
                arm_dict[arm] = [start, end]
            else:
                new_start = arm_dict[arm][0]
                new_end = end
                arm_dict[arm] = [new_start, new_end]
            genome_dict[chr] = arm_dict

ofile = open("/Users/Tammy/annotations/human/hg19_UCSC_genome/chrom_arm_dict.txt", "w")
for key in genome_dict.keys():
    for key2 in genome_dict[key].keys():
        ofile.write(key + "\t" + genome_dict[key][key2][0] + "\t" + genome_dict[key][key2][1] + "\t" + key2 +"\n")
ofile.close()
Note that, There is no order of dictionary, so the output may not be sorted. You can sort by chr and start:
cat chrom_arm_dict.txt | sort -k1,1V -k2,2n
V is only for GNU sort which will sort chromsome in alpha-numeric order
If I compare the two results from different ways, they are identical:
cmp <(sort -k1,1V -k2,2n chrom_arm_dict.txt) <(sort -k1,1V -k2,2n chrom_arm_list.txt)

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