In [15]:

    

import os
import sys

filename_m5 = '../../data/degRNAprobe/HUMAN_ens87_cdna_kmer.20.multi5'

#for tmp_f in os.listdir('../../data'):
#    print(tmp_f)
#sys.exit(1)

p2freq = dict()
p2t = dict()
f_m5 = open(filename_m5,'r')
for line in f_m5:
    tokens = line.strip().split("\t")
    tmp_seq = tokens[0]
    tmp_freq = int(tokens[1])
    if tmp_freq > 500:
        continue
        
    t_list = ['.'.join(x.split('.')[:-1]) for x in tokens[2].split(',')]
    p2freq[tmp_seq] = tmp_freq
    p2t[tmp_seq] = t_list
f_m5.close()

cum_t_list = []
tmp_count = 0
prev_t_count = 0
for tmp_p in sorted(p2freq.keys(), key=p2freq.get, reverse=False):
    if len(p2t[tmp_p]) < 100:
        continue
        
    cum_t_list = list(set(cum_t_list + p2t[tmp_p]))
    tmp_t_count = len(cum_t_list)
    if tmp_t_count == prev_t_count:
        continue

    tmp_count += 1    
    #print(tmp_p, tmp_count/len(p2freq), len(p2t[tmp_p]), len(cum_t_list))
    #if tmp_count > 5000:
    #    break
    
print( tmp_count, len(cum_t_list) )


    

    




1049 8385

In [2]:

    

import os
import sys

filename_m5 = '../../data/degRNAprobe/HUMAN_ens87_cdna_kmer.20.multi5_genes'
f_m5 = open(filename_m5,'r')
for line in f_m5:
    tokens = line.strip().split("\t")
    gene_id = tokens[0]
    probe_count = int(tokens[1])
    probe_list = tokens[2].split(';')
    if gene_id.startswith('RPS'):
        print(gene_id, probe_count)
f_m5.close()


    

    




RPS15AP16|ENSG00000239483.1 1
RPS15AP25|ENSG00000236191.3 1
RPS15AP27|ENSG00000236783.1 1
RPS15AP30|ENSG00000227560.1 1
RPS15AP3|ENSG00000214903.4 1
RPS15AP40|ENSG00000233921.2 1
RPS15AP5|ENSG00000223540.1 1
RPS16P9|ENSG00000242675.1 1
RPS20P35|ENSG00000244086.1 1
RPS24P8|ENSG00000224094.1 1
RPS26P45|ENSG00000241765.2 1
RPS27P25|ENSG00000239881.1 1
RPS29P32|ENSG00000276703.1 1
RPS29P9|ENSG00000223433.1 1
RPS2P39|ENSG00000240698.1 1
RPS3AP12|ENSG00000236804.1 1
RPS3AP33|ENSG00000214268.2 1
RPS3AP37|ENSG00000227583.1 1
RPS6P2|ENSG00000231541.1 1
RPS12P27|ENSG00000240435.2 2
RPS15AP17|ENSG00000225405.3 2
RPS17P2|ENSG00000197575.6 2
RPS17P5|ENSG00000060303.5 2
RPS19P3|ENSG00000240463.1 2
RPS29P10|ENSG00000226884.1 2
RPS29P13|ENSG00000217089.1 2
RPS29P17|ENSG00000227852.1 2
RPS29P29|ENSG00000233717.1 2
RPS29P31|ENSG00000224279.2 2
RPS29P6|ENSG00000230451.2 2
RPS29P8|ENSG00000232238.1 2
RPS3P2|ENSG00000231307.1 2
RPS4XP21|ENSG00000186008.7 2
RPS4XP3|ENSG00000214541.3 2
RPS4XP8|ENSG00000219146.1 2
RPS5P3|ENSG00000215088.3 2
RPS8P3|ENSG00000215457.5 2
RPS15AP11|ENSG00000234093.3 3
RPS15AP12|ENSG00000232134.1 3
RPS15AP24|ENSG00000241511.1 3
RPS19P7|ENSG00000228462.1 3
RPS20P5|ENSG00000236888.1 3
RPS23|ENSG00000186468.12 3
RPS3P1|ENSG00000230935.1 3
RPSAP32|ENSG00000238075.1 3
RPSAP50|ENSG00000224776.3 3
RPSAP68|ENSG00000279990.1 3
RPS12P17|ENSG00000233163.1 4
RPS12P5|ENSG00000226216.1 4
RPS15AP1|ENSG00000214535.3 4
RPS16P8|ENSG00000213664.4 4
RPS24P14|ENSG00000223688.2 4
RPS27P20|ENSG00000240121.1 4
RPS3AP38|ENSG00000226318.1 4
RPS3AP49|ENSG00000242060.1 4
RPS3AP53|ENSG00000227578.1 4
RPS3P7|ENSG00000243101.1 4
RPS4XP11|ENSG00000234335.1 4
RPS4XP17|ENSG00000244097.1 4
RPS4XP19|ENSG00000242058.2 4
RPS4XP20|ENSG00000249987.1 4
RPS4XP4|ENSG00000215520.3 4
RPS4XP6|ENSG00000244073.1 4
RPS4XP9|ENSG00000217404.2 4
RPS7P6|ENSG00000215278.4 4
RPSAP60|ENSG00000228965.1 4
RPS15AP38|ENSG00000237668.1 5
RPS18P13|ENSG00000243455.3 5
RPS19P1|ENSG00000214612.3 5
RPS20P14|ENSG00000223803.1 5
RPS26P30|ENSG00000234839.1 5
RPS29P19|ENSG00000243353.1 5
RPS3AP25|ENSG00000232385.2 5
RPS3AP40|ENSG00000243672.1 5
RPS3AP43|ENSG00000242661.1 5
RPSAP24|ENSG00000235414.3 5
RPSAP37|ENSG00000241888.2 5
RPSAP72|ENSG00000219361.1 5
RPS26P43|ENSG00000244641.2 6
RPS27P15|ENSG00000218459.1 6
RPS29P11|ENSG00000242640.1 6
RPS29P12|ENSG00000243664.1 6
RPS3AP39|ENSG00000237226.1 6
RPS3AP41|ENSG00000239481.1 6
RPS4XP22|ENSG00000239830.1 6
RPS4Y1|ENSG00000129824.15 6
RPS7P14|ENSG00000213695.3 6
RPS7P5|ENSG00000217327.3 6
RPS7P9|ENSG00000233353.1 6
RPSAP38|ENSG00000239694.1 6
RPS12P26|ENSG00000225193.5 7
RPS14|ENSG00000164587.11 7
RPS26P56|ENSG00000226339.1 7
RPS4XP13|ENSG00000240371.1 7
RPS4XP16|ENSG00000224892.6 7
RPS7P7|ENSG00000240167.1 7
RPS8P4|ENSG00000227437.1 7
RPSAP20|ENSG00000229871.1 7
RPSAP42|ENSG00000219463.1 7
RPSAP71|ENSG00000254256.1 7
RPS26P40|ENSG00000231366.1 8
RPS27P23|ENSG00000239413.1 8
RPS3AP44|ENSG00000234031.1 8
RPS4XP2|ENSG00000226948.1 8
RPS4XP7|ENSG00000218265.1 8
RPSAP40|ENSG00000231368.1 8
RPS12P23|ENSG00000180172.7 9
RPS15P9|ENSG00000240846.2 9
RPS29P16|ENSG00000235354.1 9
RPS29P7|ENSG00000231622.1 9
RPS3AP14|ENSG00000242229.1 9
RPS6|ENSG00000137154.12 9
RPS6P22|ENSG00000244390.2 9
RPS6P25|ENSG00000240616.1 9
RPS7P8|ENSG00000213183.3 9
RPSAP23|ENSG00000230391.1 9
RPSAP27|ENSG00000233869.1 9
RPSAP41|ENSG00000239626.1 9
RPSAP57|ENSG00000267524.1 9
RPS3AP15|ENSG00000244674.1 10
RPS3AP35|ENSG00000244289.1 10
RPS4X|ENSG00000198034.10 10
RPS5|ENSG00000083845.8 10
RPSAP65|ENSG00000223683.1 10
RPS26P55|ENSG00000239210.2 11
RPS3AP47|ENSG00000205871.5 11
RPSAP25|ENSG00000230384.1 11
RPS26P54|ENSG00000224161.3 12
RPSAP22|ENSG00000229648.1 12
RPSAP70|ENSG00000250327.1 12
RPS26P34|ENSG00000240427.1 13
RPS26P38|ENSG00000234192.1 13
RPS27P14|ENSG00000244717.1 13
RPSAP62|ENSG00000226299.2 13
RPSAP75|ENSG00000270954.1 13
RPS29P5|ENSG00000230777.1 14
RPS7P12|ENSG00000237432.2 14
RPSAP66|ENSG00000266943.1 14
RPS12|ENSG00000112306.7 15
RPS29P3|ENSG00000225770.1 15
RPS7P4|ENSG00000229133.1 15
RPSAP13|ENSG00000233924.1 15
RPS26P4|ENSG00000228349.1 16
RPS26P52|ENSG00000242307.1 16
RPS3P6|ENSG00000213363.4 16
RPS3AP5|ENSG00000178429.9 17
RPS10P27|ENSG00000267752.1 18
RPS25|ENSG00000118181.10 19
RPS26P13|ENSG00000227887.1 19
RPS7P15|ENSG00000237170.3 20
RPS8P10|ENSG00000223877.4 21
RPS7P10|ENSG00000226525.5 22
RPS7P3|ENSG00000231940.1 23
RPS2P44|ENSG00000243609.1 24
RPSAP7|ENSG00000237032.1 24
RPSAP73|ENSG00000274319.1 25
RPS27|ENSG00000177954.11 27
RPS27P29|ENSG00000240231.1 27
RPS7P11|ENSG00000213326.4 27
RPSAP33|ENSG00000226765.1 27
RPS18P9|ENSG00000220848.4 28
RPS3AP6|ENSG00000234797.5 28
RPS3AP26|ENSG00000214389.2 29
RPSAP2|ENSG00000237425.1 29
RPSAP74|ENSG00000253621.1 29
RPS18P12|ENSG00000230897.1 31
RPSAP10|ENSG00000224439.2 31
RPS10P14|ENSG00000213744.3 32
RPS2P52|ENSG00000213726.5 32
RPSAP28|ENSG00000214484.3 32
RPSAP44|ENSG00000220773.1 32
RPS7P1|ENSG00000263266.2 33
RPS15P5|ENSG00000229806.1 35
RPS28|ENSG00000233927.4 35
RPS28P7|ENSG00000227097.5 35
RPSAP1|ENSG00000228820.2 35
RPS2P45|ENSG00000244378.1 36
RPSAP16|ENSG00000235145.2 38
RPS13|ENSG00000110700.6 39
RPS27A|ENSG00000143947.12 40
RPS24|ENSG00000138326.18 43
RPS10P28|ENSG00000243167.1 44
RPS10P20|ENSG00000240443.1 45
RPSAP39|ENSG00000244002.1 46
RPSAP52|ENSG00000241749.4 46
RPSAP53|ENSG00000214263.2 46
RPS3|ENSG00000149273.14 47
RPS11P6|ENSG00000243024.6 49
RPS26P39|ENSG00000227586.5 50
RPS18|ENSG00000231500.6 52
RPS3A|ENSG00000145425.9 52
RPSAP6|ENSG00000214629.3 53
RPS19BP1|ENSG00000187051.8 56
RPS6KA6|ENSG00000072133.10 56
RPSAP76|ENSG00000235332.2 56
RPS16|ENSG00000105193.8 59
RPS20P22|ENSG00000239218.2 61
RPS26P35|ENSG00000242206.2 61
RPSAP31|ENSG00000234371.6 63
RPS10P3|ENSG00000217716.3 64
RPSAP55|ENSG00000214896.4 65
RPS10P2|ENSG00000213950.2 66
RPS9|ENSG00000170889.13 66
RPS10P16|ENSG00000239917.3 68
RPS26P2|ENSG00000233278.1 69
RPS17|ENSG00000182774.10 71
RPSAP43|ENSG00000216471.3 72
RPS26P31|ENSG00000235459.5 74
RPS2P24|ENSG00000244019.1 74
RPS6KL1|ENSG00000198208.11 74
RPSAP14|ENSG00000233984.1 74
RPSAP21|ENSG00000226498.2 74
RPS10P5|ENSG00000101278.6 75
RPSAP63|ENSG00000233260.1 75
RPS26P28|ENSG00000243538.1 77
RPS26P11|ENSG00000196933.5 80
RPS26P3|ENSG00000212829.8 80
RPS19|ENSG00000105372.6 86
RPSAP11|ENSG00000237433.1 88
RPSAP36|ENSG00000243175.1 88
RPSAP69|ENSG00000233487.6 88
RPSAP18|ENSG00000224261.2 90
RPSAP46|ENSG00000213394.3 90
RPS8|ENSG00000142937.11 92
RPSAP49|ENSG00000226327.3 92
RPS15|ENSG00000115268.9 94
RPS26P15|ENSG00000223416.3 94
RPS6P20|ENSG00000226356.2 94
RPS26P47|ENSG00000234354.3 97
RPSAP4|ENSG00000239269.1 98
RPS26P8|ENSG00000204652.6 99
RPSAP45|ENSG00000219773.1 103
RPS2P28|ENSG00000179157.4 106
RPSAP29|ENSG00000244722.1 106
RPS2P32|ENSG00000232818.2 112
RPSAP3|ENSG00000242952.1 114
RPS2P6|ENSG00000214255.5 116
RPS10-NUDT3|ENSG00000270800.1 117
RPSAP12|ENSG00000240087.3 119
RPS26P6|ENSG00000212994.5 120
RPSAP47|ENSG00000188856.6 120
RPS6KB2|ENSG00000175634.14 123
RPSAP5|ENSG00000243904.1 123
RPS6KB1|ENSG00000108443.13 124
RPS2P2|ENSG00000177776.8 127
RPS10|ENSG00000124614.13 128
RPSAP26|ENSG00000242735.1 129
RPSAP61|ENSG00000214016.3 138
RPSAP17|ENSG00000226855.1 141
RPS2P1|ENSG00000225246.1 147
RPSAP8|ENSG00000230592.2 147
RPSAP54|ENSG00000213621.3 148
RPSAP9|ENSG00000234618.1 148
RPS20|ENSG00000008988.9 150
RPS26|ENSG00000197728.9 150
RPSAP15|ENSG00000237506.3 152
RPS6KA3|ENSG00000177189.12 153
RPSAP19|ENSG00000183298.5 155
RPS7|ENSG00000171863.12 160
RPSAP58|ENSG00000225178.5 183
RPSA|ENSG00000168028.13 204
RPS2P35|ENSG00000238172.2 213
RPS15A|ENSG00000134419.15 265
RPS2P4|ENSG00000196183.5 270
RPS29|ENSG00000213741.8 293
RPS2P48|ENSG00000233380.1 293
RPS2P46|ENSG00000189343.7 305
RPS2P7|ENSG00000235508.3 308
RPS2|ENSG00000140988.15 408
RPS2P5|ENSG00000240342.3 411
RPS2P55|ENSG00000216866.5 422
RPS27L|ENSG00000185088.13 517
RPS6KA5|ENSG00000100784.10 930

In [ ]: