输入文件

input_v1.0.txt （三列，分别是 *.1.fastq.gz,*2.fastq.gz , *.sam）

hisat2运行参数与流程（hisat2_IWGSCv1.0.py）

#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = 'shengwei ma'
__author_email__ = 'shengweima@icloud.com'import subprocesswith open('input_v1.0_1.txt', 'r') as f:for line in f:lin = line.strip().split()fq1, fq2, sam = lin[0], lin[1], lin[2]proc = subprocess.Popen(['hisat2', '-p', '20', '--dta', '-x', '/data2/Fshare/IWGSCv1.0_hisat2/IWGSCv1.0_hiast2', '--known-splicesite-infile','/data2/Fshare/IWGSCv1.0_hisat2/TGACv1.ss', '--novel-splicesite-infile', '/data2/masw_data/rna_seq/all.ss','-t', '--no-discordant', '--no-mixed', '-1', fq1, '-2', fq2, '-S', sam], shell=False)proc.wait()print samnew = sam[:-3] + 'unmap.txt'mat = sam[:-3] + 'match.sam'mis = sam[:-3] + 'mismatch.sam'unmap = open(new, 'w')mat1 = open(mat, 'w')mis1 = open(mis, 'w')with open(sam, 'r') as f1:for (num, value) in enumerate(f1):lin = value.strip().split()if value.startswith('@'):mat1.writelines(value)mis1.writelines(value)else:if '*' in lin[2]:unmap.writelines(lin[0])else:if 'I' not in lin[5] and 'D' not in lin[5] and 'XM:i:0' in value: #筛选完全匹配的reads，但是对于softclip 无效mat1.writelines(value)if 'I' not in lin[5] and 'D' not in lin[5] and 'XM:i:0' not in value:mis1.writelines(value)mat1.close()unmap.close()mis1.close()proc = subprocess.Popen(['samtools', 'view', '-@', '10', '-b', '-o', mat[:-3] + 'bam', mat], shell=False)proc.wait()proc = subprocess.Popen(['samtools', 'sort', '-@', '10', '-o', mat[:-3] + 'sorted.bam', mat[:-3] + 'bam'], shell=False)proc.wait()proc = subprocess.Popen(['shred', '-u', '-z', mat, sam, mat[:-3] + 'bam'], shell=False)proc.wait()

hisat2输出信息，也可见该目录下的mapping_information.txt

Sample total_reads unmapped_reads uniquely-mapped_reads Multimapped_reads
ATW_AAOSW_6 45401788(100.00%) 1625896(3.58%) 36054911(79.41%) 7720981(17.01%)
ATW_ABOSW_7 43317025(100.00%) 3384472(7.81%) 32613798(75.29%) 7318755(16.90%)
ATW_ACOSW 51224256(100.00%) 3682442(7.19%) 37964008(74.11%) 9577806(18.70%)
ATW_ADOSW 85237299(100.00%) 5327852(6.25%) 63649972(74.67%) 16259475(19.08%)
ATW_AEOSW 44470405(100.00%) 3714550(8.35%) 33422930(75.16%) 7332925(16.49%)
ATW_AFOSW_2 38815740(100.00%) 2344586(6.04%) 30028428(77.36%) 6442726(16.60%)
ATW_AGOSW_2 35749803(100.00%) 3298492(9.23%) 26017323(72.78%) 6433988(18.00%)
ATW_AHOSW_3 52146021(100.00%) 4219037(8.09%) 39229076(75.23%) 8697908(16.68%)
ATW_AIOSW_2 67283195(100.00%) 19946431(29.65%) 31218902(46.40%) 16117862(23.96%)
ATW_AKOSW_2 75347431(100.00%) 24014018(31.87%) 33383763(44.31%) 17949650(23.82%)
ATW_ALOSW_3 42039096(100.00%) 2031197(4.83%) 32613783(77.58%) 7394116(17.59%)
ATW_AMOSW_4 38844640(100.00%) 7661962(19.72%) 25025383(64.42%) 6157295(15.85%)
ATW_ANOSW 89075171(100.00%) 11783105(13.23%) 63333349(71.10%) 13958717(15.67%)
ATW_AOSW 50836846(100.00%) 1967671(3.87%) 40375224(79.42%) 8493951(16.71%)
ATW_COSW 45388739(100.00%) 4336069(9.55%) 33513277(73.84%) 7539393(16.61%)
ATW_DOSW_2 48400597(100.00%) 1782615(3.68%) 38184280(78.89%) 8433702(17.42%)
ATW_FOSW_2 47627837(100.00%) 11084697(23.27%) 29081034(61.06%) 7462106(15.67%)
ATW_GOSW_3 47851480(100.00%) 2025594(4.23%) 38041640(79.50%) 7784246(16.27%)
ATW_HOSW_3 46349244(100.00%) 3243306(7.00%) 35294358(76.15%) 7811580(16.85%)
ATW_IOSW_4 53653235(100.00%) 2427235(4.52%) 42707453(79.60%) 8518547(15.88%)
ATW_KOSW_4 39894644(100.00%) 3043191(7.63%) 30655324(76.84%) 6196129(15.53%)
ATW_LOSW_5 40476784(100.00%) 2375565(5.87%) 31157278(76.98%) 6943941(17.16%)
ATW_MOSW_5 49643196(100.00%) 6008219(12.10%) 34849848(70.20%) 8785129(17.70%)
ATW_NOSW_6 45463315(100.00%) 5519168(12.14%) 32357850(71.17%) 7586297(16.69%)
ATW_POSW_6 42820604(100.00%) 4444437(10.38%) 31740451(74.12%) 6635716(15.50%)
ATW_QOSW_7 45189058(100.00%) 2519770(5.58%) 35464036(78.48%) 7205252(15.94%)
ATW_ROSW_7 41964678(100.00%) 2418292(5.76%) 32377059(77.15%) 7169327(17.08%)
ATW_SOSW_8 46010346(100.00%) 2071554(4.50%) 36664030(79.69%) 7274762(15.81%)
ATW_TOSW_8 41117096(100.00%) 3337900(8.12%) 30307865(73.71%) 7471331(18.17%)
ATW_VOSW_6 44532829(100.00%) 1723299(3.87%) 34529586(77.54%) 8279944(18.59%)
ERR392055 26786162(100.00%) 4047245(15.11%) 15990303(59.70%) 6748614(25.19%)
ERR392056 29879250(100.00%) 4692482(15.70%) 17363629(58.11%) 7823139(26.18%)
ERR392057 30226502(100.00%) 3185007(10.54%) 19814488(65.55%) 7227007(23.91%)
ERR392058 18558499(100.00%) 1998085(10.77%) 12203151(65.76%) 4357263(23.48%)
ERR392059 30793173(100.00%) 2344455(7.61%) 22029424(71.54%) 6419294(20.85%)
ERR392060 22417889(100.00%) 2366252(10.56%) 14884436(66.40%) 5167201(23.05%)
ERR392061 20355570(100.00%) 3719356(18.27%) 11386270(55.94%) 5249944(25.79%)
ERR392062 25108363(100.00%) 3797487(15.12%) 14548403(57.94%) 6762473(26.93%)
ERR392063 29965698(100.00%) 4989790(16.65%) 16957287(56.59%) 8018621(26.76%)
ERR392064 34565714(100.00%) 4811540(13.92%) 20727298(59.96%) 9026876(26.12%)
ERR392064 34565714(100.00%) 4811540(13.92%) 20727298(59.96%) 9026876(26.12%)
ERR392065 27177427(100.00%) 4520724(16.63%) 15412488(56.71%) 7244215(26.66%)
ERR392066 37515837(100.00%) 7292639(19.44%) 19656276(52.39%) 10566922(28.17%)
ERR392067 29548095(100.00%) 5994021(20.29%) 15715972(53.19%) 7838102(26.53%)
ERR392068 30476750(100.00%) 3991164(13.10%) 18606572(61.05%) 7879014(25.85%)
ERR392069 31424506(100.00%) 2679321(8.53%) 21520594(68.48%) 7224591(22.99%)
ERR392070 29660313(100.00%) 4427930(14.93%) 17592218(59.31%) 7640165(25.76%)
ERR392071 29373530(100.00%) 4610961(15.70%) 17098379(58.21%) 7664190(26.09%)
ERR392072 33407315(100.00%) 4025192(12.05%) 21596921(64.65%) 7785202(23.30%)
ERR392073 28004777(100.00%) 3852619(13.76%) 17378994(62.06%) 6773164(24.19%)
ERR392074 26658599(100.00%) 5465146(20.50%) 13906279(52.16%) 7287174(27.34%)
ERR392075 27595485(100.00%) 4936815(17.89%) 15247427(55.25%) 7411243(26.86%)
ERR392076 29674240(100.00%) 5400293(18.20%) 16416891(55.32%) 7857056(26.48%)
ERR392077 31078820(100.00%) 3574955(11.50%) 20081821(64.62%) 7422044(23.88%)
ERR392078 32327629(100.00%) 2421810(7.49%) 23264665(71.97%) 6641154(20.54%)
ERR392079 23704655(100.00%) 3131080(13.21%) 14112639(59.54%) 6460936(27.26%)
ERR392080 27746131(100.00%) 2992584(10.79%) 18525078(66.77%) 6228469(22.45%)
ERR392081 31358914(100.00%) 3746073(11.95%) 20709901(66.04%) 6902940(22.01%)
ERR392082 32871524(100.00%) 2346792(7.14%) 23727550(72.18%) 6797182(20.68%)
ERR392083 32240850(100.00%) 3128224(9.70%) 21232287(65.86%) 7880339(24.44%)
ERR392084 32641566(100.00%) 2632926(8.07%) 23252740(71.24%) 6755900(20.70%)
NG-5789_1A_lib7482 34356521(100.00%) 2743533(7.99%) 26100505(75.97%) 5512483(16.04%)
NG-5789_1B_lib7486 42444661(100.00%) 2276170(5.36%) 32538608(76.66%) 7629883(17.98%)
NG-5789_2A_lib7483 58377229(100.00%) 1980165(3.39%) 46325570(79.36%) 10071494(17.25%)
NG-5789_2B_lib7487 45374776(100.00%) 1459680(3.22%) 35121823(77.40%) 8793273(19.38%)
NG-5789_3A_lib7484 39082313(100.00%) 2105348(5.39%) 30799509(78.81%) 6177456(15.81%)
NG-5789_3B_lib7488 39159546(100.00%) 1543503(3.94%) 30324689(77.44%) 7291354(18.62%)
NG-5789_4A_lib7485 28215511(100.00%) 1319564(4.68%) 22135951(78.45%) 4759996(16.87%)
NG-5789_4B_lib7489 34385209(100.00%) 2265183(6.59%) 26117900(75.96%) 6002126(17.46%)
SRR1175868 62225856(100.00%) 4434070(7.13%) 46741787(75.12%) 11049999(17.76%)
SRR1177760 68599252(100.00%) 4784428(6.97%) 51327798(74.82%) 12487026(18.20%)
SRR1177761 77573636(100.00%) 5418773(6.99%) 58236525(75.07%) 13918338(17.94%)
SRR1460549 30618243(100.00%) 2210006(7.22%) 20459229(66.82%) 7949008(25.96%)
SRR1460550 72955159(100.00%) 5074113(6.96%) 48678341(66.72%) 19202705(26.32%)
SRR1460551 27179120(100.00%) 2914078(10.72%) 17292077(63.62%) 6972965(25.66%)
SRR1460552 37693050(100.00%) 2304774(6.11%) 25576360(67.85%) 9811916(26.03%)
SRR1460553 23942473(100.00%) 1441952(6.02%) 16313271(68.14%) 6187250(25.84%)
SRR1460554 17985663(100.00%) 1158728(6.44%) 12218492(67.93%) 4608443(25.62%)
Wheat_Room1_AL_20DPA_RNA_Extra2 32685090(100.00%) 3056423(9.35%) 21550138(65.93%) 8078529(24.72%)
Wheat_Room_SE_30DPA_RNA 23711650(100.00%) 3477993(14.67%) 13233266(55.81%) 7000391(29.52%)

使用featurecount计算reads数

其中-a 是输入文件，-o 是输出结果，每次运行注意修改。

featureCounts -T 20 -t exon -g Name --readExtension5 70  --readExtension3 70 -p -O --donotsort -C -a /data2/masw_data/transcript/TGACv1.cdna.gff3 -o /data2/masw_data/transcript/TGACv1.cdna.reformat_expression_new.txt ATW_AOSW.match.sorted.bam ATW_AAOSW_6.match.sorted.bam ATW_ANOSW.match.sorted.bam ATW_LOSW_5.match.sorted.bam ATW_ADOSW.match.sorted.bam ATW_AEOSW.match.sorted.bam ATW_DOSW_2.match.sorted.bam ATW_POSW_6.match.sorted.bam ATW_IOSW_4.match.sorted.bam ATW_KOSW_4.match.sorted.bam ATW_ROSW_7.match.sorted.bam ATW_ALOSW_3.match.sorted.bam ATW_TOSW_8.match.sorted.bam ATW_VOSW_6.match.sorted.bam ATW_MOSW_5.match.sorted.bam ATW_NOSW_6.match.sorted.bam ATW_COSW.match.sorted.bam ATW_AGOSW_2.match.sorted.bam ATW_GOSW_3.match.sorted.bam ATW_HOSW_3.match.sorted.bam ATW_ABOSW_7.match.sorted.bam ATW_ACOSW.match.sorted.bam ATW_QOSW_7.match.sorted.bam ATW_AHOSW_3.match.sorted.bam SRR1175868.match.sorted.bam SRR1177760.match.sorted.bam SRR1177761.match.sorted.bam NG-5789_1A_lib7482.match.sorted.bam NG-5789_1B_lib7486.match.sorted.bam NG-5789_2A_lib7483.match.sorted.bam NG-5789_2B_lib7487.match.sorted.bam NG-5789_3A_lib7484.match.sorted.bam NG-5789_3B_lib7488.match.sorted.bam NG-5789_4A_lib7485.match.sorted.bam NG-5789_4B_lib7489.match.sorted.bam ATW_SOSW_8.match.sorted.bam ATW_AFOSW_2.match.sorted.bam ATW_AIOSW_2.match.sorted.bam ATW_AKOSW_2.match.sorted.bam ATW_FOSW_2.match.sorted.bam ATW_AMOSW_4.match.sorted.bam ERR392061.match.sorted.bam ERR392055.match.sorted.bam ERR392057.match.sorted.bam ERR392072.match.sorted.bam ERR392082.match.sorted.bam ERR392059.match.sorted.bam ERR392080.match.sorted.bam ERR392081.match.sorted.bam ERR392078.match.sorted.bam ERR392084.match.sorted.bam ERR392063.match.sorted.bam ERR392076.match.sorted.bam ERR392074.match.sorted.bam ERR392075.match.sorted.bam ERR392058.match.sorted.bam ERR392077.match.sorted.bam ERR392056.match.sorted.bam ERR392070.match.sorted.bam ERR392064.match.sorted.bam ERR392068.match.sorted.bam ERR392073.match.sorted.bam ERR392083.match.sorted.bam ERR392079.match.sorted.bam ERR392065.match.sorted.bam ERR392066.match.sorted.bam ERR392062.match.sorted.bam ERR392069.match.sorted.bam ERR392060.match.sorted.bam ERR392067.match.sorted.bam ERR392071.match.sorted.bam SRR1460549.match.sorted.bam SRR1460550.match.sorted.bam SRR1460551.match.sorted.bam SRR1460552.match.sorted.bam SRR1460553.match.sorted.bam SRR1460554.match.sorted.bam

计算FPKM。使用 fpkm.py .输入文件为上述featurecount输出文件

#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = 'shengwei ma'
__author_email__ = 'shengweima@icloud.com'import numpy as npraw_total = [('root_Z10_rep1', 48869175), ('root_Z10_rep2', 43775892), ('root_Z13_rep1', 78098556),('root_Z13_rep2', 38101219), ('root_Z39_rep1', 79909447), ('root_Z39_rep2', 40755855),('stem_Z30_rep1', 46617982), ('stem_Z30_rep2', 38376167), ('stem_Z32_rep1', 51226000),('stem_Z32_rep2', 36851453), ('stem_Z65_rep1', 39546386), ('stem_Z65_rep2',40007899),('leaf_Z10_rep1', 37779196), ('leaf_Z10_rep2', 42809530), ('leaf_Z23_rep1', 43634977),('leaf_Z23_rep2', 39944147), ('leaf_Z71_rep1', 41052670), ('leaf_Z71_rep2', 32451311),('spike_Z32_rep1', 45825886), ('spike_Z32_rep2', 43105938), ('spike_Z39_rep1', 39932553),('spike_Z39_rep2', 47541814), ('spike_Z65_rep1', 42669288), ('spike_Z65_rep2', 47926984),('carpel', 47926984), ('carpel-like structure', 63914055), ('stamen', 72154863),('latent_lepto_rep1', 31612988), ('latent_lepto_rep2', 40168491), ('diplo_dia_rep1', 56397064),('diplo_dia_rep2', 43915096), ('zygo_pachy_rep1', 36976965), ('zygo_pachy_rep2', 37616043),('metaphaseI_rep1', 26895947), ('metaphaseI_rep2', 32120026), ('grain_Z71_rep1', 43938792),('grain_Z71_rep2', 36471154), ('grain_Z75_rep1', 47336764), ('grain_Z75_rep2', 51333413),('grain_Z85_rep1', 36543140), ('grain_Z85_rep2', 31182678), ('Wheat_Room1_10DPA', 16712256),('Wheat_Room1_10DPA_Rep', 22819483), ('Wheat_Room2_10DPA', 27121510), ('Wheat_Room2_10DPA_Rep', 29453109),('Wheat_Room1_AL_20DPA', 30598515), ('Wheat_Room1_AL_20DPA_Rep', 28518937), ('Wheat_Room2_AL_20DPA', 24838220),('Wheat_Room2_AL_20DPA_Rep', 27715580), ('Wheat_Room1_AL_20DPA_Extra1', 29978007), ('Wheat_Room1_AL_20DPA_Extra2', 30079461),('Wheat_Room1_SE_20DPA', 25140145), ('Wheat_Room1_SE_20DPA_Rep', 24446796), ('Wheat_Room2_SE_20DPA', 21339690),('Wheat_Room2_SE_20DPA_Rep', 22815780),('Wheat_Room1_TC_20DPA', 16629117), ('Wheat_Room1_TC_20DPA_Rep', 27612315), ('Wheat_Room2_TC_20DPA', 25304622),('Wheat_Room2_TC_20DPA_Rep', 25352139), ('Wheat_Room1_REF_20DPA', 29929219), ('Wheat_Room1_REF_20DPA_Rep', 26636425),('Wheat_Room2_REF_20DPA', 24316737), ('Wheat_Room2_REF_20DPA_Rep', 29330096), ('Wheat_Room1_SE_30DPA', 20661506),('Wheat_Room1_SE_30DPA_Rep', 22777481), ('Wheat_Room2_SE_30DPA', 30513836), ('Wheat_Room2_SE_30DPA_Rep', 21486098),('Wheat_Room1_AL_SE_30DPA', 28821672), ('Wheat_Room1_AL_SE_30DPA_Rep', 20134665), ('Wheat_Room2_AL_SE_30DPA', 23721856),('Wheat_Room2_AL_SE_30DPA_Rep', 24896811), ('wheat_23_1', 28444918), ('wheat_23_2', 67968193),('wheat_23_3', 24321425), ('wheat_4_1', 35430306), ('wheat_4_2', 22527710), ('wheat_4_3', 16848204)]organs = open('1.txt', 'w')
organs.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ('Geneid', 'Chr', 'root_max', 'stem_max', 'leaf_max', 'spike_max', 'grain_max', 'stamen_max', 'new_carpel'))with open('specific_gene_expression_new.txt', 'r') as f: # 此处注意修改输入文件print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" \"\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" \"\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" \"\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t" % \('Geneid', 'Chr', 'Start', 'End', 'Strand', 'Length', 'root_Z10', 'root_Z13','root_Z39','stem_Z30', 'stem_Z32', 'stem_Z65', 'leaf_Z10', 'leaf_Z23', 'leaf_Z71','spike_Z32', 'spike_Z39', 'spike_Z65', 'carpel', 'carpel_like_structure','stamen', 'latet_lepto', 'diplo_dia', 'zygo_pachy', 'metaphaseI','grain_Z71', 'grain_Z75', 'grain_Z85', 'Wheat_10DPA', 'Wheat_AL_20DPA','Wheat_SE_20DPA', 'Wheat_TC_20DPA', 'Wheat_REF_20DPA', 'Wheat_SE_30DPA','Wheat_AL.SE_30DPA', 'wheat_23', 'wheat_4', 'root_Z10_std', 'root_Z13_std', 'root_Z39_std','stem_Z30_std', 'stem_Z32_std', 'stem_Z65_std', 'leaf_Z10_std', 'leaf_Z23_std', 'leaf_Z71_std','spike_Z32_std', 'spike_Z39_std', 'spike_Z65_std', 'carpel_std', 'carpel-like_std', 'stamen_std','latet_lepto_std', 'diplo_dia_std', 'zygo_pachy_std', 'metaphaseI_std', 'grain_Z71_std','grain_Z75_std', 'grain_Z85_std','Wheat_10DPA_std', 'Wheat_AL_20DPA_std','Wheat_SE_20DPA_std','Wheat_TC_20DPA_std', 'Wheat_REF_20DPA_std', 'Wheat_SE_30DPA_std','Wheat_AL.SE_30DPA_std', 'wheat_23_std', 'wheat_4_std')for line in f:if line.startswith('#') or line.startswith('Geneid'):passelse:new = line.strip().split('\t')(Geneid, Chr, Start, End, Strand, Length, root_Z10_rep1, root_Z10_rep2, root_Z13_rep1, root_Z13_rep2,root_Z39_rep1, root_Z39_rep2, stem_Z30_rep1, stem_Z30_rep2, stem_Z32_rep1, stem_Z32_rep2, stem_Z65_rep1,stem_Z65_rep2, leaf_Z10_rep1, leaf_Z10_rep2, leaf_Z23_rep1, leaf_Z23_rep2, leaf_Z71_rep1, leaf_Z71_rep2,spike_Z32_rep1, spike_Z32_rep2, spike_Z39_rep1, spike_Z39_rep2, spike_Z65_rep1, spike_Z65_rep2, carpel,carpel_like_structure, stamen, latet_lepto_rep1, latent_lepto_rep2, diplo_dia_rep1, diplo_dia_rep2,zygo_pachy_rep1, zygo_pachy_rep2, metaphaseI_rep1, metaphaseI_rep2, grain_Z71_rep1, grain_Z71_rep2,grain_Z75_rep1, grain_Z75_rep2, grain_Z85_rep1, grain_Z85_rep2, Wheat_Room1_10DPA, Wheat_Room1_10DPA_Rep,Wheat_Room2_10DPA, Wheat_Room2_10DPA_Rep, Wheat_Room1_AL_20DPA, Wheat_Room1_AL_20DPA_Rep,Wheat_Room2_AL_20DPA, Wheat_Room2_AL_20DPA_Rep, Wheat_Room1_AL_20DPA_Extra1, Wheat_Room1_AL_20DPA_Extra2,Wheat_Room1_SE_20DPA, Wheat_Room1_SE_20DPA_Rep, Wheat_Room2_SE_20DPA, Wheat_Room2_SE_20DPA_Rep,Wheat_Room1_TC_20DPA, Wheat_Room1_TC_20DPA_Rep, Wheat_Room2_TC_20DPA, Wheat_Room2_TC_20DPA_Rep,Wheat_Room1_REF_20DPA, Wheat_Room1_REF_20DPA_Rep, Wheat_Room2_REF_20DPA, Wheat_Room2_REF_20DPA_Rep,Wheat_Room1_SE_30DPA, Wheat_Room1_SE_30DPA_Rep, Wheat_Room2_SE_30DPA, Wheat_Room2_SE_30DPA_Rep,Wheat_Room1_AL_SE_30DPA, Wheat_Room1_AL_SE_30DPA_Rep, Wheat_Room2_AL_SE_30DPA, Wheat_Room2_AL_SE_30DPA_Rep,wheat_23_1, wheat_23_2, wheat_23_3, wheat_4_1, wheat_4_2, wheat_4_3) = newnew_root_Z10_rep1 = int(root_Z10_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[0][-1]))new_root_Z10_rep2 = int(root_Z10_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[1][-1]))new_root_Z13_rep1 = int(root_Z13_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[2][-1]))new_root_Z13_rep2 = int(root_Z13_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[3][-1]))new_root_Z39_rep1 = int(root_Z39_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[4][-1]))new_root_Z39_rep2 = int(root_Z39_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[5][-1]))new_stem_Z30_rep1 = int(stem_Z30_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[6][-1]))new_stem_Z30_rep2 = int(stem_Z30_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[7][-1]))new_stem_Z32_rep1 = int(stem_Z32_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[8][-1]))new_stem_Z32_rep2 = int(stem_Z32_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[9][-1]))new_stem_Z65_rep1 = int(stem_Z65_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[10][-1]))new_stem_Z65_rep2 = int(stem_Z65_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[11][-1]))new_leaf_Z10_rep1 = int(leaf_Z10_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[12][-1]))new_leaf_Z10_rep2 = int(leaf_Z10_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[13][-1]))new_leaf_Z23_rep1 = int(leaf_Z23_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[14][-1]))new_leaf_Z23_rep2 = int(leaf_Z23_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[15][-1]))new_leaf_Z71_rep1 = int(leaf_Z71_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[16][-1]))new_leaf_Z71_rep2 = int(leaf_Z71_rep2) * pow(10.0 , 9) / (int(Length) * int(raw_total[17][-1]))new_spike_Z32_rep1 = int(spike_Z32_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[18][-1]))new_spike_Z32_rep2 = int(spike_Z32_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[19][-1]))new_spike_Z39_rep1 = int(spike_Z39_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[20][-1]))new_spike_Z39_rep2 = int(spike_Z39_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[21][-1]))new_spike_Z65_rep1 = int(spike_Z65_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[22][-1]))new_spike_Z65_rep2 = int(spike_Z65_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[23][-1]))new_carpel = int(carpel) * pow(10.0, 9) / (int(Length) * int(raw_total[24][-1]))new_carpel_like_structure = int(carpel_like_structure) * pow(10.0, 9) / (int(Length) * int(raw_total[25][-1]))new_stamen = int(stamen) * pow(10.0, 9) / (int(Length) * int(raw_total[26][-1]))new_latet_lepto_rep1 = int(latet_lepto_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[27][-1]))new_latet_lepto_rep2 = int(latent_lepto_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[28][-1]))new_diplo_dia_rep1 = int(diplo_dia_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[29][-1]))new_diplo_dia_rep2 = int(diplo_dia_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[30][-1]))new_zygo_pachy_rep1 = int(zygo_pachy_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[31][-1]))new_zygo_pachy_rep2 = int(zygo_pachy_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[32][-1]))new_metaphaseI_rep1 = int(metaphaseI_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[33][-1]))new_metaphaseI_rep2 = int(metaphaseI_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[34][-1]))new_grain_Z71_rep1 = int(grain_Z71_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[35][-1]))new_grain_Z71_rep2 = int(grain_Z71_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[36][-1]))new_grain_Z75_rep1 = int(grain_Z75_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[37][-1]))new_grain_Z75_rep2 = int(grain_Z75_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[38][-1]))new_grain_Z85_rep1 = int(grain_Z85_rep1) * pow(10.0, 9) / (int(Length) * int(raw_total[39][-1]))new_grain_Z85_rep2 = int(grain_Z85_rep2) * pow(10.0, 9) / (int(Length) * int(raw_total[40][-1]))Wheat_Room1_10DPA = int(Wheat_Room1_10DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[41][-1]))Wheat_Room1_10DPA_Rep = int(Wheat_Room1_10DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[42][-1]))Wheat_Room2_10DPA = int(Wheat_Room2_10DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[43][-1]))Wheat_Room2_10DPA_Rep = int(Wheat_Room2_10DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[44][-1]))Wheat_Room1_AL_20DPA = int(Wheat_Room1_AL_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[45][-1]))Wheat_Room1_AL_20DPA_Rep = int(Wheat_Room1_AL_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[46][-1]))Wheat_Room2_AL_20DPA = int(Wheat_Room2_AL_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[47][-1]))Wheat_Room2_AL_20DPA_Rep = int(Wheat_Room2_AL_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[48][-1]))Wheat_Room1_AL_20DPA_Extra1 = int(Wheat_Room1_AL_20DPA_Extra1) * pow(10.0, 9) / (int(Length) * int(raw_total[49][-1]))Wheat_Room1_AL_20DPA_Extra2 = int(Wheat_Room1_AL_20DPA_Extra2) * pow(10.0, 9) / (int(Length) * int(raw_total[50][-1]))Wheat_Room1_SE_20DPA = int(Wheat_Room1_SE_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[51][-1]))Wheat_Room1_SE_20DPA_Rep = int(Wheat_Room1_SE_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[52][-1]))Wheat_Room2_SE_20DPA = int(Wheat_Room2_SE_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[53][-1]))Wheat_Room2_SE_20DPA_Rep = int(Wheat_Room2_SE_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[54][-1]))Wheat_Room1_TC_20DPA = int(Wheat_Room1_TC_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[55][-1]))Wheat_Room1_TC_20DPA_Rep = int(Wheat_Room1_TC_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[56][-1]))Wheat_Room2_TC_20DPA = int(Wheat_Room2_TC_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[57][-1]))Wheat_Room2_TC_20DPA_Rep = int(Wheat_Room2_TC_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[58][-1]))Wheat_Room1_REF_20DPA = int(Wheat_Room1_REF_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[59][-1]))Wheat_Room1_REF_20DPA_Rep = int(Wheat_Room1_REF_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[60][-1]))Wheat_Room2_REF_20DPA = int(Wheat_Room2_REF_20DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[61][-1]))Wheat_Room2_REF_20DPA_Rep = int(Wheat_Room2_REF_20DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[62][-1]))Wheat_Room1_SE_30DPA = int( Wheat_Room1_SE_30DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[63][-1]))Wheat_Room1_SE_30DPA_Rep = int(Wheat_Room1_SE_30DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[64][-1]))Wheat_Room2_SE_30DPA = int(Wheat_Room2_SE_30DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[65][-1]))Wheat_Room2_SE_30DPA_Rep = int(Wheat_Room2_SE_30DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[66][-1]))Wheat_Room1_AL_SE_30DPA = int(Wheat_Room1_AL_SE_30DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[67][-1]))Wheat_Room1_AL_SE_30DPA_Rep = int(Wheat_Room1_AL_SE_30DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[68][-1]))Wheat_Room2_AL_SE_30DPA = int(Wheat_Room2_AL_SE_30DPA) * pow(10.0, 9) / (int(Length) * int(raw_total[69][-1]))Wheat_Room2_AL_SE_30DPA_Rep = int(Wheat_Room2_AL_SE_30DPA_Rep) * pow(10.0, 9) / (int(Length) * int(raw_total[70][-1]))wheat_23_1 = int(wheat_23_1) * pow(10.0, 9) / (int(Length) * int(raw_total[71][-1]))wheat_23_2 = int(wheat_23_2) * pow(10.0, 9) / (int(Length) * int(raw_total[72][-1]))wheat_23_3 = int(wheat_23_3) * pow(10.0, 9) / (int(Length) * int(raw_total[73][-1]))wheat_4_1 = int(wheat_4_1) * pow(10.0, 9) / (int(Length) * int(raw_total[74][-1]))wheat_4_2 = int(wheat_4_2) * pow(10.0, 9) / (int(Length) * int(raw_total[75][-1]))wheat_4_3 = int(wheat_4_3) * pow(10.0, 9) / (int(Length) * int(raw_total[76][-1]))root_Z10_mean = np.mean(np.array([new_root_Z10_rep1, new_root_Z10_rep2]))root_Z10_std = np.std(np.array([new_root_Z10_rep1, new_root_Z10_rep2]))root_Z13_mean = np.mean(np.array([new_root_Z13_rep1, new_root_Z13_rep2]))root_Z13_std = np.std(np.array([new_root_Z13_rep1, new_root_Z13_rep2]))root_Z39_mean = np.mean(np.array([new_root_Z39_rep1, new_root_Z39_rep2]))root_Z39_std = np.std(np.array([new_root_Z39_rep1, new_root_Z39_rep2]))stem_Z30_mean = np.mean(np.array([new_stem_Z30_rep1, new_stem_Z30_rep2]))stem_Z30_std = np.std(np.array([new_stem_Z30_rep1, new_stem_Z30_rep2]))stem_Z32_mean = np.mean(np.array([new_stem_Z32_rep1, new_stem_Z32_rep2]))stem_Z32_std = np.std(np.array([new_stem_Z32_rep1, new_stem_Z32_rep2]))stem_Z65_mean = np.mean(np.array([new_stem_Z65_rep1, new_stem_Z65_rep2]))stem_Z65_std = np.std(np.array([new_stem_Z65_rep1, new_stem_Z65_rep2]))leaf_Z10_mean = np.mean(np.array([new_leaf_Z10_rep1, new_leaf_Z10_rep2]))leaf_Z10_std = np.std(np.array([new_leaf_Z10_rep1, new_leaf_Z10_rep2]))leaf_Z23_mean = np.mean(np.array([new_leaf_Z23_rep1, new_leaf_Z23_rep2]))leaf_Z23_std = np.std(np.array([new_leaf_Z23_rep1, new_leaf_Z23_rep2]))leaf_Z71_mean = np.mean(np.array([new_leaf_Z71_rep1, new_leaf_Z71_rep2]))leaf_Z71_std = np.std(np.array([new_leaf_Z71_rep1, new_leaf_Z71_rep2]))spike_Z32_mean = np.mean(np.array([new_spike_Z32_rep1, new_spike_Z32_rep2]))spike_Z32_std = np.std(np.array([new_spike_Z32_rep1, new_spike_Z32_rep2]))spike_Z39_mean = np.mean(np.array([new_spike_Z39_rep1, new_spike_Z39_rep2]))spike_Z39_std = np.std(np.array([new_spike_Z39_rep1, new_spike_Z39_rep2]))spike_Z65_mean = np.mean(np.array([new_spike_Z65_rep1, new_spike_Z65_rep2]))spike_Z65_std = np.std(np.array([new_spike_Z65_rep1, new_spike_Z65_rep2]))latet_lepto_mean = np.mean(np.array([new_latet_lepto_rep1, new_latet_lepto_rep2]))latet_lepto_std = np.std(np.array([new_latet_lepto_rep1, new_latet_lepto_rep2]))diplo_dia_mean = np.mean(np.array([new_diplo_dia_rep1, new_diplo_dia_rep2]))diplo_dia_std = np.std(np.array([new_diplo_dia_rep1, new_diplo_dia_rep2]))zygo_pachy_mean = np.mean(np.array([new_zygo_pachy_rep1, new_zygo_pachy_rep2]))zygo_pachy_std = np.std(np.array([new_zygo_pachy_rep1, new_zygo_pachy_rep2]))metaphaseI_mean = np.mean(np.array([new_metaphaseI_rep1, new_metaphaseI_rep2]))metaphaseI_std = np.std(np.array([new_metaphaseI_rep1, new_metaphaseI_rep2]))grain_Z71_mean = np.mean(np.array([new_grain_Z71_rep1, new_grain_Z71_rep2]))grain_Z71_std = np.std(np.array([new_grain_Z71_rep1, new_grain_Z71_rep2]))grain_Z75_mean = np.mean(np.array([new_grain_Z75_rep1, new_grain_Z75_rep2]))grain_Z75_std = np.std(np.array([new_grain_Z75_rep1, new_grain_Z75_rep2]))grain_Z85_mean = np.mean(np.array([new_grain_Z85_rep1, new_grain_Z85_rep2]))grain_Z85_std = np.std(np.array([new_grain_Z85_rep1, new_grain_Z85_rep2]))root_max = np.max(np.array([new_root_Z10_rep1, new_root_Z10_rep2, new_root_Z13_rep1, new_root_Z13_rep2, new_root_Z39_rep1, new_root_Z39_rep2]))stem_max = np.max(np.array([new_stem_Z30_rep1, new_stem_Z30_rep2, new_stem_Z32_rep1, new_stem_Z32_rep2, new_stem_Z65_rep1, new_stem_Z65_rep2]))leaf_max = np.max(np.array([new_leaf_Z10_rep1, new_leaf_Z10_rep2, new_leaf_Z23_rep1, new_leaf_Z23_rep2, new_leaf_Z71_rep1, new_leaf_Z71_rep2]))spike_max = np.max(np.array([new_spike_Z32_rep1, new_spike_Z32_rep2, new_spike_Z39_rep1, new_spike_Z39_rep2, new_spike_Z65_rep1, new_spike_Z65_rep2]))grain_max = np.max(np.array([new_grain_Z71_rep1, new_grain_Z71_rep2, Wheat_Room2_10DPA, Wheat_Room2_10DPA_Rep,new_grain_Z85_rep1, new_grain_Z85_rep2]))stamen_max = np.mean(np.array([new_stamen, new_latet_lepto_rep1, new_latet_lepto_rep2, new_diplo_dia_rep1, new_diplo_dia_rep2,new_zygo_pachy_rep1, new_zygo_pachy_rep2, new_metaphaseI_rep1, new_metaphaseI_rep2]))organs.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (Geneid, Chr, root_max, stem_max, leaf_max, spike_max, grain_max, stamen_max, new_carpel))Wheat_10DPA_mean = np.mean(np.array([Wheat_Room1_10DPA, Wheat_Room1_10DPA_Rep,Wheat_Room2_10DPA, Wheat_Room2_10DPA_Rep]))Wheat_10DPA_std = np.std(np.array([Wheat_Room1_10DPA, Wheat_Room1_10DPA_Rep,Wheat_Room2_10DPA, Wheat_Room2_10DPA_Rep]))Wheat_AL_20DPA_mean = np.mean(np.array([Wheat_Room1_AL_20DPA, Wheat_Room1_AL_20DPA_Rep,Wheat_Room2_AL_20DPA, Wheat_Room2_AL_20DPA_Rep, Wheat_Room1_AL_20DPA_Extra1, Wheat_Room1_AL_20DPA_Extra2]))Wheat_AL_20DPA_std = np.std(np.array([Wheat_Room1_AL_20DPA, Wheat_Room1_AL_20DPA_Rep,Wheat_Room2_AL_20DPA, Wheat_Room2_AL_20DPA_Rep, Wheat_Room1_AL_20DPA_Extra1, Wheat_Room1_AL_20DPA_Extra2]))Wheat_SE_20DPA_mean = np.mean(np.array([Wheat_Room1_SE_20DPA, Wheat_Room1_SE_20DPA_Rep, Wheat_Room2_SE_20DPA, Wheat_Room2_SE_20DPA_Rep]))Wheat_SE_20DPA_std = np.std(np.array([Wheat_Room1_SE_20DPA, Wheat_Room1_SE_20DPA_Rep, Wheat_Room2_SE_20DPA, Wheat_Room2_SE_20DPA_Rep]))Wheat_TC_20DPA_mean = np.mean(np.array([Wheat_Room1_TC_20DPA, Wheat_Room1_TC_20DPA_Rep, Wheat_Room2_TC_20DPA, Wheat_Room2_TC_20DPA_Rep]))Wheat_TC_20DPA_std = np.std(np.array([Wheat_Room1_TC_20DPA, Wheat_Room1_TC_20DPA_Rep, Wheat_Room2_TC_20DPA, Wheat_Room2_TC_20DPA_Rep]))Wheat_REF_20DPA_mean = np.mean(np.array([Wheat_Room1_REF_20DPA, Wheat_Room1_REF_20DPA_Rep, Wheat_Room2_REF_20DPA, Wheat_Room2_REF_20DPA_Rep]))Wheat_REF_20DPA_std = np.std(np.array([Wheat_Room1_REF_20DPA, Wheat_Room1_REF_20DPA_Rep, Wheat_Room2_REF_20DPA, Wheat_Room2_REF_20DPA_Rep]))Wheat_SE_30DPA_mean = np.mean(np.array([Wheat_Room1_SE_30DPA, Wheat_Room1_SE_30DPA_Rep, Wheat_Room2_SE_30DPA, Wheat_Room2_SE_30DPA_Rep]))Wheat_SE_30DPA_std = np.std(np.array([Wheat_Room1_SE_30DPA, Wheat_Room1_SE_30DPA_Rep, Wheat_Room2_SE_30DPA, Wheat_Room2_SE_30DPA_Rep]))Wheat_AL_SE_30DPA_mean = np.mean(np.array([Wheat_Room1_AL_SE_30DPA, Wheat_Room1_AL_SE_30DPA_Rep, Wheat_Room2_AL_SE_30DPA, Wheat_Room2_AL_SE_30DPA_Rep]))Wheat_AL_SE_30DPA_std = np.std(np.array([Wheat_Room1_AL_SE_30DPA, Wheat_Room1_AL_SE_30DPA_Rep, Wheat_Room2_AL_SE_30DPA, Wheat_Room2_AL_SE_30DPA_Rep]))wheat_23_mean = np.mean(np.array([wheat_23_1, wheat_23_2, wheat_23_3]))wheat_23_std = np.std(np.array([wheat_23_1, wheat_23_2, wheat_23_3]))wheat_4_mean = np.mean(np.array([wheat_4_1, wheat_4_2, wheat_4_3]))wheat_4_std = np.std(np.array([wheat_4_1, wheat_4_2, wheat_4_3]))print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" \"\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" \"\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" \"\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % \(Geneid, Chr, Start, End, Strand, Length, root_Z10_mean, root_Z13_mean,root_Z39_mean, stem_Z30_mean,stem_Z32_mean, stem_Z65_mean, leaf_Z10_mean, leaf_Z23_mean, leaf_Z71_mean, spike_Z32_mean,spike_Z39_mean, spike_Z65_mean, new_carpel, new_carpel_like_structure, new_stamen, latet_lepto_mean,diplo_dia_mean, zygo_pachy_mean, metaphaseI_mean, grain_Z71_mean, grain_Z75_mean, grain_Z85_mean,Wheat_10DPA_mean, Wheat_AL_20DPA_mean, Wheat_SE_20DPA_mean, Wheat_TC_20DPA_mean, Wheat_REF_20DPA_mean,Wheat_SE_30DPA_mean, Wheat_AL_SE_30DPA_mean, wheat_23_mean, wheat_4_mean,root_Z10_std, root_Z13_std, root_Z39_std, stem_Z30_std, stem_Z32_std, stem_Z65_std, leaf_Z10_std,leaf_Z23_std, leaf_Z71_std, spike_Z32_std, spike_Z39_std, spike_Z65_std, 'null', 'null', 'null',latet_lepto_std, diplo_dia_std, zygo_pachy_std, metaphaseI_std, grain_Z71_std, grain_Z75_std,grain_Z85_std, Wheat_10DPA_std, Wheat_AL_20DPA_std, Wheat_SE_20DPA_std, Wheat_TC_20DPA_std,Wheat_REF_20DPA_std, Wheat_SE_30DPA_std, Wheat_AL_SE_30DPA_std, wheat_23_std, wheat_4_std)organs.close()

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