Python：检查文件并输出到新fi

Question

我有一个示例文件名文件：

chr7    149601  MERGED_DEL_2_39754  T   .   141.35  .   AC=0;AF=0.00;AN=2;DP=37;MQ=37.00;MQ0=0;1000gALT=<DEL>;AF1000g=0.09;AFR_AF=0.01;AMR_AF=0.03;ASN_AF=0.27;EUR_AF=0.04;TS=HPGOM;TSseq=T,T,G,T,T;CAnc=T;GAnc=T;OAnc=T;mSC=0.000;GRP=-2.16;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:37:99:0,111,1458:0,0:0,0:0,0:18,18:0
chr7    149616  rs190051229 C   .   108.65  .   AC=0;AF=0.00;AN=2;DP=35;MQ=37.00;MQ0=0;1000gALT=T;AF1000g=0.00;ASN_AF=0.01;CpG;TS=HPGOM;TSseq=C,C,C,C,C;CAnc=C;GAnc=C;OAnc=C;mSC=0.000;GRP=-2.15;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:35:78.65:0,79,1305:0,0:17,17:0,0:0,0:0
chr7    149628  rs3814456   A   .   129.31  .   AC=0;AF=0.00;AN=2;DP=37;MQ=37.00;MQ0=0;1000gALT=G;AF1000g=0.14;AFR_AF=0.16;AMR_AF=0.07;ASN_AF=0.27;EUR_AF=0.06;TS=HPGOM;TSseq=A,A,A,A,A;CAnc=A;GAnc=A;OAnc=A;mSC=0.000;GRP=-2.23;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:37:99:0,99,1290:14,22:0,0:0,0:0,0:0
chr7    149634  rs146001818 G   T   1375.63 .   AC=2;AF=1.00;AN=2;BaseQRankSum=0.456;DP=39;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9997;MQ=37.00;MQ0=0;MQRankSum=1.641;QD=35.27;ReadPosRankSum=1.459;1000gALT=T;AF1000g=0.01;AFR_AF=0.01;AMR_AF=0.01;EUR_AF=0.03;TS=HPGOM;TSseq=G,G,G,G,G;CAnc=G;GAnc=G;OAnc=G;mSC=0.001;GRP=0.0686;Map20=1;ANN=T|upstream_gene_variant|MODIFIER|LOC100507642|LOC100507642|transcript|NR_108064.1|Noncoding||n.-1G>T|||||84|,T|upstream_gene_variant|MODIFIER|LOC100507642|LOC100507642|transcript|NR_108065.1|Noncoding||n.-1G>T|||||84|,T|intergenic_region|MODIFIER|LOC100507642|LOC100507642|intergenic_region|LOC100507642||||||||| GT:DP:GQ:PL:A:C:G:T:IR  1/1:39:74.36:1409,74,0:0,0:0,0:0,1:15,22:0
chr7    149645  rs112562180 C   .   165.42  .   AC=0;AF=0.00;AN=2;DP=46;MQ=37.00;MQ0=0;1000gALT=A;AF1000g=0.02;AFR_AF=0.03;AMR_AF=0.03;EUR_AF=0.02;TS=HPGOM;TSseq=C,C,C,C,C;CAnc=C;GAnc=C;OAnc=C;mSC=0.000;GRP=-1.93;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:46:99:0,135,1758:0,0:22,22:0,0:1,0:0
chr7    149659  rs79606188  T   .   195.53  .   AC=0;AF=0.00;AN=2;DP=55;MQ=37.00;MQ0=0;1000gALT=A;AF1000g=0.02;AFR_AF=0.07;AMR_AF=0.01;TS=HPGOM;TSseq=T,T,T,T,G;CAnc=T;GAnc=T;OAnc=T;mSC=0.005;GRP=0.0203;Map20=1   GT:DP:GQ:PL:A:C:G:T:IR  0/0:55:99:0,166,2189:0,0:0,0:0,0:26,28:0
chr7    149724  rs193238495 C   .   216.56  .   AC=0;AF=0.00;AN=2;DP=62;MQ=37.18;MQ0=0;1000gALT=T;AF1000g=0.00;AFR_AF=0.01;CpG;TS=HPGOM;TSseq=C,C,C,C,C;CAnc=C;GAnc=C;OAnc=C;mSC=0.000;GRP=-0.139;Map20=1   GT:DP:GQ:PL:A:C:G:T:IR  0/0:62:99:0,187,2385:0,0:37,24:0,0:0,0:0
chr7    149765  rs3814455   C   .   198.52  .   AC=0;AF=0.00;AN=2;DP=56;MQ=37.73;MQ0=0;1000gALT=T;AF1000g=0.54;AFR_AF=0.35;AMR_AF=0.60;ASN_AF=0.31;EUR_AF=0.79;TS=HPGOM;TSseq=C,C,C,C,C;CAnc=C;GAnc=C;OAnc=C;mSC=0.000;GRP=-0.494;Map20=1   GT:DP:GQ:PL:A:C:G:T:IR  0/0:56:99:0,169,2174:0,0:22,32:0,0:0,0:0
chr7    149785  rs185668085 C   .   192.52  .   AC=0;AF=0.00;AN=2;DP=54;MQ=37.76;MQ0=0;1000gALT=G;AF1000g=0.01;ASN_AF=0.04;TS=HPGOM;TSseq=C,C,C,C,C;CAnc=C;GAnc=C;OAnc=C;mSC=0.002;GRP=-0.216;Map20=1   GT:DP:GQ:PL:A:C:G:T:IR  0/0:54:99:0,163,2135:0,0:19,33:0,0:0,0:0
chr7    149825  rs189449059 C   .   156.38  .   AC=0;AF=0.00;AN=2;DP=42;MQ=37.71;MQ0=0;1000gALT=T;AF1000g=0.00;TS=HPGOM;TSseq=C,C,C,C,-;CAnc=C;GAnc=C;OAnc=C;mSC=0.000;GRP=0.693;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:42:99:0,126,1609:0,0:17,24:0,0:0,0:0
chr7    149863  .   G   A   407.49  .   AC=1;AF=0.50;AN=2;BaseQRankSum=-1.315;DP=37;Dels=0.00;FS=1.341;HRun=1;HaplotypeScore=1.9995;MQ=37.00;MQ0=0;MQRankSum=-0.201;QD=11.01;ReadPosRankSum=1.469;TS=HPGOM;TSseq=G,G,G,G,G;CAnc=G;GAnc=G;OAnc=G;mSC=0.000;GRP=-1.5;Map20=1;ANN=A|non_coding_exon_variant|MODIFIER|LOC100507642|LOC100507642|transcript|NR_108064.1|Noncoding|1/3|n.146G>A||||||,A|non_coding_exon_variant|MODIFIER|LOC100507642|LOC100507642|transcript|NR_108065.1|Noncoding|1/2|n.146G>A||||||    GT:DP:GQ:PL:A:C:G:T:IR  0/1:37:99:437,0,759:6,8:0,0:13,9:0,0:0
chr7    149880  rs115127983 C   .   108.24  .   AC=0;AF=0.00;AN=2;DP=26;MQ=37.00;MQ0=0;1000gALT=G;AF1000g=0.04;AFR_AF=0.15;AMR_AF=0.02;CpG;TS=HPGOM;TSseq=C,C,C,C,C;CAnc=C;GAnc=C;OAnc=C;mSC=0.003;GRP=-1.24;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:26:78.25:0,78,1029:0,0:15,10:0,0:0,0:0
chr7    150067  rs181041230 G   .   138.34  .   AC=0;AF=0.00;AN=2;DP=36;MQ=38.37;MQ0=0;1000gALT=A;AF1000g=0.00;AFR_AF=0.01;TS=HPGOM;TSseq=G,G,G,G,G;CAnc=G;GAnc=G;OAnc=G;mSC=0.005;GRP=0.119;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:36:99:0,108,1425:0,0:0,0:16,19:0,0:0
chr7    150253  rs28397846  A   .   159.4   .   AC=0;AF=0.00;AN=2;DP=43;MQ=39.05;MQ0=0;1000gALT=G;AF1000g=0.03;AFR_AF=0.14;AMR_AF=0.02;TS=HPGOM;TSseq=A,A,A,-,G;CAnc=A;GAnc=A;OAnc=A;mSC=0.000;GRP=-2.18;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:43:99:0,129,1687:24,19:0,0:0,0:0,0:0
chr7    150280  rs139905037 A   .   159.4   .   AC=0;AF=0.00;AN=2;DP=45;MQ=38.96;MQ0=0;1000gALT=G;AF1000g=0.00;ASN_AF=0.01;TS=HPGOM;TSseq=A,A,A,-,-;CAnc=A;GAnc=A;OAnc=A;mSC=0.000;GRP=-0.168;Map20=1   GT:DP:GQ:PL:A:C:G:T:IR  0/0:45:99:0,129,1682:19,25:0,1:0,0:0,0:0
chr7    150353  rs75914010  A   .   162.42  .   AC=0;AF=0.00;AN=2;DP=45;MQ=37.00;MQ0=0;1000gALT=T;AF1000g=0.02;AFR_AF=0.03;AMR_AF=0.02;EUR_AF=0.02;TS=HPGOM;TSseq=A,A,A,A,A;CAnc=A;GAnc=A;OAnc=A;mSC=0.000;GRP=-0.647;Map20=1   GT:DP:GQ:PL:A:C:G:T:IR  0/0:45:99:0,132,1739:21,24:0,0:0,0:0,0:0
chr7    150356  rs185358707 C   .   113.39  .   AC=0;AF=0.00;AN=2;DP=43;MQ=37.00;MQ0=0;1000gALT=T;AF1000g=0.00;CpG;TS=HPGOM;TSseq=C,C,C,C,C;CAnc=C;GAnc=C;OAnc=C;mSC=0.000;GRP=-1.59;Map20=1    GT:DP:GQ:PL:A:C:G:T:IR  0/0:43:83.39:0,83,1538:0,1:19,21:0,0:2,0:0

我的目标是保存指定范围内的所有行。 这就是我目前所拥有的

#!/usr/bin/env python
import sys

file=open('filename')
sys.stdout=open('mega1.txt', 'w')

for line in file:
    fields = line.strip().split()
    chrm = fields[0]
    pos = int(fields[1])
    id1    = fields[2]
    if id1 in range(149601, 1149601):
        print line

我不知道为什么它会继续运行

对于此样本文件名，所有行都将保存到新的mega1.txt文件中，因为第2列中的值都适合该范围

Answer 1

如果出现以下情况，您可能正在签入错误的数据

您正在用range(149601, 1149601)检查str的id1

你必须用这个范围检查pos

请试试这个，它很管用

#!/usr/bin/env python
import sys

fp=open('filename')
sys.stdout = open('mega1.txt', 'w')

for line in fp:
    fields = line.strip().split()
    chrm = fields[0]
    pos = int(fields[1])
    id1    = fields[2]
    if pos in range(149601, 1149601):
        print line