GFF3 TO GTF

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GFF3 TO GTF

gff3格式是使用gmap软件得到的。

输入文件gff3的格式如下：

chr1A   IWGSCv1.0_gmap  gene    11740   12074   .   +   .   ID=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1.path1;Name=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1 chr1A   IWGSCv1.0_gmap  mRNA    11740   12074   .   +   .   ID=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1.mrna1;Name=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1;Parent=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1.path1;coverage=100.0;identity=100.0;matches=335;mismatches=0;indels=0;unknowns=0    chr1A   IWGSCv1.0_gmap  exon    11740   12074   100 +   .   ID=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1.mrna1.exon1;Name=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1;Parent=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1.mrna1;Target=TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1 1   335 +   chr1A   IWGSCv1.0_gmap  gene    22427   24851   .   -   .   ID=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1.path1;Name=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1 chr1A   IWGSCv1.0_gmap  mRNA    22427   24851   .   -   .   ID=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1.mrna1;Name=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1;Parent=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1.path1;coverage=100.0;identity=100.0;matches=2425;mismatches=0;indels=0;unknowns=0   chr1A   IWGSCv1.0_gmap  exon    22427   24851   100 -   .   ID=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1.mrna1.exon1;Name=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1;Parent=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1.mrna1;Target=TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1 1   2425    +   chr1A   IWGSCv1.0_gmap  gene    28794   39054   .   +   .   ID=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1.path1;Name=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1 chr1A   IWGSCv1.0_gmap  mRNA    28794   39054   .   +   .   ID=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1.mrna1;Name=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1;Parent=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1.path1;coverage=100.0;identity=100.0;matches=1624;mismatches=0;indels=0;unknowns=0   chr1A   IWGSCv1.0_gmap  exon    28794   28929   100 +   .   ID=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1.mrna1.exon1;Name=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1;Parent=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1.mrna1;Target=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1 1   136 +   chr1A   IWGSCv1.0_gmap  exon    37567   39054   100 +   .   ID=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1.mrna1.exon2;Name=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1;Parent=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1.mrna1;Target=TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1 137 1624    +

转换成gtf的格式，类似下边的结果：

chr1A   IWGSCv1.0_gmap  transcript  11740   12074   .   +   .   transcript_id "TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1"; gene_id "TRIAE_CS42_1AS_TGACv1_023354_AA0082670";chr1A   IWGSCv1.0_gmap  exon    11740   12074   100 +   .   transcript_id "TRIAE_CS42_1AS_TGACv1_023354_AA0082670.1"; gene_id "TRIAE_CS42_1AS_TGACv1_023354_AA0082670";exon_number 1;chr1A   IWGSCv1.0_gmap  transcript  22427   24851   .   -   .   transcript_id "TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1"; gene_id "TRIAE_CS42_1AS_TGACv1_024449_AA0082770";chr1A   IWGSCv1.0_gmap  exon    22427   24851   100 -   .   transcript_id "TRIAE_CS42_1AS_TGACv1_024449_AA0082770.1"; gene_id "TRIAE_CS42_1AS_TGACv1_024449_AA0082770";exon_number 1;chr1A   IWGSCv1.0_gmap  transcript  28794   39054   .   +   .   transcript_id "TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1"; gene_id "TRIAE_CS42_1AS_TGACv1_021338_AA0081570";chr1A   IWGSCv1.0_gmap  exon    28794   28929   100 +   .   transcript_id "TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1"; gene_id "TRIAE_CS42_1AS_TGACv1_021338_AA0081570";exon_number 1;chr1A   IWGSCv1.0_gmap  exon    37567   39054   100 +   .   transcript_id "TRIAE_CS42_1AS_TGACv1_021338_AA0081570.1"; gene_id "TRIAE_CS42_1AS_TGACv1_021338_AA0081570";exon_number 2;chr1A   IWGSCv1.0_gmap  transcript  59624   60578   .   -   .   transcript_id "TRIAE_CS42_1AS_TGACv1_021658_AA0082030.1"; gene_id "TRIAE_CS42_1AS_TGACv1_021658_AA0082030";chr1A   IWGSCv1.0_gmap  exon    59624   60578   99  -   .   transcript_id "TRIAE_CS42_1AS_TGACv1_021658_AA0082030.1"; gene_id "TRIAE_CS42_1AS_TGACv1_021658_AA0082030";exon_number 1;chr1A   IWGSCv1.0_gmap  transcript  86763   89148   .   -   .   transcript_id "TRIAE_CS42_1AS_TGACv1_021895_AA0082240.1"; gene_id "TRIAE_CS42_1AS_TGACv1_021895_AA0082240";

转换的脚本如下：

#!/usr/bin/env python# -*- coding: utf-8 -*-__author__ = 'shengwei ma'__author_email__ = 'shengweima@icloud.com'with open('TGACv1.cdna.gff3', 'r') as f:    for line in f:        lin = line.strip().split('\t')        if lin[2] == 'gene':            print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\ttranscript_id \"%s\";gene_id \"%s\"" % \                  (lin[0], lin[1], "transcript", lin[3], lin[4], lin[5], lin[6], lin[7], lin[8].split(';')[0][3:-6],                   lin[8].split(';')[1].split('.')[0][5:])        if lin[2] == 'exon':            exon = lin[8].split(';')[0]            exon1 = exon.split('exon')[-1]            print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\ttranscript_id \"%s\";gene_id \"%s\";exon_number %s" % \                  (lin[0], lin[1], lin[2], lin[3], lin[4], lin[5], lin[6], lin[7], lin[8].split(';')[0][3:-12],                   lin[8].split(';')[1].split('.')[0][5:], exon1)

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