convert_dN-gmap_to_dex-compat_map_gff_DEL¶

import pandas as pd
import numpy as np

import sys
sys.path.append('/Users/hughcross/analysis/git_projects/git_projects/consensus_builder/consensus_functions')
from file_funcs import make_list

gff_file = '/Users/hughcross/analysis/git_projects/rangefinder/gmap.spliced_alignments.gff3'

gold_dtypes = {'seqid':'str','source':'str','type':'str','start':'float','end':'float','score':'str','strand':'str','phase':'str','attributes':'str'}

col_names = ['seqid','source','type','start','end','score','strand','phase','attributes']

gmap = pd.read_table(gff_file, sep='\t', comment='#', dtype=gold_dtypes, names=col_names)

gmap.head()

gmap_scafs = gmap['seqid'].tolist()
print(len(gmap_scafs))

12310

de_epi = make_list('/Users/hughcross/analysis/epiclim/dex_epi_phase1/DE_epigenes_scaffold_list.txt')

de_epi_gmapped = []
for i in de_epi:
    if i in gmap_scafs:
        de_epi_gmapped.append(i)
print(len(de_epi_gmapped))

30

#de_epi_gmapped
# more than one gene per scaffold, so maybe split the df by geneID 
#gff['gene_ID'], gff['attr_info'] = zip(*gff['attributes'].apply(lambda x: x.split(';', 1)))

gmap['attr_ID'], gmap['attr_Name'], gmap['attr_Target'], gmap['attr_Gap'] = zip(*gmap['attributes'].apply(lambda x: x.split(';', 3)))

gmap.head()

# now do the others
gmap['attr_ID'] = gmap.attr_ID.str.replace('ID=','') ## replacing it later, so retains ID= for making new attributes 
gmap['attr_Name'] = gmap.attr_Name.str.replace('Name=','')
gmap['attr_Target'] = gmap.attr_Target.str.replace('Target=','')
gmap['attr_Gap'] = gmap.attr_Gap.str.replace('Gap=','')

# try to get range info from attr_Target above
gmap['gene_name'], gmap['attr_start'], gmap['attr_end'] = zip(*gmap['attr_Target'].apply(lambda x: x.split(' ', 3)))

gmap_names = gmap['gene_name'].tolist()
print(len(gmap_names))

12310

# get a subset of those of correct scaffolds
## eug_sub = eug[eug['seqid'].isin(scaflist)]
gmap_sub = gmap[gmap['seqid'].isin(de_epi_gmapped)]

gmap_sub

gmap_sub_ls = gmap_sub['gene_name'].tolist()
trans_genes = trans['seqid'].tolist()

subset = set(gmap_sub_ls)
transet = set(trans_genes)
print(len(subset))
print(len(transet))

68
552

epi_dn = []
for nam in subset:
    if nam in transet:
        epi_dn.append(nam)
print(len(epi_dn))

2

# iterate through the gmap gff df, and create dictionary of all genes
gene_starts = {}
gene_ends = {}
gene_dict = {}
gene_scaffs = {}
path_scaffs = {}
for ind,rw in gmap_sub.iterrows():
    gene_id = rw.attr_ID#.replace('ID=','')
    gene = rw.attr_Name
    gene_dict.setdefault(gene_id, {})['gene']=gene
    gene_dict.setdefault(gene_id, {})['scaffold']=rw.seqid
    gene_dict.setdefault(gene_id, {})['strand']=rw.strand
    gene_scaffs.setdefault(gene, []).append(rw.seqid)
    path_scaffs[gene_id]=rw.seqid
    gene_starts.setdefault(gene_id, []).append(int(rw.start))
    gene_ends.setdefault(gene_id, []).append(int(rw.end))
print(len(gene_dict))
print(len(gene_scaffs))
print(len(path_scaffs))
print(len(gene_starts))
print(len(gene_ends))

73
68
73
73
73

# now have to insert whole gene ranges in right place in lists
## have to create dictionary of whole gene ranges from previous for loop results
### get list of gene_ids
gene_list = gene_dict.keys()
print(gene_list[0])
print(len(gene_list))

TR55663|c3_g2_i1.path1
73

gene_range = {}
for gene in gene_list:
    gene_start = min(gene_starts[gene])
    gene_end = max(gene_ends[gene])
    gene_range.setdefault(gene, {})['g_start']=gene_start
    gene_range.setdefault(gene, {})['g_end']=gene_end
print(len(gene_range))

73

Repeat above loop, but now insert the gene type at the beginning of new genes¶

# rerun for loop iterating through df above, but create lists of all categories, 
## then make dict of lists, and apply to df
### repeat above loop, but add exons
scaff_ls = []
source_ls = []
type_ls = []
start_ls = []
end_ls = []
score_ls = []
orient_ls = []
phase_ls = []
id_ls = []
glist = []
for ind,rw in gmap_sub.iterrows():
    gene_id = rw.attr_ID#.replace('ID=','')
    # here, condition on if new gene
    if gene_id in glist:
        # first put in exon
        scaff_ls.append(rw.seqid)
        source_ls.append('dN_gmap')
        type_ls.append('exon') # this will have to be adjusted
        start_ls.append(int(rw.start))
        end_ls.append(int(rw.end))
        score_ls.append(rw.score)
        orient_ls.append(rw.strand)
        phase_ls.append('.')
        id_ls.append(gene_id)
        # repeat same, but for CDS
        scaff_ls.append(rw.seqid)
        source_ls.append('dN_gmap')
        type_ls.append('CDS') # this will have to be adjusted
        start_ls.append(int(rw.start))
        end_ls.append(int(rw.end))
        score_ls.append(rw.score)
        orient_ls.append(rw.strand)
        phase_ls.append('.')
        id_ls.append(gene_id)
    else:
        glist.append(gene_id)
        scaff_ls.append(gene_dict[gene_id]['scaffold'])
        source_ls.append('dN_gmap')
        type_ls.append('gene') # this will have to be adjusted
        start_ls.append(int(gene_range[gene_id]['g_start']))
        end_ls.append(int(gene_range[gene_id]['g_end']))
        score_ls.append(rw.score)
        orient_ls.append(gene_dict[gene_id]['strand'])
        phase_ls.append('.')
        id_ls.append(gene_id)
        # then do the normal line once overall gene is put in
        ## first do the exon
        scaff_ls.append(rw.seqid)
        source_ls.append('dN_gmap')
        type_ls.append('exon') # this will have to be adjusted
        start_ls.append(int(rw.start))
        end_ls.append(int(rw.end))
        score_ls.append(rw.score)
        orient_ls.append(rw.strand)
        phase_ls.append('.')
        id_ls.append(gene_id)
        # now do CDS
        scaff_ls.append(rw.seqid)
        source_ls.append('dN_gmap')
        type_ls.append('CDS') # this will have to be adjusted
        start_ls.append(int(rw.start))
        end_ls.append(int(rw.end))
        score_ls.append(rw.score)
        orient_ls.append(rw.strand)
        phase_ls.append('.')
        id_ls.append(gene_id)
print(len(scaff_ls))
print(len(id_ls))

733
733

# now try to make a df from these lists
## first make a dict of lists
### adding exons
data6 = {'source':source_ls,'Type':type_ls,'phase':phase_ls,'start':start_ls,'end':end_ls,'seqid':scaff_ls,'score':score_ls,'strand':orient_ls,'attributes':id_ls}
df6 = pd.DataFrame(data6, columns=['seqid','source','Type','start','end','score','strand','phase','attributes'])
df6.head()

# now have to modify attributes column for different types and number
## iterate through rows, grab type and attributes, then modify attributes and make new
### modifying a single cell:
#### df1.set_value(6, 'starts', 4600)
##### adding exons here
count = 1 # for exon counts
for ind,rw in df6.iterrows():
    tipo = rw.Type
    attr = rw.attributes
    if tipo == 'gene':
        new_attr = 'ID='+attr+'.g1;'+'Name=ORF'
        count = 1
    elif tipo == 'exon': # need to add exon numbers
        new_attr = 'ID='+attr+'.m1.exon'+str(count)+';'+'Parent='+attr+'.g1;'+'Name=ORF'
        count += 1
    elif tipo == 'CDS':
        new_attr = 'ID='+attr+'.m1;'+'Parent='+attr+'.g1;'+'Name=ORF'
    df6.set_value(ind, 'attributes', new_attr)

# now write to file and test with dexseq scripts and cufflinks
## filt_blast_results.to_csv(blastout, sep='\t', index=False, header=False)
df6.to_csv('epireg_converted_from_gmap2.gff3', sep='\t', index=False, header=False)

	seqid	source	type	start	end	score	strand	phase	attributes
0	MA_339960	Pabies1.0_gene_only.fa.gmap	cDNA_match	3398.0	3520.0	100	-	.	ID=TR547\|c0_g1_i2.path1;Name=TR547\|c0_g1_i2;Ta...
1	MA_339960	Pabies1.0_gene_only.fa.gmap	cDNA_match	2959.0	3347.0	96	-	.	ID=TR547\|c0_g1_i2.path1;Name=TR547\|c0_g1_i2;Ta...
2	MA_82491	Pabies1.0_gene_only.fa.gmap	cDNA_match	5764.0	6396.0	99	-	.	ID=TR392\|c0_g1_i1.path1;Name=TR392\|c0_g1_i1;Ta...
3	MA_474985	Pabies1.0_gene_only.fa.gmap	cDNA_match	5839.0	6224.0	93	-	.	ID=TR466\|c0_g1_i1.path1;Name=TR466\|c0_g1_i1;Ta...
4	MA_77330	Pabies1.0_gene_only.fa.gmap	cDNA_match	3304.0	4106.0	96	+	.	ID=TR393\|c0_g1_i1.path1;Name=TR393\|c0_g1_i1;Ta...

	seqid	source	type	start	end	score	strand	phase	attributes	attr_ID	attr_Name	attr_Target	attr_Gap
0	MA_339960	Pabies1.0_gene_only.fa.gmap	cDNA_match	3398.0	3520.0	100	-	.	ID=TR547\|c0_g1_i2.path1;Name=TR547\|c0_g1_i2;Ta...	TR547\|c0_g1_i2.path1	TR547\|c0_g1_i2	TR547\|c0_g1_i2 1 123	M123
1	MA_339960	Pabies1.0_gene_only.fa.gmap	cDNA_match	2959.0	3347.0	96	-	.	ID=TR547\|c0_g1_i2.path1;Name=TR547\|c0_g1_i2;Ta...	TR547\|c0_g1_i2.path1	TR547\|c0_g1_i2	TR547\|c0_g1_i2 124 501	M214 D11 M164
2	MA_82491	Pabies1.0_gene_only.fa.gmap	cDNA_match	5764.0	6396.0	99	-	.	ID=TR392\|c0_g1_i1.path1;Name=TR392\|c0_g1_i1;Ta...	TR392\|c0_g1_i1.path1	TR392\|c0_g1_i1	TR392\|c0_g1_i1 1 633	M633
3	MA_474985	Pabies1.0_gene_only.fa.gmap	cDNA_match	5839.0	6224.0	93	-	.	ID=TR466\|c0_g1_i1.path1;Name=TR466\|c0_g1_i1;Ta...	TR466\|c0_g1_i1.path1	TR466\|c0_g1_i1	TR466\|c0_g1_i1 8 403	M36 I5 M228 I8 M104 D3 M15
4	MA_77330	Pabies1.0_gene_only.fa.gmap	cDNA_match	3304.0	4106.0	96	+	.	ID=TR393\|c0_g1_i1.path1;Name=TR393\|c0_g1_i1;Ta...	TR393\|c0_g1_i1.path1	TR393\|c0_g1_i1	TR393\|c0_g1_i1 1 781	M351 D22 M430

	seqid	source	type	start	end	score	strand	phase	attributes	attr_ID	attr_Name	attr_Target	attr_Gap	gene_name	attr_start	attr_end
60	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	1174.0	1448.0	99	+	.	ID=TR574\|c2_g1_i2.path2;Name=TR574\|c2_g1_i2;Ta...	TR574\|c2_g1_i2.path2	TR574\|c2_g1_i2	TR574\|c2_g1_i2 67 341	M275	TR574\|c2_g1_i2	67	341
61	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	1577.0	2225.0	98	+	.	ID=TR574\|c2_g1_i2.path2;Name=TR574\|c2_g1_i2;Ta...	TR574\|c2_g1_i2.path2	TR574\|c2_g1_i2	TR574\|c2_g1_i2 342 990	M649	TR574\|c2_g1_i2	342	990
62	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	2327.0	2526.0	100	+	.	ID=TR574\|c2_g1_i2.path2;Name=TR574\|c2_g1_i2;Ta...	TR574\|c2_g1_i2.path2	TR574\|c2_g1_i2	TR574\|c2_g1_i2 991 1190	M200	TR574\|c2_g1_i2	991	1190
63	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	2670.0	2914.0	98	+	.	ID=TR574\|c2_g1_i2.path2;Name=TR574\|c2_g1_i2;Ta...	TR574\|c2_g1_i2.path2	TR574\|c2_g1_i2	TR574\|c2_g1_i2 1191 1435	M245	TR574\|c2_g1_i2	1191	1435
64	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	3018.0	4085.0	97	+	.	ID=TR574\|c2_g1_i2.path2;Name=TR574\|c2_g1_i2;Ta...	TR574\|c2_g1_i2.path2	TR574\|c2_g1_i2	TR574\|c2_g1_i2 1436 2500	M951 D3 M114	TR574\|c2_g1_i2	1436	2500
65	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	4478.0	4537.0	79	+	.	ID=TR574\|c2_g1_i2.path2;Name=TR574\|c2_g1_i2;Ta...	TR574\|c2_g1_i2.path2	TR574\|c2_g1_i2	TR574\|c2_g1_i2 2501 2567	M47 I7 M13	TR574\|c2_g1_i2	2501	2567
66	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	4638.0	4964.0	99	+	.	ID=TR574\|c2_g1_i2.path2;Name=TR574\|c2_g1_i2;Ta...	TR574\|c2_g1_i2.path2	TR574\|c2_g1_i2	TR574\|c2_g1_i2 2568 2894	M327	TR574\|c2_g1_i2	2568	2894
1034	MA_713159	Pabies1.0_gene_only.fa.gmap	cDNA_match	316.0	577.0	96	+	.	ID=TR18492\|c2_g1_i11.path1;Name=TR18492\|c2_g1_...	TR18492\|c2_g1_i11.path1	TR18492\|c2_g1_i11	TR18492\|c2_g1_i11 1 262	M262	TR18492\|c2_g1_i11	1	262
1035	MA_713159	Pabies1.0_gene_only.fa.gmap	cDNA_match	736.0	758.0	86	+	.	ID=TR18492\|c2_g1_i11.path1;Name=TR18492\|c2_g1_...	TR18492\|c2_g1_i11.path1	TR18492\|c2_g1_i11	TR18492\|c2_g1_i11 263 285	M23	TR18492\|c2_g1_i11	263	285
1036	MA_713159	Pabies1.0_gene_only.fa.gmap	cDNA_match	358.0	548.0	96	+	.	ID=TR18492\|c2_g1_i7.path1;Name=TR18492\|c2_g1_i...	TR18492\|c2_g1_i7.path1	TR18492\|c2_g1_i7	TR18492\|c2_g1_i7 1 191	M191	TR18492\|c2_g1_i7	1	191
1037	MA_713159	Pabies1.0_gene_only.fa.gmap	cDNA_match	707.0	758.0	94	+	.	ID=TR18492\|c2_g1_i7.path1;Name=TR18492\|c2_g1_i...	TR18492\|c2_g1_i7.path1	TR18492\|c2_g1_i7	TR18492\|c2_g1_i7 192 243	M52	TR18492\|c2_g1_i7	192	243
1041	MA_74102	Pabies1.0_gene_only.fa.gmap	cDNA_match	2244.0	2430.0	94	+	.	ID=TR18492\|c2_g1_i3.path1;Name=TR18492\|c2_g1_i...	TR18492\|c2_g1_i3.path1	TR18492\|c2_g1_i3	TR18492\|c2_g1_i3 1 187	M187	TR18492\|c2_g1_i3	1	187
1095	MA_97951	Pabies1.0_gene_only.fa.gmap	cDNA_match	10453.0	10925.0	93	+	.	ID=TR18492\|c2_g7_i2.path1;Name=TR18492\|c2_g7_i...	TR18492\|c2_g7_i2.path1	TR18492\|c2_g7_i2	TR18492\|c2_g7_i2 1 473	M400 I1 M20 D1 M52	TR18492\|c2_g7_i2	1	473
1164	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	3018.0	4012.0	90	-	.	ID=TR23182\|c0_g1_i2.path1;Name=TR23182\|c0_g1_i...	TR23182\|c0_g1_i2.path1	TR23182\|c0_g1_i2	TR23182\|c0_g1_i2 1 1085	M241 I90 M754	TR23182\|c0_g1_i2	1	1085
1165	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	2670.0	2914.0	97	-	.	ID=TR23182\|c0_g1_i2.path1;Name=TR23182\|c0_g1_i...	TR23182\|c0_g1_i2.path1	TR23182\|c0_g1_i2	TR23182\|c0_g1_i2 1086 1330	M245	TR23182\|c0_g1_i2	1086	1330
1166	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	2327.0	2526.0	98	-	.	ID=TR23182\|c0_g1_i2.path1;Name=TR23182\|c0_g1_i...	TR23182\|c0_g1_i2.path1	TR23182\|c0_g1_i2	TR23182\|c0_g1_i2 1331 1530	M200	TR23182\|c0_g1_i2	1331	1530
1167	MA_10426199	Pabies1.0_gene_only.fa.gmap	cDNA_match	1822.0	2225.0	99	-	.	ID=TR23182\|c0_g1_i2.path1;Name=TR23182\|c0_g1_i...	TR23182\|c0_g1_i2.path1	TR23182\|c0_g1_i2	TR23182\|c0_g1_i2 1531 1934	M404	TR23182\|c0_g1_i2	1531	1934
1640	MA_15346	Pabies1.0_gene_only.fa.gmap	cDNA_match	8899.0	8920.0	95	-	.	ID=TR34065\|c5_g1_i1.path1;Name=TR34065\|c5_g1_i...	TR34065\|c5_g1_i1.path1	TR34065\|c5_g1_i1	TR34065\|c5_g1_i1 1 22	M22	TR34065\|c5_g1_i1	1	22
1641	MA_15346	Pabies1.0_gene_only.fa.gmap	cDNA_match	4683.0	6303.0	98	-	.	ID=TR34065\|c5_g1_i1.path1;Name=TR34065\|c5_g1_i...	TR34065\|c5_g1_i1.path1	TR34065\|c5_g1_i1	TR34065\|c5_g1_i1 23 1643	M1621	TR34065\|c5_g1_i1	23	1643
1696	MA_74102	Pabies1.0_gene_only.fa.gmap	cDNA_match	2146.0	2426.0	100	-	.	ID=TR34944\|c3_g1_i3.path1;Name=TR34944\|c3_g1_i...	TR34944\|c3_g1_i3.path1	TR34944\|c3_g1_i3	TR34944\|c3_g1_i3 1 281	M281	TR34944\|c3_g1_i3	1	281
2089	MA_920994	Pabies1.0_gene_only.fa.gmap	cDNA_match	2912.0	2929.0	100	-	.	ID=TR45686\|c0_g1_i1.path1;Name=TR45686\|c0_g1_i...	TR45686\|c0_g1_i1.path1	TR45686\|c0_g1_i1	TR45686\|c0_g1_i1 1 18	M18	TR45686\|c0_g1_i1	1	18
2090	MA_920994	Pabies1.0_gene_only.fa.gmap	cDNA_match	2280.0	2391.0	100	-	.	ID=TR45686\|c0_g1_i1.path1;Name=TR45686\|c0_g1_i...	TR45686\|c0_g1_i1.path1	TR45686\|c0_g1_i1	TR45686\|c0_g1_i1 19 130	M112	TR45686\|c0_g1_i1	19	130
2091	MA_920994	Pabies1.0_gene_only.fa.gmap	cDNA_match	2107.0	2168.0	100	-	.	ID=TR45686\|c0_g1_i1.path1;Name=TR45686\|c0_g1_i...	TR45686\|c0_g1_i1.path1	TR45686\|c0_g1_i1	TR45686\|c0_g1_i1 131 192	M62	TR45686\|c0_g1_i1	131	192
2092	MA_920994	Pabies1.0_gene_only.fa.gmap	cDNA_match	1740.0	1827.0	100	-	.	ID=TR45686\|c0_g1_i1.path1;Name=TR45686\|c0_g1_i...	TR45686\|c0_g1_i1.path1	TR45686\|c0_g1_i1	TR45686\|c0_g1_i1 193 280	M88	TR45686\|c0_g1_i1	193	280
2096	MA_106416	Pabies1.0_gene_only.fa.gmap	cDNA_match	9216.0	9221.0	100	-	.	ID=TR45686\|c2_g2_i1.path1;Name=TR45686\|c2_g2_i...	TR45686\|c2_g2_i1.path1	TR45686\|c2_g2_i1	TR45686\|c2_g2_i1 1 6	M6	TR45686\|c2_g2_i1	1	6
2097	MA_106416	Pabies1.0_gene_only.fa.gmap	cDNA_match	4353.0	4422.0	100	-	.	ID=TR45686\|c2_g2_i1.path1;Name=TR45686\|c2_g2_i...	TR45686\|c2_g2_i1.path1	TR45686\|c2_g2_i1	TR45686\|c2_g2_i1 7 76	M70	TR45686\|c2_g2_i1	7	76
2098	MA_106416	Pabies1.0_gene_only.fa.gmap	cDNA_match	4163.0	4256.0	100	-	.	ID=TR45686\|c2_g2_i1.path1;Name=TR45686\|c2_g2_i...	TR45686\|c2_g2_i1.path1	TR45686\|c2_g2_i1	TR45686\|c2_g2_i1 77 170	M94	TR45686\|c2_g2_i1	77	170
2099	MA_106416	Pabies1.0_gene_only.fa.gmap	cDNA_match	3005.0	3116.0	98	-	.	ID=TR45686\|c2_g2_i1.path1;Name=TR45686\|c2_g2_i...	TR45686\|c2_g2_i1.path1	TR45686\|c2_g2_i1	TR45686\|c2_g2_i1 171 282	M112	TR45686\|c2_g2_i1	171	282
2100	MA_106416	Pabies1.0_gene_only.fa.gmap	cDNA_match	2829.0	2890.0	98	-	.	ID=TR45686\|c2_g2_i1.path1;Name=TR45686\|c2_g2_i...	TR45686\|c2_g2_i1.path1	TR45686\|c2_g2_i1	TR45686\|c2_g2_i1 283 344	M62	TR45686\|c2_g2_i1	283	344
2101	MA_106416	Pabies1.0_gene_only.fa.gmap	cDNA_match	2356.0	2497.0	100	-	.	ID=TR45686\|c2_g2_i1.path1;Name=TR45686\|c2_g2_i...	TR45686\|c2_g2_i1.path1	TR45686\|c2_g2_i1	TR45686\|c2_g2_i1 345 486	M142	TR45686\|c2_g2_i1	345	486
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
9115	MA_173651	Pabies1.0_gene_only.fa.gmap	cDNA_match	21350.0	21418.0	100	+	.	ID=TR114591\|c0_g1_i1.path1;Name=TR114591\|c0_g1...	TR114591\|c0_g1_i1.path1	TR114591\|c0_g1_i1	TR114591\|c0_g1_i1 1113 1181	M69	TR114591\|c0_g1_i1	1113	1181
9116	MA_173651	Pabies1.0_gene_only.fa.gmap	cDNA_match	21533.0	21862.0	100	+	.	ID=TR114591\|c0_g1_i1.path1;Name=TR114591\|c0_g1...	TR114591\|c0_g1_i1.path1	TR114591\|c0_g1_i1	TR114591\|c0_g1_i1 1182 1511	M330	TR114591\|c0_g1_i1	1182	1511
9129	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	5353.0	6891.0	99	-	.	ID=TR114594\|c0_g1_i1.path1;Name=TR114594\|c0_g1...	TR114594\|c0_g1_i1.path1	TR114594\|c0_g1_i1	TR114594\|c0_g1_i1 1 1539	M1539	TR114594\|c0_g1_i1	1	1539
9130	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	3160.0	3457.0	100	-	.	ID=TR114594\|c0_g1_i1.path1;Name=TR114594\|c0_g1...	TR114594\|c0_g1_i1.path1	TR114594\|c0_g1_i1	TR114594\|c0_g1_i1 1540 1837	M298	TR114594\|c0_g1_i1	1540	1837
9131	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	2604.0	3066.0	99	-	.	ID=TR114594\|c0_g1_i1.path1;Name=TR114594\|c0_g1...	TR114594\|c0_g1_i1.path1	TR114594\|c0_g1_i1	TR114594\|c0_g1_i1 1838 2300	M463	TR114594\|c0_g1_i1	1838	2300
9132	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	2437.0	2553.0	100	-	.	ID=TR114594\|c0_g1_i1.path1;Name=TR114594\|c0_g1...	TR114594\|c0_g1_i1.path1	TR114594\|c0_g1_i1	TR114594\|c0_g1_i1 2301 2417	M117	TR114594\|c0_g1_i1	2301	2417
10030	MA_9476	Pabies1.0_gene_only.fa.gmap	cDNA_match	50394.0	51362.0	90	+	.	ID=TR121046\|c0_g1_i1.path1;Name=TR121046\|c0_g1...	TR121046\|c0_g1_i1.path1	TR121046\|c0_g1_i1	TR121046\|c0_g1_i1 1 965	M198 D49 M352 I45 M370	TR121046\|c0_g1_i1	1	965
11214	MA_6194	Pabies1.0_gene_only.fa.gmap	cDNA_match	46870.0	47715.0	100	-	.	ID=TR129570\|c0_g1_i1.path1;Name=TR129570\|c0_g1...	TR129570\|c0_g1_i1.path1	TR129570\|c0_g1_i1	TR129570\|c0_g1_i1 1 846	M846	TR129570\|c0_g1_i1	1	846
11499	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	2449.0	2553.0	100	+	.	ID=TR131307\|c0_g1_i1.path1;Name=TR131307\|c0_g1...	TR131307\|c0_g1_i1.path1	TR131307\|c0_g1_i1	TR131307\|c0_g1_i1 1 105	M105	TR131307\|c0_g1_i1	1	105
11500	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	2604.0	3114.0	99	+	.	ID=TR131307\|c0_g1_i1.path1;Name=TR131307\|c0_g1...	TR131307\|c0_g1_i1.path1	TR131307\|c0_g1_i1	TR131307\|c0_g1_i1 106 616	M511	TR131307\|c0_g1_i1	106	616
11501	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	3208.0	3457.0	100	+	.	ID=TR131307\|c0_g1_i1.path1;Name=TR131307\|c0_g1...	TR131307\|c0_g1_i1.path1	TR131307\|c0_g1_i1	TR131307\|c0_g1_i1 617 866	M250	TR131307\|c0_g1_i1	617	866
11502	MA_99694	Pabies1.0_gene_only.fa.gmap	cDNA_match	5353.0	6111.0	99	+	.	ID=TR131307\|c0_g1_i1.path1;Name=TR131307\|c0_g1...	TR131307\|c0_g1_i1.path1	TR131307\|c0_g1_i1	TR131307\|c0_g1_i1 867 1625	M759	TR131307\|c0_g1_i1	867	1625
11515	MA_2328	Pabies1.0_gene_only.fa.gmap	cDNA_match	16898.0	17712.0	99	+	.	ID=TR131470\|c0_g1_i1.path1;Name=TR131470\|c0_g1...	TR131470\|c0_g1_i1.path1	TR131470\|c0_g1_i1	TR131470\|c0_g1_i1 1 815	M815	TR131470\|c0_g1_i1	1	815
11516	MA_2328	Pabies1.0_gene_only.fa.gmap	cDNA_match	17920.0	19635.0	99	+	.	ID=TR131470\|c0_g1_i1.path1;Name=TR131470\|c0_g1...	TR131470\|c0_g1_i1.path1	TR131470\|c0_g1_i1	TR131470\|c0_g1_i1 816 2529	M1614 D2 M100	TR131470\|c0_g1_i1	816	2529
11699	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	1298.0	1995.0	98	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 1 690	M296 D8 M394	TR132765\|c0_g1_i1	1	690
11700	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	2115.0	2203.0	100	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 691 779	M89	TR132765\|c0_g1_i1	691	779
11701	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	2237.0	3054.0	100	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 780 1597	M818	TR132765\|c0_g1_i1	780	1597
11702	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	3520.0	3662.0	100	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 1598 1740	M143	TR132765\|c0_g1_i1	1598	1740
11703	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	4176.0	4304.0	100	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 1741 1869	M129	TR132765\|c0_g1_i1	1741	1869
11704	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	4420.0	5381.0	99	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 1870 2831	M962	TR132765\|c0_g1_i1	1870	2831
11705	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	5467.0	5563.0	100	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 2832 2928	M97	TR132765\|c0_g1_i1	2832	2928
11706	MA_10428736	Pabies1.0_gene_only.fa.gmap	cDNA_match	5814.0	6147.0	99	+	.	ID=TR132765\|c0_g1_i1.path1;Name=TR132765\|c0_g1...	TR132765\|c0_g1_i1.path1	TR132765\|c0_g1_i1	TR132765\|c0_g1_i1 2929 3262	M334	TR132765\|c0_g1_i1	2929	3262
11962	MA_7658	Pabies1.0_gene_only.fa.gmap	cDNA_match	21300.0	23353.0	99	-	.	ID=TR135599\|c0_g2_i1.path1;Name=TR135599\|c0_g2...	TR135599\|c0_g2_i1.path1	TR135599\|c0_g2_i1	TR135599\|c0_g2_i1 1 2054	M2054	TR135599\|c0_g2_i1	1	2054
11969	MA_14500	Pabies1.0_gene_only.fa.gmap	cDNA_match	38918.0	38958.0	87	-	.	ID=TR135287\|c0_g1_i2.path1;Name=TR135287\|c0_g1...	TR135287\|c0_g1_i2.path1	TR135287\|c0_g1_i2	TR135287\|c0_g1_i2 13 53	M41	TR135287\|c0_g1_i2	13	53
12160	MA_111652	Pabies1.0_gene_only.fa.gmap	cDNA_match	10123.0	10277.0	100	+	.	ID=TR137080\|c0_g1_i1.path1;Name=TR137080\|c0_g1...	TR137080\|c0_g1_i1.path1	TR137080\|c0_g1_i1	TR137080\|c0_g1_i1 1 155	M155	TR137080\|c0_g1_i1	1	155
12161	MA_111652	Pabies1.0_gene_only.fa.gmap	cDNA_match	10491.0	10691.0	100	+	.	ID=TR137080\|c0_g1_i1.path1;Name=TR137080\|c0_g1...	TR137080\|c0_g1_i1.path1	TR137080\|c0_g1_i1	TR137080\|c0_g1_i1 156 356	M201	TR137080\|c0_g1_i1	156	356
12162	MA_111652	Pabies1.0_gene_only.fa.gmap	cDNA_match	11729.0	11822.0	100	+	.	ID=TR137080\|c0_g1_i1.path1;Name=TR137080\|c0_g1...	TR137080\|c0_g1_i1.path1	TR137080\|c0_g1_i1	TR137080\|c0_g1_i1 357 450	M94	TR137080\|c0_g1_i1	357	450
12163	MA_111652	Pabies1.0_gene_only.fa.gmap	cDNA_match	11923.0	11994.0	100	+	.	ID=TR137080\|c0_g1_i1.path1;Name=TR137080\|c0_g1...	TR137080\|c0_g1_i1.path1	TR137080\|c0_g1_i1	TR137080\|c0_g1_i1 451 522	M72	TR137080\|c0_g1_i1	451	522
12164	MA_111652	Pabies1.0_gene_only.fa.gmap	cDNA_match	13383.0	13481.0	100	+	.	ID=TR137080\|c0_g1_i1.path1;Name=TR137080\|c0_g1...	TR137080\|c0_g1_i1.path1	TR137080\|c0_g1_i1	TR137080\|c0_g1_i1 523 621	M99	TR137080\|c0_g1_i1	523	621
12165	MA_111652	Pabies1.0_gene_only.fa.gmap	cDNA_match	13953.0	14402.0	100	+	.	ID=TR137080\|c0_g1_i1.path1;Name=TR137080\|c0_g1...	TR137080\|c0_g1_i1.path1	TR137080\|c0_g1_i1	TR137080\|c0_g1_i1 622 1071	M450	TR137080\|c0_g1_i1	622	1071

	seqid	source	Type	start	end	score	strand	phase	attributes
0	MA_10426199	dN_gmap	gene	1174	4964	99	+	.	TR574\|c2_g1_i2.path2
1	MA_10426199	dN_gmap	exon	1174	1448	99	+	.	TR574\|c2_g1_i2.path2
2	MA_10426199	dN_gmap	CDS	1174	1448	99	+	.	TR574\|c2_g1_i2.path2
3	MA_10426199	dN_gmap	exon	1577	2225	98	+	.	TR574\|c2_g1_i2.path2
4	MA_10426199	dN_gmap	CDS	1577	2225	98	+	.	TR574\|c2_g1_i2.path2