Skip to content

Commit b1761de

Browse files
drosofffdrosofff
authored
Merge pull request #686 from ARTbio/print_unique_counts
repenrich2 prints unique counts
2 parents 03183e2 + 0c14ce1 commit b1761de

8 files changed

+302
-1
lines changed

‎tools/repenrich2/RepEnrich2.py

+6
Original file line numberDiff line numberDiff line change
@@ -115,6 +115,12 @@ def run_bowtie(args):
115115
sumofrepeatreads += int(line[4])
116116
print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.")
117117

118+
# print unique mapper counts
119+
with open("unique_mapper_counts.tsv", 'w') as fout:
120+
fout.write("#element\tcount\n")
121+
for count in sorted(counts):
122+
fout.write(f"{count}\t{counts[count]}\n")
123+
118124
# multimapper parsing
119125
if not paired_end:
120126
args_list = [(metagenome, fastqfile_1) for

‎tools/repenrich2/macros.xml

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
<macros>
22
<token name="@TOOL_VERSION@">2.31.1</token>
3-
<token name="@VERSION_SUFFIX@">4</token>
3+
<token name="@VERSION_SUFFIX@">5</token>
44
<token name="@PROFILE@">23.0</token>
55

66
<xml name="repenrich_requirements">

‎tools/repenrich2/repenrich2.xml

+3
Original file line numberDiff line numberDiff line change
@@ -102,6 +102,7 @@
102102
</inputs>
103103

104104
<outputs>
105+
<data format="tabular" name="unique_mapper_counts" label="RepEnrich on ${on_string}: unique mapper counts" from_work_dir="unique_mapper_counts.tsv" />
105106
<data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tsv" />
106107
<data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tsv" />
107108
<data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tsv" />
@@ -114,6 +115,7 @@
114115
<param name="genomeSource" value="history"/>
115116
<param name="genome" value="chrY-1-500k.fa" ftype="fasta"/>
116117
<param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/>
118+
<output name="unique_mapper_counts" file="chrY_single_unique_mapper_counts.tab" ftype="tabular"/>
117119
<output name="class_fraction_counts" file="chrY_single_class_fraction_counts.tab" ftype="tabular"/>
118120
<output name="family_fraction_counts" file="chrY_single_family_fraction_counts.tab" ftype="tabular"/>
119121
<output name="fraction_counts" file="chrY_single_fraction_counts.tab" ftype="tabular"/>
@@ -125,6 +127,7 @@
125127
<param name="genomeSource" value="history"/>
126128
<param name="genome" value="chrY-1-500k.fa" ftype="fasta"/>
127129
<param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/>
130+
<output name="unique_mapper_counts" file="chrY_paired_unique_mapper_counts.tab" ftype="tabular"/>
128131
<output name="class_fraction_counts" file="chrY_paired_class_fraction_counts.tab" ftype="tabular"/>
129132
<output name="family_fraction_counts" file="chrY_paired_family_fraction_counts.tab" ftype="tabular"/>
130133
<output name="fraction_counts" file="chrY_paired_fraction_counts.tab" ftype="tabular"/>

‎tools/repenrich2/test-data/Samp.fastq.gz

-74.5 KB
Binary file not shown.

‎tools/repenrich2/test-data/Samp_L.fastq.gz

-103 KB
Binary file not shown.

‎tools/repenrich2/test-data/Samp_R.fastq.gz

-103 KB
Binary file not shown.

‎tools/repenrich2/test-data/chrY_paired_unique_mapper_counts.tab

+146
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,146 @@
1+
#element count
2+
A-rich 0
3+
ACCORD2_I-int 0
4+
ACCORD2_LTR 0
5+
ACCORD_I-int 0
6+
BARI1 0
7+
BATUMI_LTR 0
8+
BS 0
9+
BS2 58
10+
BURDOCK_I-int 0
11+
Baggins1 0
12+
Bica_I-int 38
13+
Bica_LTR 0
14+
CIRCE 0
15+
Chouto_I-int 0
16+
Copia1-I_DM 0
17+
Copia_I-int 25181
18+
Copia_LTR 647
19+
DIVER2_I-int 0
20+
DIVER2_LTR 0
21+
DM1731_I-int 6
22+
DM1731_LTR 0
23+
DM176_I-int 0
24+
DM412 0
25+
DM412B_LTR 0
26+
DMCR1A 4
27+
DMLTR5 0
28+
DMRT1A 0
29+
DMRT1B 86
30+
DMRT1C 0
31+
DNAREP1_DM 0
32+
DOC2_DM 0
33+
DOC3_DM 0
34+
FB4_DM 38
35+
FROGGER_I-int 0
36+
FW2_DM 0
37+
G3_DM 0
38+
G5A_DM 0
39+
G5_DM 0
40+
G6_DM 0
41+
GA-rich 0
42+
GTWIN_I-int 0
43+
G_DM 0
44+
Gypsy11_I-int 0
45+
Gypsy11_LTR 0
46+
Gypsy12_LTR 0
47+
Gypsy2-I_DM 2
48+
Gypsy2-LTR_DM 0
49+
Gypsy3_LTR 0
50+
Gypsy4_I-int 0
51+
Gypsy5_I-int 0
52+
Gypsy6A_LTR 0
53+
Gypsy6_I-int 26
54+
Gypsy8_I-int 0
55+
Gypsy8_LTR 0
56+
Gypsy9_I-int 0
57+
Gypsy_I-int 32
58+
Gypsy_LTR 1
59+
HELENA_RT 0
60+
HETA 24
61+
HMSBEAGLE_I-int 2
62+
IDEFIX_I-int 4
63+
IDEFIX_LTR 0
64+
Invader1_I-int 0
65+
Invader1_LTR 0
66+
Invader2_I-int 0
67+
Invader4_I-int 0
68+
Invader4_LTR 0
69+
Invader5_I-int 0
70+
Invader5_LTR 0
71+
Invader6_I-int 0
72+
Invader6_LTR 0
73+
MAX_I-int 49
74+
MAX_LTR 2
75+
MDG1_I-int 0
76+
MDG1_LTR 0
77+
MDG3_I-int 152
78+
MDG3_LTR 0
79+
MICROPIA_I-int 0
80+
MICROPIA_LTR 0
81+
Mariner2_DM 0
82+
NINJA_I-int 0
83+
NOMAD_I-int 0
84+
PROTOP_A 32
85+
PROTOP_B 0
86+
QUASIMODO2-I_DM 42
87+
QUASIMODO2-LTR_DM 0
88+
QUASIMODO_I-int 10
89+
QUASIMODO_LTR 2
90+
R1_DM 0
91+
ROOA_I-int 0
92+
ROOA_LTR 0
93+
ROVER-I_DM 381
94+
ROVER-LTR_DM 2
95+
S2_DM 0
96+
STALKER4_I-int 77
97+
STALKER4_LTR 4
98+
S_DM 48
99+
Stalker2_I-int 80
100+
Stalker2_LTR 2
101+
TART-A 4
102+
TART_B1 19
103+
TC1-2_DM 0
104+
TC1_DM 0
105+
TLD2 0
106+
TRANSIB1 0
107+
TRANSIB2 30
108+
ZAM_I-int 0
109+
_AACACA_n 0
110+
_AAT_n 0
111+
_ACAATAG_n 0
112+
_ACC_n 0
113+
_AGAGAAG_n 0
114+
_AGAGA_n 0
115+
_ATAAT_n 0
116+
_ATATATT_n 0
117+
_ATATTAT_n 0
118+
_ATTTTT_n 0
119+
_ATT_n 0
120+
_AT_n 0
121+
_A_n 0
122+
_CATA_n 0
123+
_CTTTT_n 0
124+
_GAGAA_n 0
125+
_GCCTTT_n 0
126+
_TAATAT_n 0
127+
_TAATA_n 0
128+
_TATAAAA_n 0
129+
_TATAA_n 0
130+
_TATCATG_n 0
131+
_TA_n 0
132+
_TGTTG_n 0
133+
_TTATATA_n 0
134+
_TTATAT_n 0
135+
_TTATA_n 0
136+
_TTA_n 0
137+
_TTCTT_n 0
138+
_TTC_n 0
139+
_TTTAT_n 0
140+
_TTTA_n 0
141+
_TTTC_n 0
142+
_TTTGA_n 0
143+
_TTTTAG_n 0
144+
_TTTTCTT_n 0
145+
_TTTTC_n 0
146+
_T_n 0

‎tools/repenrich2/test-data/chrY_single_unique_mapper_counts.tab

+146
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,146 @@
1+
#element count
2+
A-rich 0
3+
ACCORD2_I-int 0
4+
ACCORD2_LTR 0
5+
ACCORD_I-int 0
6+
BARI1 0
7+
BATUMI_LTR 0
8+
BS 0
9+
BS2 29
10+
BURDOCK_I-int 0
11+
Baggins1 0
12+
Bica_I-int 19
13+
Bica_LTR 0
14+
CIRCE 0
15+
Chouto_I-int 0
16+
Copia1-I_DM 0
17+
Copia_I-int 12652
18+
Copia_LTR 134
19+
DIVER2_I-int 1
20+
DIVER2_LTR 0
21+
DM1731_I-int 3
22+
DM1731_LTR 0
23+
DM176_I-int 0
24+
DM412 0
25+
DM412B_LTR 0
26+
DMCR1A 2
27+
DMLTR5 0
28+
DMRT1A 0
29+
DMRT1B 35
30+
DMRT1C 0
31+
DNAREP1_DM 0
32+
DOC2_DM 0
33+
DOC3_DM 0
34+
FB4_DM 15
35+
FROGGER_I-int 0
36+
FW2_DM 0
37+
G3_DM 0
38+
G5A_DM 0
39+
G5_DM 0
40+
G6_DM 0
41+
GA-rich 0
42+
GTWIN_I-int 0
43+
G_DM 0
44+
Gypsy11_I-int 0
45+
Gypsy11_LTR 0
46+
Gypsy12_LTR 0
47+
Gypsy2-I_DM 1
48+
Gypsy2-LTR_DM 0
49+
Gypsy3_LTR 0
50+
Gypsy4_I-int 0
51+
Gypsy5_I-int 0
52+
Gypsy6A_LTR 0
53+
Gypsy6_I-int 12
54+
Gypsy8_I-int 0
55+
Gypsy8_LTR 0
56+
Gypsy9_I-int 0
57+
Gypsy_I-int 15
58+
Gypsy_LTR 0
59+
HELENA_RT 0
60+
HETA 12
61+
HMSBEAGLE_I-int 1
62+
IDEFIX_I-int 0
63+
IDEFIX_LTR 0
64+
Invader1_I-int 0
65+
Invader1_LTR 0
66+
Invader2_I-int 0
67+
Invader4_I-int 0
68+
Invader4_LTR 0
69+
Invader5_I-int 0
70+
Invader5_LTR 0
71+
Invader6_I-int 0
72+
Invader6_LTR 0
73+
MAX_I-int 27
74+
MAX_LTR 1
75+
MDG1_I-int 0
76+
MDG1_LTR 0
77+
MDG3_I-int 70
78+
MDG3_LTR 0
79+
MICROPIA_I-int 0
80+
MICROPIA_LTR 0
81+
Mariner2_DM 0
82+
NINJA_I-int 0
83+
NOMAD_I-int 0
84+
PROTOP_A 18
85+
PROTOP_B 0
86+
QUASIMODO2-I_DM 19
87+
QUASIMODO2-LTR_DM 0
88+
QUASIMODO_I-int 3
89+
QUASIMODO_LTR 1
90+
R1_DM 0
91+
ROOA_I-int 0
92+
ROOA_LTR 0
93+
ROVER-I_DM 188
94+
ROVER-LTR_DM 1
95+
S2_DM 0
96+
STALKER4_I-int 28
97+
STALKER4_LTR 0
98+
S_DM 25
99+
Stalker2_I-int 32
100+
Stalker2_LTR 2
101+
TART-A 2
102+
TART_B1 10
103+
TC1-2_DM 0
104+
TC1_DM 0
105+
TLD2 0
106+
TRANSIB1 0
107+
TRANSIB2 12
108+
ZAM_I-int 0
109+
_AACACA_n 0
110+
_AAT_n 0
111+
_ACAATAG_n 0
112+
_ACC_n 0
113+
_AGAGAAG_n 0
114+
_AGAGA_n 0
115+
_ATAAT_n 0
116+
_ATATATT_n 0
117+
_ATATTAT_n 0
118+
_ATTTTT_n 0
119+
_ATT_n 0
120+
_AT_n 0
121+
_A_n 0
122+
_CATA_n 0
123+
_CTTTT_n 0
124+
_GAGAA_n 0
125+
_GCCTTT_n 0
126+
_TAATAT_n 0
127+
_TAATA_n 0
128+
_TATAAAA_n 0
129+
_TATAA_n 0
130+
_TATCATG_n 0
131+
_TA_n 0
132+
_TGTTG_n 0
133+
_TTATATA_n 0
134+
_TTATAT_n 0
135+
_TTATA_n 0
136+
_TTA_n 0
137+
_TTCTT_n 0
138+
_TTC_n 0
139+
_TTTAT_n 0
140+
_TTTA_n 0
141+
_TTTC_n 0
142+
_TTTGA_n 0
143+
_TTTTAG_n 0
144+
_TTTTCTT_n 0
145+
_TTTTC_n 0
146+
_T_n 0

0 commit comments

Comments
 (0)