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Commit 34cc20f

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fgvieirafgvieira
committed
Small fixes
1 parent 9b0d2dc commit 34cc20f

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14 files changed

+219
-15
lines changed

14 files changed

+219
-15
lines changed

‎bio/metadmg/compressbam/test/Snakefile

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@
22
rule compressbam:
33
input:
44
aln="{sample}.bam",
5+
ref="genome.fasta",
56
output:
67
"results/compressbam/{sample}.bam",
78
log:

‎bio/metadmg/compressbam/test/a.bam

4.27 KB
Binary file not shown.

‎bio/metadmg/compressbam/test/genome.fasta

Lines changed: 101 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,101 @@
1+
>NC_023100.1 partial
2+
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTTTGGGGG
3+
GTGTGCACGCGATAGCATTGCGAAACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
4+
CTGCCCCATCTCATTATTTATCGCACCTACGTTCAATATTACAGGCGAGCATANNTACTAAAGTGTGTTA
5+
ATTAATTAATGCTTGTAGGACATAATAATAACNATTNAATGNCTGCACAGCCGCTTTCCACACAGACATC
6+
ACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
7+
AACCCCAAAAACAAAGAACCCTAACACCAGCCTAGCCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
8+
TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATTAATA
9+
CAACCCCCGCCCATNCTACCCANNACACACACACCGCTGCTAACTCCATACCCCGAACCAACCAAACCCC
10+
AAAGACACCCCCCANAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
11+
ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
12+
GCATCCCCATTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC
13+
AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATAAGCCTTTAGCAATAA
14+
ACGAAAGTTTAACTAAGCTATACTAACTCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA
15+
TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCANNNNNNNNNNAATAAAGCTAAAACT
16+
CACCTGAGTTGTAAAAAACTCCAGTTGATACAAAATAAACTACGAAAGTGGCTTTAACACATCTGAATAC
17+
ACAATAGCTAAGGCCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC
18+
AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC
19+
CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCCCTTGCTCAGCCTATATA
20+
CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC
21+
AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAACCCTTAT
22+
GAAATTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAATAGAGTGCTTAGTTGAACAGGGCCCTGA
23+
AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA
24+
TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA
25+
GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
26+
GCCCCAAACCCACTCCACCTTACTACCANACAACCTTAACCAAACCATTTACCCAAATAAAGTATAGGCG
27+
ATAGAAATTGTAACCCGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA
28+
ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAACC
29+
AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA
30+
AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAANCTANCGAGCCTGGTGATAGCTGGTTNTCCAAGAT
31+
AGAATCTTAGTTCAACTTTAAATTTACCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
32+
CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG
33+
TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC
34+
ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCTTATAGAAGAACTAATGTTAGTATAAG
35+
TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC
36+
AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
37+
AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
38+
ATTACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA
39+
AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT
40+
TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA
41+
TGGAGCTTTAATTTATTAATGCAAACAATACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
42+
AAAAATTTCGGTTGGGGCGACCTCGGAGCACAGCCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG
43+
TCAAAGCGAACTACCATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
44+
GCGCAATCCTATTCCAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG
45+
ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG
46+
AGTAATCCAGGTCGGTTTCTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTA
47+
CTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTNNNNNNNNNNNNNNCCAAGAA
48+
CAGGNTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAATCAGAGGTTCAACT
49+
CCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGCACCCATTCTAATCGCAATGGCAT
50+
TCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCC
51+
CTACGGGCTACTACAGCCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCTCCACA
52+
TCNACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACTCCCC
53+
TCCCCATACCCAACCCCCTGGTCAACCTCAANCTAGGCCTCCTATTTATCCTAGCCACCTCTAGCCTAGC
54+
CGTTTACTCAATCCTCTGATCAGGGTGAGCGTCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCA
55+
GTGGCCCAAACAATCTCATATGAAGTCACCCTAGCTATCATCCTACTATCAACATTACTAATAAGTGGCT
56+
CCTTTAACCTCTCCACCCTTATCACAACACAAGAGCACCTCTGATTACTCCTGCCATCATGACCCTTGGC
57+
CATAATATGATTTATCTCCACACTAGCAGAGACCAACCGNANCCCCTTCGACCTTGCNGAAGGGGAGTCC
58+
GAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTTATAGCCGAATACA
59+
CAAACATCATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATAACGCACTCTCCCC
60+
TGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTNACCTCCCTATTCTTATGAATTCGAACA
61+
GCATACCCCCGATTCCGCTACGACCAACTCATNCACCTNCTATGAAAAAACTTCCTACCACTCACCCTAG
62+
CATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATATG
63+
TCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTAGGACTATGAG
64+
AATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCTACCTATCACACCCCATCCTAAAGTAAGGTCA
65+
GCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATATCCTTCCCGTACTAATTAATCCCCTG
66+
GCCCAACCCGNCATNNACTCTACCATCTTTACAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTT
67+
TTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTCG
68+
TTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATC
69+
CTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAACACTANNNATNNNNNNNNGTCATTAATAA
70+
TCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGG
71+
CACCCCTCTGACATCCGGCCTGCTACTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAA
72+
ATTTCCCCCTCATTAAACGTAAGCCTTCTCCTCACTCTTTCAATCTTATCCATCATGGCAGGCAGTTGAG
73+
GTGGACTAAACCAAACCCAACTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAAT
74+
AGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATNCTAACTACTACC
75+
GCATTCCTACTACTCAACTTAAACTCCAGCACCACAACCCTACTACTATCTCGCACCTGAAACAAACTAA
76+
CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTT
77+
GCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACC
78+
ATCACCCTCCTTAACCTCTACTTCTACCTGCGCCTAATCTACTCCACCTCAATCACACTACTCCCTATAT
79+
CTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCGC
80+
CCTTACCACACTGCTCCTACCTATCTCCCCTTTTATACTNNNNNNNNNNNAGAAATTTAGGTTAAATACA
81+
GACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAAAT
82+
CCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGAC
83+
TTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCG
84+
CCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAA
85+
AATCACCTCAGAGCTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAG
86+
CCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGA
87+
ACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCG
88+
AACTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATT
89+
TGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATA
90+
ATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCNCCCTCCCTCC
91+
TACTCCTGCTTGCATCTGCTATAGTGGAGGCCGGCGCAGGGACAGGTTGAACAGTCTACCCTCCCTTAGC
92+
AGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTGCACCTAGCAGNTATTTCC
93+
TCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATGACCCAATACC
94+
AAACGCCCCTTTTCGTCTGATCCGTCCTAATCACAGCAGTCTTGCTTCTCCTATCTCTCCCAGTCCTGGC
95+
CGCTGGCATCACTATACTACTAACAGACCGNAACCTCAACACCACCTTCTTCGACCCNGCCGGAGGAGGA
96+
GACCCCATTCTATACCAACACCTATTCTGATTCTTCGGTCACCCTGAAGTTTATATTCTCATCCTACCAG
97+
GCTTCGGAATAATCTCTCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTAT
98+
GGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGA
99+
ATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAG
100+
TATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGG
101+
ATTTATTTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTA

‎bio/metadmg/compressbam/wrapper.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@
44

55

66
import tempfile
7+
from pathlib import Path
78
from snakemake.shell import shell
89

910

@@ -13,12 +14,12 @@
1314

1415
ref = snakemake.input.get("ref", "")
1516
if ref:
16-
ref = f"--ref {ref}"
17+
ref = f"-ref {ref}"
1718

1819

1920
out_fmt = Path(snakemake.input.aln).suffix.lstrip(".").lower()
2021

2122

2223
shell(
23-
"compressbam -threads {snakemake.threads} -hts {snakemake.input.aln} {ref} {extra} -type {out_fmt} -out {snakemake.output[0]} {log}"
24+
"compressbam -@ {snakemake.threads} -hts {snakemake.input.aln} {ref} {extra} -type {out_fmt} -out {snakemake.output[0]} {log}"
2425
)

‎bio/metadmg/getdamage/test/Snakefile

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ rule metadmg_getdamage:
1010
log:
1111
"logs/getdamage/{sample}.log",
1212
params:
13-
extra="--minlength 30 --printlength 30 --runmode 1",
13+
extra="-l 30 -p 30 -r 1",
1414
threads: 4
1515
resources:
1616
mem_mb=1024,

‎bio/metadmg/getdamage/test/a.bam

4.27 KB
Binary file not shown.

‎bio/metadmg/getdamage/test/genome.fasta

Lines changed: 101 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,101 @@
1-
>ref
2-
AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
3-
>ref2
4-
aggttttataaaacaattaagtctacagagcaactacgcg
1+
>NC_023100.1 partial
2+
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTTTGGGGG
3+
GTGTGCACGCGATAGCATTGCGAAACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
4+
CTGCCCCATCTCATTATTTATCGCACCTACGTTCAATATTACAGGCGAGCATANNTACTAAAGTGTGTTA
5+
ATTAATTAATGCTTGTAGGACATAATAATAACNATTNAATGNCTGCACAGCCGCTTTCCACACAGACATC
6+
ACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
7+
AACCCCAAAAACAAAGAACCCTAACACCAGCCTAGCCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
8+
TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATTAATA
9+
CAACCCCCGCCCATNCTACCCANNACACACACACCGCTGCTAACTCCATACCCCGAACCAACCAAACCCC
10+
AAAGACACCCCCCANAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
11+
ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
12+
GCATCCCCATTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC
13+
AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATAAGCCTTTAGCAATAA
14+
ACGAAAGTTTAACTAAGCTATACTAACTCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA
15+
TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCANNNNNNNNNNAATAAAGCTAAAACT
16+
CACCTGAGTTGTAAAAAACTCCAGTTGATACAAAATAAACTACGAAAGTGGCTTTAACACATCTGAATAC
17+
ACAATAGCTAAGGCCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC
18+
AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC
19+
CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCCCTTGCTCAGCCTATATA
20+
CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC
21+
AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAACCCTTAT
22+
GAAATTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAATAGAGTGCTTAGTTGAACAGGGCCCTGA
23+
AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA
24+
TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA
25+
GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
26+
GCCCCAAACCCACTCCACCTTACTACCANACAACCTTAACCAAACCATTTACCCAAATAAAGTATAGGCG
27+
ATAGAAATTGTAACCCGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA
28+
ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAACC
29+
AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA
30+
AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAANCTANCGAGCCTGGTGATAGCTGGTTNTCCAAGAT
31+
AGAATCTTAGTTCAACTTTAAATTTACCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
32+
CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG
33+
TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC
34+
ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCTTATAGAAGAACTAATGTTAGTATAAG
35+
TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC
36+
AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
37+
AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
38+
ATTACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA
39+
AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT
40+
TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA
41+
TGGAGCTTTAATTTATTAATGCAAACAATACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
42+
AAAAATTTCGGTTGGGGCGACCTCGGAGCACAGCCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG
43+
TCAAAGCGAACTACCATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
44+
GCGCAATCCTATTCCAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG
45+
ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG
46+
AGTAATCCAGGTCGGTTTCTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTA
47+
CTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTNNNNNNNNNNNNNNCCAAGAA
48+
CAGGNTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAATCAGAGGTTCAACT
49+
CCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGCACCCATTCTAATCGCAATGGCAT
50+
TCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCC
51+
CTACGGGCTACTACAGCCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCTCCACA
52+
TCNACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACTCCCC
53+
TCCCCATACCCAACCCCCTGGTCAACCTCAANCTAGGCCTCCTATTTATCCTAGCCACCTCTAGCCTAGC
54+
CGTTTACTCAATCCTCTGATCAGGGTGAGCGTCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCA
55+
GTGGCCCAAACAATCTCATATGAAGTCACCCTAGCTATCATCCTACTATCAACATTACTAATAAGTGGCT
56+
CCTTTAACCTCTCCACCCTTATCACAACACAAGAGCACCTCTGATTACTCCTGCCATCATGACCCTTGGC
57+
CATAATATGATTTATCTCCACACTAGCAGAGACCAACCGNANCCCCTTCGACCTTGCNGAAGGGGAGTCC
58+
GAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTTATAGCCGAATACA
59+
CAAACATCATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATAACGCACTCTCCCC
60+
TGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTNACCTCCCTATTCTTATGAATTCGAACA
61+
GCATACCCCCGATTCCGCTACGACCAACTCATNCACCTNCTATGAAAAAACTTCCTACCACTCACCCTAG
62+
CATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATATG
63+
TCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTAGGACTATGAG
64+
AATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCTACCTATCACACCCCATCCTAAAGTAAGGTCA
65+
GCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATATCCTTCCCGTACTAATTAATCCCCTG
66+
GCCCAACCCGNCATNNACTCTACCATCTTTACAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTT
67+
TTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTCG
68+
TTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATC
69+
CTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAACACTANNNATNNNNNNNNGTCATTAATAA
70+
TCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGG
71+
CACCCCTCTGACATCCGGCCTGCTACTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAA
72+
ATTTCCCCCTCATTAAACGTAAGCCTTCTCCTCACTCTTTCAATCTTATCCATCATGGCAGGCAGTTGAG
73+
GTGGACTAAACCAAACCCAACTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAAT
74+
AGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATNCTAACTACTACC
75+
GCATTCCTACTACTCAACTTAAACTCCAGCACCACAACCCTACTACTATCTCGCACCTGAAACAAACTAA
76+
CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTT
77+
GCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACC
78+
ATCACCCTCCTTAACCTCTACTTCTACCTGCGCCTAATCTACTCCACCTCAATCACACTACTCCCTATAT
79+
CTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCGC
80+
CCTTACCACACTGCTCCTACCTATCTCCCCTTTTATACTNNNNNNNNNNNAGAAATTTAGGTTAAATACA
81+
GACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAAAT
82+
CCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGAC
83+
TTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCG
84+
CCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAA
85+
AATCACCTCAGAGCTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAG
86+
CCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGA
87+
ACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCG
88+
AACTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATT
89+
TGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATA
90+
ATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCNCCCTCCCTCC
91+
TACTCCTGCTTGCATCTGCTATAGTGGAGGCCGGCGCAGGGACAGGTTGAACAGTCTACCCTCCCTTAGC
92+
AGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTGCACCTAGCAGNTATTTCC
93+
TCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATGACCCAATACC
94+
AAACGCCCCTTTTCGTCTGATCCGTCCTAATCACAGCAGTCTTGCTTCTCCTATCTCTCCCAGTCCTGGC
95+
CGCTGGCATCACTATACTACTAACAGACCGNAACCTCAACACCACCTTCTTCGACCCNGCCGGAGGAGGA
96+
GACCCCATTCTATACCAACACCTATTCTGATTCTTCGGTCACCCTGAAGTTTATATTCTCATCCTACCAG
97+
GCTTCGGAATAATCTCTCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTAT
98+
GGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGA
99+
ATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAG
100+
TATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGG
101+
ATTTATTTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTA

‎bio/metadmg/getdamage/wrapper.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,12 +13,12 @@
1313

1414
ref = snakemake.input.get("ref", "")
1515
if ref:
16-
ref = f"--fasta {ref}"
16+
ref = f"-f {ref}"
1717

1818

1919
with tempfile.TemporaryDirectory() as tmpdir:
2020
shell(
21-
"metaDMG-cpp getdamage --threads {snakemake.threads} {ref} {extra} --outname {tmpdir}/out {snakemake.input.aln} {log}"
21+
"metaDMG-cpp getdamage --threads {snakemake.threads} {ref} {extra} -o {tmpdir}/out {snakemake.input.aln} {log}"
2222
)
2323

2424
if snakemake.output.get("dmg"):

‎bio/metadmg/lca/test/Snakefile

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,9 @@
22
rule metadmg_lca:
33
input:
44
aln="{sample}.bam",
5+
names="names.dmp.gz",
6+
nodes="nodes.dmp.gz",
7+
acc2taxid="acc2taxid.tsv",
58
output:
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res="results/lca/{sample}.out.gz",
710
lca="results/lca/{sample}.lca.gz",
@@ -10,7 +13,7 @@ rule metadmg_lca:
1013
log:
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"logs/lca/{sample}.log",
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params:
13-
extra="-simscorelow 0.95 -simscorehigh 1.0 -minmapq 30 -howmany 30 -lca_rank species",
16+
extra="-simscorelow 0.95 -simscorehigh 1.0 -minmapq 30 -howmany 30 -lca_rank genus -fix_ncbi 0",
1417
threads: 4
1518
resources:
1619
mem_mb=1024,

‎bio/metadmg/lca/test/a.bam

4.27 KB
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