Small fixes

bio/metadmg/compressbam/test/Snakefile

@@ -2,6 +2,7 @@
 rule compressbam:
     input:
         aln="{sample}.bam",
+        ref="genome.fasta",
     output:
         "results/compressbam/{sample}.bam",
     log:

bio/metadmg/compressbam/test/genome.fasta

@@ -0,0 +1,101 @@
+>NC_023100.1 partial
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTTTGGGGG
+GTGTGCACGCGATAGCATTGCGAAACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
+CTGCCCCATCTCATTATTTATCGCACCTACGTTCAATATTACAGGCGAGCATANNTACTAAAGTGTGTTA
+ATTAATTAATGCTTGTAGGACATAATAATAACNATTNAATGNCTGCACAGCCGCTTTCCACACAGACATC
+ACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAGCCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATTAATA
+CAACCCCCGCCCATNCTACCCANNACACACACACCGCTGCTAACTCCATACCCCGAACCAACCAAACCCC
+AAAGACACCCCCCANAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
+GCATCCCCATTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC
+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATAAGCCTTTAGCAATAA
+ACGAAAGTTTAACTAAGCTATACTAACTCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA
+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCANNNNNNNNNNAATAAAGCTAAAACT
+CACCTGAGTTGTAAAAAACTCCAGTTGATACAAAATAAACTACGAAAGTGGCTTTAACACATCTGAATAC
+ACAATAGCTAAGGCCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC
+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC
+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCCCTTGCTCAGCCTATATA
+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC
+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAACCCTTAT
+GAAATTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAATAGAGTGCTTAGTTGAACAGGGCCCTGA
+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA
+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA
+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
+GCCCCAAACCCACTCCACCTTACTACCANACAACCTTAACCAAACCATTTACCCAAATAAAGTATAGGCG
+ATAGAAATTGTAACCCGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA
+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAACC
+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA
+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAANCTANCGAGCCTGGTGATAGCTGGTTNTCCAAGAT
+AGAATCTTAGTTCAACTTTAAATTTACCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG
+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC
+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCTTATAGAAGAACTAATGTTAGTATAAG
+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC
+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
+ATTACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA
+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT
+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA
+TGGAGCTTTAATTTATTAATGCAAACAATACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
+AAAAATTTCGGTTGGGGCGACCTCGGAGCACAGCCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG
+TCAAAGCGAACTACCATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
+GCGCAATCCTATTCCAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG
+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG
+AGTAATCCAGGTCGGTTTCTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTA
+CTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTNNNNNNNNNNNNNNCCAAGAA
+CAGGNTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAATCAGAGGTTCAACT
+CCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGCACCCATTCTAATCGCAATGGCAT
+TCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCC
+CTACGGGCTACTACAGCCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCTCCACA
+TCNACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACTCCCC
+TCCCCATACCCAACCCCCTGGTCAACCTCAANCTAGGCCTCCTATTTATCCTAGCCACCTCTAGCCTAGC
+CGTTTACTCAATCCTCTGATCAGGGTGAGCGTCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCA
+GTGGCCCAAACAATCTCATATGAAGTCACCCTAGCTATCATCCTACTATCAACATTACTAATAAGTGGCT
+CCTTTAACCTCTCCACCCTTATCACAACACAAGAGCACCTCTGATTACTCCTGCCATCATGACCCTTGGC
+CATAATATGATTTATCTCCACACTAGCAGAGACCAACCGNANCCCCTTCGACCTTGCNGAAGGGGAGTCC
+GAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTTATAGCCGAATACA
+CAAACATCATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATAACGCACTCTCCCC
+TGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTNACCTCCCTATTCTTATGAATTCGAACA
+GCATACCCCCGATTCCGCTACGACCAACTCATNCACCTNCTATGAAAAAACTTCCTACCACTCACCCTAG
+CATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATATG
+TCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTAGGACTATGAG
+AATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCTACCTATCACACCCCATCCTAAAGTAAGGTCA
+GCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATATCCTTCCCGTACTAATTAATCCCCTG
+GCCCAACCCGNCATNNACTCTACCATCTTTACAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTT
+TTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTCG
+TTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATC
+CTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAACACTANNNATNNNNNNNNGTCATTAATAA
+TCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGG
+CACCCCTCTGACATCCGGCCTGCTACTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAA
+ATTTCCCCCTCATTAAACGTAAGCCTTCTCCTCACTCTTTCAATCTTATCCATCATGGCAGGCAGTTGAG
+GTGGACTAAACCAAACCCAACTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAAT
+AGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATNCTAACTACTACC
+GCATTCCTACTACTCAACTTAAACTCCAGCACCACAACCCTACTACTATCTCGCACCTGAAACAAACTAA
+CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTT
+GCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACC
+ATCACCCTCCTTAACCTCTACTTCTACCTGCGCCTAATCTACTCCACCTCAATCACACTACTCCCTATAT
+CTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCGC
+CCTTACCACACTGCTCCTACCTATCTCCCCTTTTATACTNNNNNNNNNNNAGAAATTTAGGTTAAATACA
+GACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAAAT
+CCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGAC
+TTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCG
+CCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAA
+AATCACCTCAGAGCTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAG
+CCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGA
+ACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCG
+AACTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATT
+TGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATA
+ATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCNCCCTCCCTCC
+TACTCCTGCTTGCATCTGCTATAGTGGAGGCCGGCGCAGGGACAGGTTGAACAGTCTACCCTCCCTTAGC
+AGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTGCACCTAGCAGNTATTTCC
+TCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATGACCCAATACC
+AAACGCCCCTTTTCGTCTGATCCGTCCTAATCACAGCAGTCTTGCTTCTCCTATCTCTCCCAGTCCTGGC
+CGCTGGCATCACTATACTACTAACAGACCGNAACCTCAACACCACCTTCTTCGACCCNGCCGGAGGAGGA
+GACCCCATTCTATACCAACACCTATTCTGATTCTTCGGTCACCCTGAAGTTTATATTCTCATCCTACCAG
+GCTTCGGAATAATCTCTCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTAT
+GGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGA
+ATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAG
+TATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGG
+ATTTATTTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTA

bio/metadmg/compressbam/wrapper.py

@@ -4,6 +4,7 @@
 
 
 import tempfile
+from pathlib import Path
 from snakemake.shell import shell
 
 
@@ -13,12 +14,12 @@
 
 ref = snakemake.input.get("ref", "")
 if ref:
-    ref = f"--ref {ref}"
+    ref = f"-ref {ref}"
 
 
 out_fmt = Path(snakemake.input.aln).suffix.lstrip(".").lower()
 
 
 shell(
-    "compressbam -threads {snakemake.threads} -hts {snakemake.input.aln} {ref} {extra} -type {out_fmt} -out {snakemake.output[0]} {log}"
+    "compressbam -@ {snakemake.threads} -hts {snakemake.input.aln} {ref} {extra} -type {out_fmt} -out {snakemake.output[0]} {log}"
 )

bio/metadmg/getdamage/test/Snakefile

@@ -10,7 +10,7 @@ rule metadmg_getdamage:
     log:
         "logs/getdamage/{sample}.log",
     params:
-        extra="--minlength 30 --printlength 30 --runmode 1",
+        extra="-l 30 -p 30 -r 1",
     threads: 4
     resources:
         mem_mb=1024,

bio/metadmg/getdamage/test/genome.fasta

@@ -1,4 +1,101 @@
->ref
-AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
->ref2
-aggttttataaaacaattaagtctacagagcaactacgcg
+>NC_023100.1 partial
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTTTGGGGG
+GTGTGCACGCGATAGCATTGCGAAACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
+CTGCCCCATCTCATTATTTATCGCACCTACGTTCAATATTACAGGCGAGCATANNTACTAAAGTGTGTTA
+ATTAATTAATGCTTGTAGGACATAATAATAACNATTNAATGNCTGCACAGCCGCTTTCCACACAGACATC
+ACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAGCCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATTAATA
+CAACCCCCGCCCATNCTACCCANNACACACACACCGCTGCTAACTCCATACCCCGAACCAACCAAACCCC
+AAAGACACCCCCCANAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
+GCATCCCCATTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC
+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATAAGCCTTTAGCAATAA
+ACGAAAGTTTAACTAAGCTATACTAACTCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA
+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCANNNNNNNNNNAATAAAGCTAAAACT
+CACCTGAGTTGTAAAAAACTCCAGTTGATACAAAATAAACTACGAAAGTGGCTTTAACACATCTGAATAC
+ACAATAGCTAAGGCCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC
+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC
+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCCCTTGCTCAGCCTATATA
+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC
+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAACCCTTAT
+GAAATTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAATAGAGTGCTTAGTTGAACAGGGCCCTGA
+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA
+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA
+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
+GCCCCAAACCCACTCCACCTTACTACCANACAACCTTAACCAAACCATTTACCCAAATAAAGTATAGGCG
+ATAGAAATTGTAACCCGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA
+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAACC
+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA
+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAANCTANCGAGCCTGGTGATAGCTGGTTNTCCAAGAT
+AGAATCTTAGTTCAACTTTAAATTTACCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG
+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC
+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCTTATAGAAGAACTAATGTTAGTATAAG
+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC
+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
+ATTACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA
+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT
+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA
+TGGAGCTTTAATTTATTAATGCAAACAATACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
+AAAAATTTCGGTTGGGGCGACCTCGGAGCACAGCCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG
+TCAAAGCGAACTACCATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
+GCGCAATCCTATTCCAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG
+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG
+AGTAATCCAGGTCGGTTTCTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTA
+CTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTNNNNNNNNNNNNNNCCAAGAA
+CAGGNTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAATCAGAGGTTCAACT
+CCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGCACCCATTCTAATCGCAATGGCAT
+TCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCC
+CTACGGGCTACTACAGCCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCTCCACA
+TCNACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACTCCCC
+TCCCCATACCCAACCCCCTGGTCAACCTCAANCTAGGCCTCCTATTTATCCTAGCCACCTCTAGCCTAGC
+CGTTTACTCAATCCTCTGATCAGGGTGAGCGTCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCA
+GTGGCCCAAACAATCTCATATGAAGTCACCCTAGCTATCATCCTACTATCAACATTACTAATAAGTGGCT
+CCTTTAACCTCTCCACCCTTATCACAACACAAGAGCACCTCTGATTACTCCTGCCATCATGACCCTTGGC
+CATAATATGATTTATCTCCACACTAGCAGAGACCAACCGNANCCCCTTCGACCTTGCNGAAGGGGAGTCC
+GAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTTATAGCCGAATACA
+CAAACATCATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATAACGCACTCTCCCC
+TGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTNACCTCCCTATTCTTATGAATTCGAACA
+GCATACCCCCGATTCCGCTACGACCAACTCATNCACCTNCTATGAAAAAACTTCCTACCACTCACCCTAG
+CATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATATG
+TCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTAGGACTATGAG
+AATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCTACCTATCACACCCCATCCTAAAGTAAGGTCA
+GCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATATCCTTCCCGTACTAATTAATCCCCTG
+GCCCAACCCGNCATNNACTCTACCATCTTTACAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTT
+TTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTCG
+TTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATC
+CTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAACACTANNNATNNNNNNNNGTCATTAATAA
+TCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGG
+CACCCCTCTGACATCCGGCCTGCTACTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAA
+ATTTCCCCCTCATTAAACGTAAGCCTTCTCCTCACTCTTTCAATCTTATCCATCATGGCAGGCAGTTGAG
+GTGGACTAAACCAAACCCAACTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAAT
+AGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATNCTAACTACTACC
+GCATTCCTACTACTCAACTTAAACTCCAGCACCACAACCCTACTACTATCTCGCACCTGAAACAAACTAA
+CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTT
+GCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACC
+ATCACCCTCCTTAACCTCTACTTCTACCTGCGCCTAATCTACTCCACCTCAATCACACTACTCCCTATAT
+CTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCGC
+CCTTACCACACTGCTCCTACCTATCTCCCCTTTTATACTNNNNNNNNNNNAGAAATTTAGGTTAAATACA
+GACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAAAT
+CCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGAC
+TTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCG
+CCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAA
+AATCACCTCAGAGCTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAG
+CCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGA
+ACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCG
+AACTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATT
+TGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATA
+ATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCNCCCTCCCTCC
+TACTCCTGCTTGCATCTGCTATAGTGGAGGCCGGCGCAGGGACAGGTTGAACAGTCTACCCTCCCTTAGC
+AGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTGCACCTAGCAGNTATTTCC
+TCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATGACCCAATACC
+AAACGCCCCTTTTCGTCTGATCCGTCCTAATCACAGCAGTCTTGCTTCTCCTATCTCTCCCAGTCCTGGC
+CGCTGGCATCACTATACTACTAACAGACCGNAACCTCAACACCACCTTCTTCGACCCNGCCGGAGGAGGA
+GACCCCATTCTATACCAACACCTATTCTGATTCTTCGGTCACCCTGAAGTTTATATTCTCATCCTACCAG
+GCTTCGGAATAATCTCTCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTAT
+GGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGA
+ATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAG
+TATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGG
+ATTTATTTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTA

bio/metadmg/getdamage/wrapper.py

@@ -13,12 +13,12 @@
 
 ref = snakemake.input.get("ref", "")
 if ref:
-    ref = f"--fasta {ref}"
+    ref = f"-f {ref}"
 
 
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(
-        "metaDMG-cpp getdamage --threads {snakemake.threads} {ref} {extra} --outname {tmpdir}/out {snakemake.input.aln} {log}"
+        "metaDMG-cpp getdamage --threads {snakemake.threads} {ref} {extra} -o {tmpdir}/out {snakemake.input.aln} {log}"
     )
 
     if snakemake.output.get("dmg"):

bio/metadmg/lca/test/Snakefile

@@ -2,6 +2,9 @@
 rule metadmg_lca:
     input:
         aln="{sample}.bam",
+        names="names.dmp.gz",
+        nodes="nodes.dmp.gz",
+        acc2taxid="acc2taxid.tsv",
     output:
         res="results/lca/{sample}.out.gz",
         lca="results/lca/{sample}.lca.gz",
@@ -10,7 +13,7 @@ rule metadmg_lca:
     log:
         "logs/lca/{sample}.log",
     params:
-        extra="-simscorelow 0.95 -simscorehigh 1.0 -minmapq 30 -howmany 30 -lca_rank species",
+        extra="-simscorelow 0.95 -simscorehigh 1.0 -minmapq 30 -howmany 30 -lca_rank genus -fix_ncbi 0",
     threads: 4
     resources:
         mem_mb=1024,

bio/metadmg/lca/test/acc2taxid.tsv

@@ -0,0 +1 @@
+NC_023100.1	1425170

bio/metadmg/lca/wrapper.py

@@ -13,29 +13,29 @@
 
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(
-        "metaDMG-cpp lca -nthreads {snakemake.threads} -bam {snakemake.input.aln} -names {snakemake.input.names} -nodes {snakemake.input.nodes} -acc2tax {snakemake.input.acc2taxid} -tempfolder {tmpdir} {extra} --outnames {tmpdir}/out {log}"
+        "metaDMG-cpp lca -nthreads {snakemake.threads} -bam {snakemake.input.aln} -names {snakemake.input.names} -nodes {snakemake.input.nodes} -acc2tax {snakemake.input.acc2taxid} -tempfolder {tmpdir} {extra} -outnames {tmpdir}/out {log}"
     )
 
     if snakemake.output.get("dmg"):
         assert snakemake.output.dmg.endswith(
             ".gz"
-        ), "'dmg' file is Gzip compressed, but extension is not '.gz'"
+        ), "'dmg' file is Gzip compressed, but has no '.gz' extension"
         shell("cat {tmpdir}/out.bdamage.gz > {snakemake.output.dmg}")
 
     if snakemake.output.get("lca"):
         assert snakemake.output.lca.endswith(
             ".gz"
-        ), "'lca' file is Gzip compressed, but extension is not '.gz'"
+        ), "'lca' file is Gzip compressed, but has no '.gz' extension"
         shell("cat {tmpdir}/out.lca.gz > {snakemake.output.lca}")
 
     if snakemake.output.get("stats"):
         assert not snakemake.output.stats.endswith(
             ".gz"
-        ), "'stats' file is NOT Gzip compressed, but extension is '.gz'"
+        ), "'stats' file is NOT Gzip compressed, but has '.gz' extension"
         shell("cat {tmpdir}/out.stat > {snakemake.output.stats}")
 
     if snakemake.output.get("log"):
         assert not snakemake.output.log.endswith(
             ".gz"
-        ), "'log' file is NOT Gzip compressed, but extension is '.gz'"
+        ), "'log' file is NOT Gzip compressed, but has '.gz' extension"
         shell("cat {tmpdir}/out.log > {snakemake.output.log}")