sourmash sig merge needs --name

[ctb]

sourmash sig merge should support --name to rename the output signature.

feature suggested by @olgabot as per below.

To get started on this,

• add a --name parameter to argument parsing for sig merge in src/sourmash/cli/sig/merge.py
• in src/sourmash/sig/__main__.py, function merge(...), adjust the SourmashSignature object creation to use name=args.name
• add a test in tests/test_test_cmd_signature.py, perhaps starting from a renamed copy of test_sig_merge_1, that uses --name on the command line and checks the .name attribute on the output signature

[olgabot]

Yes because piping doesn't work!

(base)
 Fri 16 Oct - 15:16  ~/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged 
 olga@ndnd  sourmash sig merge --quiet -k 27 --dayhoff /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__aligned__aligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__unaligned__unaligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig | sourmash sig rename --quiet --output /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged/alphabet-dayhoff__ksize-27__scaled-5/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC.sig - HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC
Traceback (most recent call last):
  File "/home/olga/anaconda/bin/sourmash", line 11, in <module>
    sys.exit(main())
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/__main__.py", line 14, in main
    return mainmethod(args)
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/cli/sig/merge.py", line 29, in main
    return sourmash.sig.__main__.merge(args)
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/sig/__main__.py", line 269, in merge
    sourmash.save_signatures([merged_sigobj], fp=fp)
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/signature.py", line 336, in save_signatures
    fp.write(result)
BrokenPipeError: [Errno 32] Broken pipe
(base)
 Fri 16 Oct - 15:16  ~/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged 
 olga@ndnd  sourmash sig merge --quiet -k 27 --dayhoff /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__aligned__aligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__unaligned__unaligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig | sourmash sig rename --quiet --output /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged/alphabet-dayhoff__ksize-27__scaled-5/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC.sig HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC
usage:  rename [-h] [-q] [-d] [-o FILE] [-k K] [--protein] [--no-protein]
               [--dayhoff] [--no-dayhoff] [--hp] [--no-hp] [--dna] [--no-dna]
               sigfiles [sigfiles ...] name
 rename: error: the following arguments are required: name
(base)
 ✘  Fri 16 Oct - 15:16  ~/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged 
 olga@ndnd  sourmash sig merge --quiet -k 27 --dayhoff /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__aligned__aligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__unaligned__unaligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig | sourmash sig rename --quiet --name HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC --output /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged/alphabet-dayhoff__ksize-27__scaled-5/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC.sig
usage:  rename [-h] [-q] [-d] [-o FILE] [-k K] [--protein] [--no-protein]
               [--dayhoff] [--no-dayhoff] [--hp] [--no-hp] [--dna] [--no-dna]
               sigfiles [sigfiles ...] name
 rename: error: the following arguments are required: name
Traceback (most recent call last):
  File "/home/olga/anaconda/bin/sourmash", line 11, in <module>
    sys.exit(main())
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/__main__.py", line 14, in main
    return mainmethod(args)
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/cli/sig/merge.py", line 29, in main
    return sourmash.sig.__main__.merge(args)
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/sig/__main__.py", line 269, in merge
    sourmash.save_signatures([merged_sigobj], fp=fp)
  File "/home/olga/miniconda3/lib/python3.6/site-packages/sourmash/signature.py", line 336, in save_signatures
    fp.write(result)
BrokenPipeError: [Errno 32] Broken pipe
(base)
 ✘  Fri 16 Oct - 15:17  ~/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged 
 olga@ndnd  sourmash sig merge --quiet -k 27 --dayhoff /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__aligned__aligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__unaligned__unaligned__ACACCCTTCAAACCAC__coding_reads_peptides.sig | sourmash sig rename --quiet --name HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC --output /home/olga/data_sm/tabula-microcebus/analyses/kmermaid/tenx-tgz--hlca-v2--normal-lung-remove-riborna/sketches_peptide_handmade_merged/alphabet-dayhoff__ksize-27__scaled-5/HUMAN_HCA_LUNG_LUNG_CD45_OR_CD31__ACACCCTTCAAACCAC.sig  -
sourmash: error: unrecognized arguments: --name

[ctb]

hi @olgabot ok, figured this out - the correct syntax for renaming signatures via pipe is:

sourmash sig merge 47.fa.sig 63.fa.sig  | \
     sourmash sig rename - newname

To be fair, I don't really like the syntax for sourmash sig rename, but that's what it is ;).

I do like the idea of adding a --name parameter to sourmash sig merge, though!