nebiolabs / ampseer Goto Github PK

I'm sure my Rust on linux isn't up-to-date, but I got this:

error: failed to parse manifest at /mnt/home/mcampbell/src/ampseer/Cargo.toml

Caused by:
feature edition2021 is required

this Cargo does not support nightly features, but if you
switch to nightly channel you can add
cargo-features = ["edition2021"] to enable this feature

compare key between similarly scored sets, use only complementary keys to differentiate

After running cargo test:

running 10 tests
test test_cli ... ok
test test_help_exit_code ... ok
test missing_reads ... ok
test ont_amps_find_both_orientations ... FAILED
test differentiate_artic_v3_from_vss ... FAILED
test test_version ... ok
test test_insufficient_arguments ... ok
test non_matching_primer_sets ... ok
test differentiate_vss_from_artic_v3 ... ok
test differentiate_vss2_from_vss1a ... FAILED

failures:

---- ont_amps_find_both_orientations stdout ----
thread 'ont_amps_find_both_orientations' panicked at 'Unexpected stdout, failed fn(var)
└── var as str:

command="/Users/mcampbell/Desktop/src/ampseer/target/debug/ampseer" "--primer-sets" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/vss_18_28.bed.fasta" "--reads" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/ont_vss_full_length_amp18rev_amp28for.fastq"
code=1
stdout=""
stderr="2022-01-25 17:12:39,767 ERROR [ampseer] Could not find reads at "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/ont_vss_full_length_amp18rev_amp28for.fastq"\nError: Invalid input\n"
', /rustc/db9d1b20bba1968c1ec1fc49616d4742c1725b4b/library/core/src/ops/function.rs:227:5
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

---- differentiate_artic_v3_from_vss stdout ----
thread 'differentiate_artic_v3_from_vss' panicked at 'Unexpected stdout, failed fn(var)
└── var as str:

command="/Users/mcampbell/Desktop/src/ampseer/target/debug/ampseer" "--primer-sets" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/primer_sets/ARTIC_v3.bed.fasta" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/primer_sets/neb_vss1a.bed.fasta" "--reads" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/artic_v3.fastq"
code=1
stdout=""
stderr="2022-01-25 17:12:39,767 ERROR [ampseer] Could not find reads at "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/artic_v3.fastq"\nError: Invalid input\n"
', /rustc/db9d1b20bba1968c1ec1fc49616d4742c1725b4b/library/core/src/ops/function.rs:227:5

---- differentiate_vss2_from_vss1a stdout ----
thread 'differentiate_vss2_from_vss1a' panicked at 'Unexpected stdout, failed fn(var)
└── var as str: unknown

nextera transposases cannot insert at the extreme ends of amplicons. To handle these libraries, it would be necessary to enable partial matches with expected start sequences.

Running the first command in the readme:

samtools bam2fq: Cannot read file "tests/fixtures/vss2_small.bam": No such file or directory

Hi!

This is a very nice tool.

Once you have enough confidence in it, it would be nice to create a package on bioconda to make it easier to integrate in workflow (e.g. I would like to add it to V-pipe, as we need primer autodetection for several components )

I can give a hand with that if needed.