jimhester / fasta_utilities Goto Github PK

Hello Jim,
I am trying the unique_headers.pl but unsuccessfully. I am using the WSL version for windows and after following the instructions for compilation, I still get the following error:
"
unique_headers.pl --help
Can't locate ReadFastx.pm in @inc (you may need to install the ReadFastx module) (@inc contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/local/bin/unique_headers.pl line 31.
BEGIN failed--compilation aborted at /usr/local/bin/unique_headers.pl line 31.
"
After cloning the repository and using the "perl Makefile.PL PREFIX=$HOME" I get the following errors:

Warning: prerequisite Class::XSAccessor 0 not found.
Warning: prerequisite Inline 0 not found.
Warning: prerequisite List::MoreUtils 0 not found.
Warning: prerequisite Moose 0 not found.
Warning: prerequisite MooseX::NonMoose 0 not found.
Warning: prerequisite Readonly 0 not found.
Warning: prerequisite Term::ProgressBar 0 not found.
Warning: prerequisite namespace::autoclean 0 not found.
Generating a Unix-style Makefile
Writing Makefile for fasta_utilities
Writing MYMETA.yml and MYMETA.json

After that, make and make install look fine.
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/absolute_coordinates.pl
cp scripts/wrap.pl blib/script/wrap.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wrap.pl
Manifying 40 pod documents
Manifying 22 pod documents

make install
"Appending installation info to /home/moraisd/lib/x86_64-linux-gnu/perl/5.22.1/perllocal.pod"

But I still get the error.

Could you show me how to solve it? Thanks.

Hi,

definitely have the correct file name and path, the always get this error:

home> ~/bin/fasta_utils/consensus.pl test_sorted.bam
Use of uninitialized value $filename in string at /OSM/HOME-MEL/all29c/bin/fasta_utils/consensus.pl line 101.
Use of uninitialized value $filename in concatenation (.) or string at home/bin/fasta_utils/consensus.pl line 101.
No such file or directory:Could not open

Thanks,

Theo

I try fasta2fastq.pl after installing your package without any problem (perl Makefile.PL/make/make install) but I obtain error massage
Can't locate object method "new" via package "ReadFastx::Fastq::Seq" (perhaps you forgot to load "ReadFastx::Fastq::Seq"?) at /usr/local/bin/fasta2fastq.pl line 60, <$_[...]> line 2.

Hi @jimhester , it failed to run split_fasta.pl

$ split_fasta.pl -amount 2 dataset_A.fa -force
dataset_A.fa:  98% [==================================*============================================  ]0m00s
 LeftNot an ARRAY reference at /usr/local/bin/split_fasta.pl line 118, <$_[...]> line 175365.
$ split_fasta.pl -amount 2 dataset_B.fa -force                                
dataset_B.fa:  56% [*=============================================                                   ]0m00s 
LeftNot an ARRAY reference at /usr/local/bin/split_fasta.pl line 118, <$_[...]> line 7.
$ split_fasta.pl -amount 2 dataset_RNA.fasta -force                           
Not an ARRAY reference at /usr/local/bin/split_fasta.pl line 118, <$_[...]> line 101.

I checked the code and printed the type of $seq_ref, it was REF, and there was error information:

Virtual timer expired

By the way, I'm writing a FASTA kit, named fakit, and I've done some benchmarks with similar tools, including fasta_utilities. Could you please take few minutes to look and give some advice?

sincerely,
Wei