nbay13/toilkit

A python package for working with inputs to and outputs from the toil-rnaseq pipeline

toilkit's Issues

star output directory read as filename prefix if no forward slash

toilkit/toilkit/commands/process_uuid_tars_utilities/star_junctions.py

Line 11 in 379839f

with open('%s%s.SJ.out.tab' % (output_path, heading), 'wb') as output:

Need to check if directory exists and create it if it does not. May need to also make sure star output directory has forward slash if necessary, and add one to the end of string if not.

cat_bbseal not working

toilkit/commands/cat_bbseal_output.py

Line 7 in a90aa47

with open(f + "_human_ambig_umap_reads_R1.fq.gz", "w") as outfile:

Cant open zipped fastq with open()

Cut manifest produces blank final entry

toilkit/commands/cut_manifest.py

Line 10 in a90aa47

for i in range(num_files//split_num+1):

Seems likely to be an off by 1 error

Printing locations of output files

toilkit/toilkit/commands/process_uuid_tars.py

Line 133 in ef9816c

print(f"\nDone! Files can be found in {input_path}")

toilkit/toilkit/commands/process_uuid_tars_utilities/collate_qc.py

Line 125 in ef9816c

print("\nDone! TOIL QC data written to " + path + '\n')

toilkit/toilkit/commands/process_uuid_tars_utilities/collate_qc.py

Line 127 in ef9816c

print("All Done! Renamed SJ.out.tab files can be found at: %s" % (output_path))

Get full path and switch with input path

Allow processing of non-sequential UUIDs

toilkit/toilkit/commands/process_uuid_tars.py

Lines 99 to 101 in ef9816c

	for uuid_num in tqdm(desc="Processing Samples: ", unit="samples", iterable=range(min_id, len(folders))):
	file_name = os.path.join(input_path, f"UUID_{uuid_num}.tar.gz")
	heading = anno_dict[f"UUID_{uuid_num}"]

Iterable should access entries in toil_ids instead of adding iterable as string to "UUID_"

Add command line argument to specify directory containing bbduk/bbseal reference files

On line 27, this should be the same as the bbduk directory provided, with the added "/resources/' subdirectory

toilkit/toilkit/commands/batch_bbduk_bbseal.py

Line 27 in 0c01a1b

'ref=/home/graeberlab/bbmap/resources/trim_galore_adapter.fa', 'ktrim=r', 'k=10', 'mink=7', 'hdist=1', 'tpe', 'tbo'])

On line 30, this should require a new command line argument providing the directory of both reference genome fastqs

toilkit/toilkit/commands/batch_bbduk_bbseal.py

Line 30 in 0c01a1b

'ref=/media/graeberlab/wdgold/nbayley/refs/gencode.v31.transcripts.fa.gz,/media/graeberlab/wdgold/nbayley/refs/gencode.vM22.transcripts.fa.gz',

Assume args.dir (WD) is the current directory the command is executed from

toilkit/toilkit/commands/make_manifest.py

Line 4 in 5429ba8

WD = args.dir

toilkit/toilkit/commands/make_manifest.py

Line 10 in 5429ba8

os.chdir(WD)

Instead of requiring user to input the working directory, assume args.dir (WD) is the current directory the command is executed from and remove the --dir argument