Not so much a bug, as something we should fix.
If the name of an individual in the barcodes file contains a slash, then parts of msg interpret this as folder/file
e.g.
CGCCTC A/A1
AAGGTT sbcy126
TCTGTC sbcy134
leads to the following error
parse_and_map.py: ERROR: Caught exception
Traceback (most recent call last):
File "/misc/local/msg/cmdline/cmdline.py", line 162, in run
exit_code = self.main(*main_args)
File "msg/parse_and_map.py", line 145, in main
self.parse()
File "msg/parse_and_map.py", line 321, in parse
number_reads = count_lines(fastq_file)/4
File "/misc/local/msg/mapping_functions.py", line 26, in count_lines
filename = open(count_file,'r')
IOError: [Errno 2] No such file or directory: 'Sample_Inuez.fastq.gz.trim.fastq.gz_parsed/indivA/A1_CGCCTC'
Error in python msg/parse_and_map.py -i Sample_Inuez.fastq.gz.trim.fastq.gz -b barcodes.txt --parent1 parent1_ref.fa --parent2 par
ent2_ref.fa --parse-only --re_cutter MseI --linker_system Dros_SR_vII --bwa_alg aln --bwa_threads 8 --use_stampy 1 --stampy_premap
_w_bwa 1 --indiv_stampy_substitution_rate 0.01 --indiv_mapq_filter 20 --index_file --index_barcodes --quality_trim_reads_thresh
0 --quality_trim_reads_consec 30: 256 at msg/Utils.pm line 19, <> line 1.
Not sure the best way to handle this. We could either
1 - Be clear in the instructions
2 - Catch these slashes before they are fed to msg
3 - ?
Not so much a bug, as something we should fix.
If the name of an individual in the barcodes file contains a slash, then parts of msg interpret this as folder/file
e.g.
CGCCTC A/A1
AAGGTT sbcy126
TCTGTC sbcy134
leads to the following error
parse_and_map.py: ERROR: Caught exception
Traceback (most recent call last):
File "/misc/local/msg/cmdline/cmdline.py", line 162, in run
exit_code = self.main(*main_args)
File "msg/parse_and_map.py", line 145, in main
self.parse()
File "msg/parse_and_map.py", line 321, in parse
number_reads = count_lines(fastq_file)/4
File "/misc/local/msg/mapping_functions.py", line 26, in count_lines
filename = open(count_file,'r')
IOError: [Errno 2] No such file or directory: 'Sample_Inuez.fastq.gz.trim.fastq.gz_parsed/indivA/A1_CGCCTC'
Error in python msg/parse_and_map.py -i Sample_Inuez.fastq.gz.trim.fastq.gz -b barcodes.txt --parent1 parent1_ref.fa --parent2 par
ent2_ref.fa --parse-only --re_cutter MseI --linker_system Dros_SR_vII --bwa_alg aln --bwa_threads 8 --use_stampy 1 --stampy_premap
_w_bwa 1 --indiv_stampy_substitution_rate 0.01 --indiv_mapq_filter 20 --index_file --index_barcodes --quality_trim_reads_thresh
0 --quality_trim_reads_consec 30: 256 at msg/Utils.pm line 19, <> line 1.
Not sure the best way to handle this. We could either
1 - Be clear in the instructions
2 - Catch these slashes before they are fed to msg
3 - ?