bialimed / anacore-utils

Scripts for easily process NGS data from medical centers.

AnaCore-utils

Description

Scripts for easily process NGS data from medical centers. This package contains several aggregators, converters, filters, wrappers, etc.

Installation

conda install -c bioconda -c conda-forge -c fescudie anacore-utils

Copyright

2017 Laboratoire d'Anatomo-Cytopathologie de l'Institut Universitaire du Cancer Toulouse - Oncopole

Contact

[email protected]

anacore-utils's Issues

AlignmentHeader does not support item assignment

Hi,

It seems that pysam v0.15.3 is not compatible.
It looks very similar of this issue : namphuon/ViFi#9

See log :

> ampliVariantCalling.py \
-g ${GENOME_REF} \
-pi ${DESIGN_PATH}/withPrimers.bed \
-po ${DESIGN_PATH}/woutPrimers.bed \
-pg ${DESIGN_PATH}/nonOverlappingGroups.tsv \
-l "${SAMPLE}" -a ${OUTPUT_TMP}/${SAMPLE}.RG.bam \
-ov ${OUTPUT_TMP}/${SAMPLE}.vcf \
-ol ${OUTPUT_TMP}/${SAMPLE}.log
Traceback (most recent call last):
File "/bin/anaconda3/envs/TEST_anacore/bin/splitBAMByRG.py", line 72, in
new_header["RG"] = [curr_RG for curr_RG in FH_in.header["RG"] if group_by_tag[curr_RG[args.RG_tag]] == group]
File "pysam/libcalignmentfile.pyx", line 544, in pysam.libcalignmentfile.AlignmentHeader.setitem
TypeError: AlignmentHeader does not support item assignment (use header.to_dict()
Traceback (most recent call last):
File "/bin/anaconda3/envs/TEST_anacore/bin/ampliVariantCalling.py", line 557, in
SplitBAMByRG(args.input_non_overlapping_design, args.input_aln, out_bam_pattern).submit(args.output_log)
File "/bin/anaconda3/envs/TEST_anacore/bin/ampliVariantCalling.py", line 112, in submit
subprocess.check_output(self.get_cmd(), shell=True)
File "/bin/anaconda3/envs/TEST_anacore/lib/python3.7/subprocess.py", line 411, in check_output
**kwargs).stdout
File "/bin/anaconda3/envs/TEST_anacore/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'splitBAMByRG.py --input-design ${DESIGN_PATH}/nonOverlappingGroups.tsv --input-aln${OUTPUT_TMP}/${SAMPLE}.RG.bam --output-pattern ${OUTPUT_TMP}/1580394752.121624_10888{GP}.bam' returned non-zero exit status 1._