<commit_before>#! /bin/bash
# 
# Simple annotator loop for .vcf and .snp files
#
#   ~/opt/somatic_pipeline/scripts/annotate.sh < list
#
# e.g.,
#
#   ls *Somatic*vcf --color=never -1 |~/opt/somatic_pipeline/scripts/annotate.sh
#

# annotate=/data/common_scripts/SAP42-testing/annotator.pl
annotate=/hpc/cog_bioinf/common_scripts/SAP42-HPC/annotator.pl
onceonly="once-only"

while read infile ; do
  echo ==== $annotate $infile...
  # echo "$annotate -in $infile"|$onceonly -in $infile --out $infile.snv1 --out $infile.snv2 --pfff -d . -v
  echo "$annotate -in $infile"|$onceonly -in $infile --out $infile.snv1 --out $infile.snv2 --pbs '-q veryshort' --pbs-type SGE --pfff -d . -v
  [ $? -ne 0 ] && exit 1
done<commit_msg>Set to medium for large VCF files<commit_after>#! /bin/bash
# 
# Simple annotator loop for .vcf and .snp files
#
#   ~/opt/somatic_pipeline/scripts/annotate.sh < list
#
# e.g.,
#
#   ls *Somatic*vcf --color=never -1 |~/opt/somatic_pipeline/scripts/annotate.sh
#

# annotate=/data/common_scripts/SAP42-testing/annotator.pl
annotate=/hpc/cog_bioinf/common_scripts/SAP42-HPC/annotator.pl
onceonly="once-only"

while read infile ; do
  echo ==== $annotate $infile...
  # echo "$annotate -in $infile"|$onceonly -in $infile --out $infile.snv1 --out $infile.snv2 --pfff -d . -v
  echo "$annotate -in $infile"|$onceonly -in $infile --out $infile.snv1 --out $infile.snv2 --pbs '-q medium' --pbs-type SGE --pfff -d . -v
  [ $? -ne 0 ] && exit 1
done
{'fraction_non_alphanumeric': 0.17932922655715264, 'fraction_numerical': 0.015058179329226557, 'mean_word_length': 3.2873900293255134, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6844874', 'n_tokens_mistral': 627, 'n_tokens_neox': 602, 'n_words': 133}