diff options
| -rwxr-xr-x | SelectiveWholeGenomeAmplification | 6 | ||||
| -rwxr-xr-x | src/remove_mers_from_file.py | 9 |
2 files changed, 9 insertions, 6 deletions
diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification index 37ddeb1..23b14bc 100755 --- a/SelectiveWholeGenomeAmplification +++ b/SelectiveWholeGenomeAmplification @@ -27,7 +27,7 @@ check_mers() { local counts="$2" local mer=0 - echo " counting mers in $fasta_file:e" + echo " counting mers in $fasta_file:" echo -e "\e[32m" # remove the counts file so we can concatenate @@ -315,11 +315,11 @@ if [[ -n "$step_filters" ]] || [[ -n "$all" ]]; then # check mers from next ignore file counts="$counts_directory/ignore-"$(basename "$ignore_file") check_mers "$ignore_file" "$counts" + counts="$counts-counts" echo " filtering ignored mers from: $ignore_file" - cat "$ignore_all_mers_counts" | remove_mers_from_file.py "$ignore_file"> "$ignore_all_mers_counts-tmp" + cat "$ignore_all_mers_counts" | remove_mers_from_file.py "$counts"> "$ignore_all_mers_counts-tmp" mv "$ignore_all_mers_counts-tmp" "$ignore_all_mers_counts" - read check_non_empty "$ignore_all_mers_counts" "ignore all mers from file $ignore_file" else echo " $ignore_file not found, continuing..." diff --git a/src/remove_mers_from_file.py b/src/remove_mers_from_file.py index bef3ea3..3576e35 100755 --- a/src/remove_mers_from_file.py +++ b/src/remove_mers_from_file.py @@ -8,9 +8,12 @@ if __name__ == "__main__": mers_to_delete = set() - for mer in open(sys.argv[1], 'r'): - mer = mer.strip().split()[0] - mers_to_delete.add(mer) + for mer in open(sys.argv[1], 'rU'): + sp = mer.strip().split() + if len(sp) == 2: + mer = sp[0] + mers_to_delete.add(mer) + for line in sys.stdin: if line.split()[0] not in mers_to_delete: |