diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-07-16 14:06:21 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-07-16 14:06:21 -0400 |
| commit | 765a73ed7bb055d11aea2627af8daa9cfc6d664b (patch) | |
| tree | b3f553314002bca59f0f2c8aeaefbc8a588c2463 /SelectiveWholeGenomeAmplification | |
| parent | 7246d741138a5692e57b2fdd3eb229f07b29ff5d (diff) | |
add working remove mers from file
Diffstat (limited to 'SelectiveWholeGenomeAmplification')
| -rwxr-xr-x | SelectiveWholeGenomeAmplification | 6 |
1 files changed, 3 insertions, 3 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..." |