added missing files

[biopieces.git] / bp_scripts / remove_adaptor_454.sh

diff --git a/bp_scripts/remove_adaptor_454.sh b/bp_scripts/remove_adaptor_454.sh
index 34013b1ec4c6a06f67daf17123ae14b6ddac0ddd..5088d477000115a4e565b5147f267b3b382c6c09 100755 (executable)
--- a/bp_scripts/remove_adaptor_454.sh
+++ b/bp_scripts/remove_adaptor_454.sh
@@ -2,14 +2,13 @@
 
 # Remove adaptor from sequences and produce a number of plots.
 
-# Usage: read_fastq -i test.fq | remove_adaptor.sh | write_fastq -xo test_no_adaptor.fq
+# Usage: read_fastq -i test.fq | remove_adaptor_454.sh | write_fastq -xo test_no_adaptor.fq
 
 adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor
 pid=$$
 
-#find_adaptor -a $adaptor |
 plot_lendist -t post -o 00_remove_adaptor_lendist_seq_before.$pid.ps -k SEQ_LEN |
-parallel -k --blocksize 50M --pipe --recend "\n---\n" "nice -n 19 find_adaptor -a $adaptor" |
+find_adaptor -a $adaptor -p |
 plot_histogram -t post -o 01_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num |
 plot_lendist -t post -o 02_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN |
 plot_lendist -t post -o 03_remove_adaptor_lendist_seq_after.$pid.ps -k SEQ_LEN |