Merge pull request #52 from statbiophys/scripts

Temporal bash script to calculate pgen value of a given sequence.

Makefile.am

@@ -12,6 +12,10 @@ demo_DATA = demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJ
 #Install the generated man pages
 man_MANS = igor.1
 
+# Scripts
+bin_SCRIPTS = \
+  scripts/igor-compute_pgen
+
 install-data-local:
 	mkdir -p $(DESTDIR)$(pkgdatadir)/models
 	cp -r models/* $(DESTDIR)$(pkgdatadir)/models

scripts/igor-compute_pgen

@@ -0,0 +1,21 @@
+#!/bin/bash
+args=("$@")
+species=${args[0]} #human
+chain=${args[1]}  #beta
+seque=${args[2]}
+export tmp_dir=$(mktemp -d)
+export tmp_seqfile=$(mktemp ${tmp_dir}/igorSeq.XXXXXXXXXXXXXXXXXXXXXX.txt)
+echo ${seque} > ${tmp_seqfile}
+export randomBatch=`head /dev/urandom | tr -dc A-Za-z0-9 | head -c10`
+echo ${species}" "${chain}" "${tmp_dir}" "${tmp_seqfile}
+igor -set_wd ${tmp_dir} -batch ${randomBatch} -read_seqs ${tmp_seqfile}
+igor -set_wd ${tmp_dir} -batch ${randomBatch} -species ${species} -chain ${chain} -align --all
+igor -set_wd ${tmp_dir} -batch ${randomBatch} -species ${species} -chain ${chain} -evaluate -output --Pgen
+#cat ${tmp_dir}/aligns/${randomBatch}_indexed_sequences.csv
+#cat ${tmp_dir}/aligns/${randomBatch}_indexed_CDR3.csv
+pgenFile=${tmp_dir}/${randomBatch}_output/Pgen_counts.csv
+#cat ${pgenFile}
+pgenValue=`awk -F ';' 'FNR==2{print $2}' ${pgenFile}`
+echo ${pgenValue}
+rm -r ${tmp_dir}
+