Mercurial > repos > pjbriggs > pal_finder

changeset 16:856cafcbf422 draft

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Uploaded
author pjbriggs
date Tue, 15 May 2018 07:24:18 -0400
parents a3af1ff4cad1
children 831c838927c7
files fastq_subset.py test-data/454_microsats.out.re_match~ test-data/illuminaPE_filtered_microsats.out.re_match~ test-data/illuminaPE_filtered_microsats_occurrences.out.re_match~ test-data/illuminaPE_filtered_microsats_primers.out.re_match~ test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match~ test-data/illuminaPE_microsat_types.out.re_match~ test-data/illuminaPE_microsats.out.re_match~
diffstat 8 files changed, 74 insertions(+), 49 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_subset.py	Tue May 15 07:24:18 2018 -0400
@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+
+import argparse
+import random
+from Bio.SeqIO.QualityIO import FastqGeneralIterator
+
+def count_reads(fastq):
+    """
+    Count number of reads in a Fastq file
+    """
+    n = 0
+    with open(fastq,'r') as fq:
+        while True:
+            buf = fq.read()
+            n += buf.count('\n')
+            if buf == "": break
+    return n/4
+
+def fastq_subset(fastq_in,fastq_out,indices):
+    """
+    Output a subset of reads from a Fastq file
+
+    The reads to output are specifed by a list
+    of integer indices; only reads at those
+    positions in the input file will be written
+    to the output.
+    """
+    with open(fastq_in,'r') as fq_in:
+        fq_out = open(fastq_out,'w')
+        i = 0
+        for title,seq,qual in FastqGeneralIterator(fq_in):
+            if i in indices:
+                fq_out.write("@%s\n%s\n+\n%s\n" % (title,
+                                                   seq,
+                                                   qual))
+            i += 1
+        fq_out.close()
+
+if __name__ == "__main__":
+
+    p = argparse.ArgumentParser()
+    p.add_argument("fastq_r1")
+    p.add_argument("fastq_r2")
+    p.add_argument("-n",
+                   dest="subset_size",
+                   default=None,
+                   help="subset size")
+    p.add_argument("-s",
+                   dest="seed",
+                   type=int,
+                   default=None,
+                   help="seed for random number generator")
+    args = p.parse_args()
+
+    print "Processing fastq pair:"
+    print "\t%s" % args.fastq_r1
+    print "\t%s" % args.fastq_r2
+
+    nreads = count_reads(args.fastq_r1)
+    print "Counted %d reads in %s" % (nreads,args.fastq_r1)
+
+    if args.subset_size is not None:
+        subset_size = float(args.subset_size)
+        if subset_size < 1.0:
+            subset_size = int(nreads*subset_size)
+        else:
+            subset_size = int(subset_size)
+        print "Extracting subset of reads: %s" % subset_size
+        if args.seed is not None:
+            print "Random number generator seed: %d" % args.seed
+            random.seed(args.seed)
+        subset = random.sample(xrange(nreads),subset_size)
+        fastq_subset(args.fastq_r1,"subset_r1.fq",subset)
+        fastq_subset(args.fastq_r2,"subset_r2.fq",subset)
--- a/test-data/454_microsats.out.re_match~	Mon May 14 11:10:19 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-SequenceID\	Repeat\ Motif\ Size\	Repeat\ Motif\	Number\ Tandem\ Repeats\	Primer\ Designed\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Total\ Repeats\ In\ Amplicon\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs
-FW1N29Q04EP35X\	2\	AC\	18\	0\	\	\	\	\	\	\	\	\	
--- a/test-data/illuminaPE_filtered_microsats.out.re_match~	Mon May 14 11:10:19 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_3\	AAGTACAGTGGGGAGGCTGG\	test\_6\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_7\	GCAGTAAACAAAGGCAAAGGG\	test\_4\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	AG\(14\)\ \	14\	\	\	1\	test\_5\	TTCTCCCACTATATTTTGCATTGG\	test\_1\	TCCAGACTGAAGCTACCCTGG\	AG\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- a/test-data/illuminaPE_filtered_microsats_occurrences.out.re_match~	Mon May 14 11:10:19 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	AG\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_6\	TCCAGACTGAAGCTACCCTGG\	AG\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_5\	GCAGTAAACAAAGGCAAAGGG\	test\_2\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_8\	AAGTACAGTGGGGAGGCTGG\	test\_4\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
--- a/test-data/illuminaPE_filtered_microsats_primers.out.re_match~	Mon May 14 11:10:19 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	AG\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_2\	TCCAGACTGAAGCTACCCTGG\	AG\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	TG\(12\)\ \	12\	\	\	1\	test\_5\	GCAGTAAACAAAGGCAAAGGG\	test\_3\	CCTGGGCAGAGGTGTTCC\	TG\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	TG\(12\)\ \	12\	\	\	1\	test\_4\	AAGTACAGTGGGGAGGCTGG\	test\_6\	TTTTCTACACAGCTCAAGTAGCCC\	TG\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\	TG\(12\)\ TG\(12\)\ \	24\	\	\	1\	test\_8\	TCTTTATCTAAACACATCCTGAAATACC\	test\_1\	AAACGCAATTATTTTGAGATGTCC\	TG\(12\)\ TG\(12\)\ \	24\	1\	\	\	1\	2\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 1\:N\:0\:TCCTGA\	TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 2\:N\:0\:TCCTGA\	TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC
--- a/test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match~	Mon May 14 11:10:19 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_3\	AAGTACAGTGGGGAGGCTGG\	test\_4\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 1\:N\:0\:TCCTGA\	TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 2\:N\:0\:TCCTGA\	TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\	TC\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 1\:N\:0\:TCCTGA\	TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 2\:N\:0\:TCCTGA\	TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 1\:N\:0\:TCCTGA\	TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 2\:N\:0\:TCCTGA\	TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_6\	GCAGTAAACAAAGGCAAAGGG\	test\_1\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\	AC\(36\)\ \	36\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 1\:N\:0\:TCCTGA\	TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 2\:N\:0\:TCCTGA\	TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	TC\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_2\	TCCAGACTGAAGCTACCCTGG\	TC\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- a/test-data/illuminaPE_microsat_types.out.re_match~	Mon May 14 11:10:19 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-allExtended\:\	0
-allSpan\:\	0
-broken\:\	2
-compound\:\	2
-readsWithMicrosat\:\	13
-totalBases\:\	2320
-totalReads\:\	20\	\(2\ x\ 10\)
-
-
-Microsat\ Type\	monomer\ length\	total\ loci\	loci\ w\/\ primers\	reads\ with\ loci\	total\ bases\	extended\	extended\ w\/\ primers\	spanning\	spanning\ w\/\ primers
-AC\	2\	7\	4\	7\	116\	0\	0\	0\	0
-AG\	2\	0\	0\	0\	0\	0\	0\	0\	0
-AT\	2\	8\	0\	6\	106\	0\	0\	0\	0
-CG\	2\	0\	0\	0\	0\	0\	0\	0\	0
-TC\	2\	2\	1\	2\	26\	\	\	\	
--- a/test-data/illuminaPE_microsats.out.re_match~	Mon May 14 11:10:19 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	TC\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_2\	TCCAGACTGAAGCTACCCTGG\	TC\(14\)\ \	14\	1\	\	\	1\	1\	1\	1
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\	AC\(36\)\ \	36\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:19063\:1614\	AT\(14\)\ AT\(14\)\ AT\(14\)\ AT\(14\)\ \	56\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_6\	GCAGTAAACAAAGGCAAAGGG\	test\_1\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5626\:1554\	AT\(14\)\ AC\(16\)\ AC\(16\)\ AT\(12\)\ \	58\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\	TC\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_3\	AAGTACAGTGGGGAGGCTGG\	test\_4\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1
-ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\	AC\(12\)\ AC\(12\)\ \	24\	\	\	1\	test\_8\	TCTTTATCTAAACACATCCTGAAATACC\	test\_5\	AAACGCAATTATTTTGAGATGTCC\	AC\(12\)\ AC\(12\)\ \	24\	1\	\	\	1\	2\	1\	1