Galaxy |

Changeset 0:9d189d08f2ad (2014-05-19)

Next changeset 1:7e801ab2b70e (2015-11-11)

Commit message:
Imported from capsule None

added:
fasta_to_tabular.py
fasta_to_tabular.xml
test-data/1.tabular
test-data/2.tabular
test-data/4.fasta
test-data/454.fasta
test-data/a.tab
test-data/fasta_to_tabular_out1.tabular
test-data/fasta_to_tabular_out2.tabular
test-data/fasta_to_tabular_out3.tabular
test-data/fasta_to_tabular_out4.tabular
test-data/fasta_to_tabular_out5.tabular
test-data/fasta_to_tabular_out6.tabular

diff -r 000000000000 -r 9d189d08f2ad fasta_to_tabular.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_to_tabular.py Mon May 19 12:34:27 2014 -0400

[

@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+# This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools
+"""
+Input: fasta (input file), tabular (output file), int (truncation of id), int (columns from description)
+Output: tabular
+format convert: fasta to tabular
+"""
+
+import sys, os
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    if len(sys.argv) != 5:
+        stop_err("Wrong number of argument. Expect four (fasta, tabular, truncation, columns)")
+    infile = sys.argv[1]
+    outfile = sys.argv[2]
+    keep_first = int( sys.argv[3] )
+    descr_split = int( sys.argv[4] )
+    fasta_title = fasta_seq = ''
+    if keep_first == 0:
+        keep_first = None
+    elif descr_split == 1:
+        #Added one for the ">" character
+        #(which is removed if using descr_split > 1)
+        keep_first += 1
+    if descr_split < 1:
+        stop_err("Bad description split value (should be 1 or more)")
+    out = open( outfile, 'w' )
+    for i, line in enumerate( open( infile ) ):
+        line = line.rstrip( '\r\n' )
+        if not line or line.startswith( '#' ):
+            continue
+        if line.startswith( '>' ):
+            #Don't want any existing tabs to trigger extra columns:
+            line = line.replace('\t', ' ')
+            if i > 0:
+                out.write('\n')
+            if descr_split == 1:
+                out.write(line[1:keep_first])
+            else:
+                words = line[1:].split(None, descr_split-1)
+                #apply any truncation to first word (the id)
+                words[0] = words[0][0:keep_first]
+                #pad with empty columns if required
+                words += [""]*(descr_split-len(words))
+                out.write("\t".join(words))
+            out.write('\t')
+        else:
+            out.write(line)
+    if i > 0:
+        out.write('\n')
+    out.close()
+
+if __name__ == "__main__" : __main__()

diff -r 000000000000 -r 9d189d08f2ad fasta_to_tabular.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_to_tabular.xml Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,128 @@
+<tool id="fasta2tab" name="FASTA-to-Tabular" version="1.1.0">
+ <description>converter</description>
+ <command interpreter="python">fasta_to_tabular.py $input $output $keep_first $descr_columns</command>
+ <inputs>
+ <param name="input" type="data" format="fasta" label="Convert these sequences"/>
+ <param name="descr_columns" type="integer" size="2" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column">
+ <validator type="in_range" min="1" />
+ </param>
+ <param name="keep_first" type="integer" size="5" value="0" label="How many title characters to keep?" help="Applies only to the first column taken from the title string ('0' = keep the whole thing), useful when your sequence identifiers are all the same length.">
+ <validator type="in_range" min="0" />
+ </param>
+ </inputs>
+ <outputs>
+ <data name="output" format="tabular"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="input" value="454.fasta" />
+ <param name="descr_columns" value="1"/>
+ <param name="keep_first" value="0"/>
+ <output name="output" file="fasta_to_tabular_out1.tabular" />
+ </test>
+
+ <test>
+ <param name="input" value="4.fasta" />
+ <param name="descr_columns" value="1"/>
+ <param name="keep_first" value="0"/>
+ <output name="output" file="fasta_to_tabular_out2.tabular" />
+ </test>
+
+ <test>
+ <param name="input" value="454.fasta" />
+ <param name="descr_columns" value="1"/>
+ <param name="keep_first" value="14"/>
+ <output name="output" file="fasta_to_tabular_out3.tabular" />
+ </test>
+
+ <test>
+ <param name="input" value="454.fasta" />
+ <param name="descr_columns" value="2"/>
+ <param name="keep_first" value="0"/>
+ <output name="output" file="fasta_to_tabular_out4.tabular" />
+ </test>
+
+ <test>
+ <param name="input" value="454.fasta" />
+ <param name="descr_columns" value="5"/>
+ <param name="keep_first" value="0"/>
+ <output name="output" file="fasta_to_tabular_out5.tabular" />
+ </test>
+
+ <test>
+ <param name="input" value="454.fasta" />
+ <param name="descr_columns" value="5"/>
+ <param name="keep_first" value="10"/>
+ <output name="output" file="fasta_to_tabular_out6.tabular" />
+ </test>
+
+ </tests>
+ <help>
+
+**What it does**
+
+This tool converts FASTA formatted sequences to TAB-delimited format.
+
+Many tools consider the first word of the FASTA ">" title line to be an identifier, and any remaining text to be a free form description.
+It is therefore useful to split this text into two columns in Galaxy (identifier and any description) by setting **How many columns to divide title string into?** to **2**.
+In some cases the description can be usefully broken up into more columns -- see the examples .
+
+The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
+With the introduction of the **How many columns to divide title string into?** option this setting is of limited use, but does still allow you to truncate the identifier.
+
+-----
+
+**Example**
+
+Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
+
+    >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
+    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
+    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
+    >EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
+    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAA
+
+Running this tool with the default settings will produce this (2 column output):
+
+========================================================================== =======================================
+EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
+EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_  AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
+========================================================================== =======================================
+
+Having the full title line (the FASTA ">" line text) as a column is not always ideal.
+
+The **How many characters to keep?** option is useful if your identifiers are all the same length.
+In this example the identifier is 14 characters, so setting **How many characters to keep?** to **14** (and leaving **How many columns to divide title string into?** as the default, **1**) will produce this (2 column output):
+
+============== =======================================
+EYKX4VC02EQLO5 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
+EYKX4VC02D4GS2 AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
+============== =======================================
+
+If however your FASTA file has identifiers of variable length, it is better to split the text into at least two columns.
+Running this tool with **How many columns to divide title string into?** to **2** will produce this (3 column output):
+
+============== =========================================================== =======================================
+EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
+EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_  AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
+============== =========================================================== =======================================
+
+Running this tool with **How many columns to divide title string into?** to **5** will produce this (5 column output):
+
+============== ========== ============ ======== ========================== =======================================
+EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
+EYKX4VC02D4GS2 length=60  xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
+============== ========== ============ ======== ========================== =======================================
+
+Running this tool with **How many columns to divide title string into?** to **5** and **How many characters to keep?** to **10** will produce this (5 column output).
+Notice that only the first column is truncated to 10 characters -- and be careful not to trim your sequence names too much (generally they should be unique):
+
+========== ========== ============ ======== ========================== =======================================
+EYKX4VC02E length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
+EYKX4VC02D length=60  xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
+========== ========== ============ ======== ========================== =======================================
+
+Note the sequences have been truncated for display purposes in the above tables.
+
+ </help>
+</tool>

diff -r 000000000000 -r 9d189d08f2ad test-data/1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.tabular Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,6 @@
+chr22 1000 NM_17
+chr22 2000 NM_18
+chr10 2200 NM_10
+chr10 hap test
+chr10 1200 NM_11
+chr22 1600 NM_19
\ No newline at end of file

diff -r 000000000000 -r 9d189d08f2ad test-data/2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,10 @@
+1 68 4.1
+2 71 4.6
+3 62 3.8
+4 75 4.4
+5 58 3.2
+6 60 3.1
+7 67 3.8
+8 68 4.1
+9 71 4.3
+10 69 3.7

diff -r 000000000000 -r 9d189d08f2ad test-data/4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4.fasta Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,7 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
+CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
+CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG
+GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC
+CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC
+ATTGGTC

diff -r 000000000000 -r 9d189d08f2ad test-data/454.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/454.fasta Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,52 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
+CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
+CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG
+GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC
+CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC
+ATTGGTC
+>EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_
+GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATC
+ATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+>EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_
+TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAA
+TACGTCAAAAACATAACTTCATGATATCTTGCAGT
+>EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_
+GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGC
+CCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+>EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_
+GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGAT
+CATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+>EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_
+CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGA
+ACTTAGCCTTCCTTTNTTAACG
+>EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_
+TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+>EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_
+CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCA
+GGGCGTGCTGATGAAGTTCAAAT
+>EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_
+AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAA
+CGCGGTAAA
+>EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_
+AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACC
+GCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGT
+TCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGG
+GCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+>EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_
+CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCA
+GGGCGTGCTGATGAAGTTCAAAT
+>EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_
+AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+>EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_
+GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+>EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_
+TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGAC
+TTCC
+>EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_
+AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+>EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_
+CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+>EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_
+TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCG
+CCCAGTTGCCCTGACTTC

diff -r 000000000000 -r 9d189d08f2ad test-data/a.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a.tab Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,15 @@
+CHR SNP BP A1 TEST NMISS BETA STAT P
+1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161
+1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05
+1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05
+1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05
+1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05
+1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233
+1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05
+1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05
+1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982
+1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826
+1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05
+1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339
+1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05
+1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05

diff -r 000000000000 -r 9d189d08f2ad test-data/fasta_to_tabular_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_to_tabular_out1.tabular Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,18 @@
+EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC
+EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_ GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_ TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAATACGTCAAAAACATAACTTCATGATATCTTGCAGT
+EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_ GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGCCCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_ GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_ CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGAACTTAGCCTTCCTTTNTTAACG
+EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_ TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_ AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAACGCGGTAAA
+EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_ AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGGGCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_ AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_ GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_ TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGACTTCC
+EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_ AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_ CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_ TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCGCCCAGTTGCCCTGACTTC

diff -r 000000000000 -r 9d189d08f2ad test-data/fasta_to_tabular_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_to_tabular_out2.tabular Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,2 @@
+EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC

diff -r 000000000000 -r 9d189d08f2ad test-data/fasta_to_tabular_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_to_tabular_out3.tabular Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,18 @@
+EYKX4VC01B65GS CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01BNCSP CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC
+EYKX4VC01CD9FT GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01B8FW0 TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAATACGTCAAAAACATAACTTCATGATATCTTGCAGT
+EYKX4VC01BCGYW GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGCCCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+EYKX4VC01AZXC6 GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01CATH5 CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGAACTTAGCCTTCCTTTNTTAACG
+EYKX4VC01BCEIV TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+EYKX4VC01BWERM CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01BT2O7 AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAACGCGGTAAA
+EYKX4VC01BO0UO AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGGGCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+EYKX4VC01CBCPK CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B474S AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+EYKX4VC01BB4QL GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+EYKX4VC01BJ37M TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGACTTCC
+EYKX4VC01BV9R8 AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+EYKX4VC01CEPP8 CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+EYKX4VC01BTLME TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCGCCCAGTTGCCCTGACTTC

diff -r 000000000000 -r 9d189d08f2ad test-data/fasta_to_tabular_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_to_tabular_out4.tabular Mon May 19 12:34:27 2014 -0400

diff -r 000000000000 -r 9d189d08f2ad test-data/fasta_to_tabular_out5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_to_tabular_out5.tabular Mon May 19 12:34:27 2014 -0400

diff -r 000000000000 -r 9d189d08f2ad test-data/fasta_to_tabular_out6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_to_tabular_out6.tabular Mon May 19 12:34:27 2014 -0400

@@ -0,0 +1,18 @@
+EYKX4VC01B length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01B length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC
+EYKX4VC01C length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_ GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01B length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_ TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAATACGTCAAAAACATAACTTCATGATATCTTGCAGT
+EYKX4VC01B length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_ GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGCCCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+EYKX4VC01A length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_ GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01C length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_ CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGAACTTAGCCTTCCTTTNTTAACG
+EYKX4VC01B length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_ TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+EYKX4VC01B length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_ AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAACGCGGTAAA
+EYKX4VC01B length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_ AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGGGCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+EYKX4VC01C length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_ AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+EYKX4VC01B length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_ GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+EYKX4VC01B length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_ TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGACTTCC
+EYKX4VC01B length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_ AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+EYKX4VC01C length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_ CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+EYKX4VC01B length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_ TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCGCCCAGTTGCCCTGACTTC