Repository 'fasta_compute_length'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length

Changeset 2:de2db1bdfbf8 (2015-11-11)
Previous changeset 1:d8cc2c8eef14 (2015-07-21) Next changeset 3:2051602a5f97 (2019-09-11)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
modified:
fasta_compute_length.py
fasta_compute_length.xml
added:
test-data/454.fasta
test-data/extract_genomic_dna_out1.fasta
test-data/fasta_tool_compute_length_1.out
test-data/fasta_tool_compute_length_2.out
test-data/fasta_tool_compute_length_3.out
b
diff -r d8cc2c8eef14 -r de2db1bdfbf8 fasta_compute_length.py
--- a/fasta_compute_length.py Tue Jul 21 14:18:55 2015 -0400
+++ b/fasta_compute_length.py Wed Nov 11 12:13:18 2015 -0500
[
@@ -6,4 +6,4 @@
 import sys
 from utils.fasta_to_len import compute_fasta_length
 
-compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], False )
\ No newline at end of file
+compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4] == 'id_only' )
b
diff -r d8cc2c8eef14 -r de2db1bdfbf8 fasta_compute_length.xml
--- a/fasta_compute_length.xml Tue Jul 21 14:18:55 2015 -0400
+++ b/fasta_compute_length.xml Wed Nov 11 12:13:18 2015 -0500
b
@@ -1,51 +1,78 @@
-<tool id="fasta_compute_length" name="Compute sequence length" version="1.0.0">
- <description></description>
- <command interpreter="python">fasta_compute_length.py $input $output $keep_first</command>
- <inputs>
- <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
- <param name="keep_first" type="integer" size="5" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
- </inputs>
- <outputs>
- <data name="output" format="tabular"/>
- </outputs>
- <tests>
- <test>
- <param name="input" value="454.fasta" />
- <param name="keep_first" value="0"/>
- <output name="output" file="fasta_tool_compute_length_1.out" />
- </test>
-
- <test>
- <param name="input" value="extract_genomic_dna_out1.fasta" />
- <param name="keep_first" value="0"/>
- <output name="output" file="fasta_tool_compute_length_2.out" />
- </test>
-
- <test>
- <param name="input" value="454.fasta" />
- <param name="keep_first" value="14"/>
- <output name="output" file="fasta_tool_compute_length_3.out" />
- </test>
- </tests>
- <help>
+<tool id="fasta_compute_length" name="Compute sequence length" version="1.0.1">
+    <description></description>
+    <command interpreter="python">fasta_compute_length.py $input $output $keep_first $keep_first_word</command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
+        <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
+        <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
+            selected="false" label="Strip fasta description from header?"
+            help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
+
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="454.fasta" />
+            <param name="keep_first" value="0"/>
+            <param name="keep_first_word" value="id_and_desc" />
+            <output name="output" file="fasta_tool_compute_length_1.out" />
+        </test>
+
+        <test>
+            <param name="input" value="extract_genomic_dna_out1.fasta" />
+            <param name="keep_first" value="0"/>
+            <param name="keep_first_word" value="id_and_desc" />
+            <output name="output" file="fasta_tool_compute_length_2.out" />
+        </test>
+
+        <test>
+            <param name="input" value="454.fasta" />
+            <param name="keep_first" value="14"/>
+            <param name="keep_first_word" value="id_and_desc" />
+            <output name="output" file="fasta_tool_compute_length_3.out" />
+        </test>
+    </tests>
+    <help>
 
 **What it does**
 
-This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry. 
+This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
 
------
+-----
 
 **Example**
 
 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
 
-    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_     TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG     TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG     &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_     AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
+    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
+    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
+    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
+    &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
+    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
 
 Running this tool while setting **How many characters to keep?** to **14** will produce this::
-
- EYKX4VC02EQLO5  108
- EYKX4VC02D4GS2  60
+
+    EYKX4VC02EQLO5  108
+    EYKX4VC02D4GS2   60
+
+However, if your IDs are not all the same length, you may wish to just keep the fasta ID, and not the description::
+
+    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
+    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
+    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
+    &gt;EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
+    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
+
+Running this tool with **Strip fasta description from header** set to **True** and **How many characters to keep?** set to **0** will produce::
+
+    EYKX4VC02EQLO5  108
+    EYKX4VC     60
 
 
- </help>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq281</citation>
+    </citations>
 </tool>
b
diff -r d8cc2c8eef14 -r de2db1bdfbf8 test-data/454.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/454.fasta Wed Nov 11 12:13:18 2015 -0500
b
@@ -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
b
diff -r d8cc2c8eef14 -r de2db1bdfbf8 test-data/extract_genomic_dna_out1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_genomic_dna_out1.fasta Wed Nov 11 12:13:18 2015 -0500
b
b'@@ -0,0 +1,456 @@\n+>hg17_chr1_147962192_147962580_-\n+ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG\n+GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT\n+GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT\n+CCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGG\n+ACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATT\n+CGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGC\n+CTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTG\n+GGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA\n+>hg17_chr1_147984545_147984630_+\n+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT\n+TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+>hg17_chr1_148078400_148078582_-\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAA\n+GAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGA\n+GCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACG\n+GCTTCCAGTACCTCACCAACGGCATCATGTGA\n+>hg17_chr1_148185136_148185276_+\n+ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC\n+CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC\n+CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA\n+>hg17_chr10_55251623_55253124_-\n+TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCT\n+CAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACT\n+ATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAA\n+ACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAA\n+GTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAAT\n+TCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAAT\n+ACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGC\n+TGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCA\n+AATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAA\n+AGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCA\n+ATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATA\n+AGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCT\n+CTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCA\n+CTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTC\n+ATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTG\n+TGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTAC\n+CTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAAC\n+ATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctcc\n+ttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctc\n+ctttttctcttttttgtcctcctccctctcctccttctatccctcttcct\n+cttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCC\n+AACAccacctcttctacctccatttccaactcctcttcctccaccacctc\n+cttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAG\n+TGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGA\n+GAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAA\n+CAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTA\n+GCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAA\n+CTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAG\n+TAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAAT\n+ATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTA\n+A\n+>hg17_chr11_116124407_116124501_-\n+ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGG\n+CAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA\n+>hg17_chr11_116206508_116206563_+\n+ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTC\n+TGCCC\n+>hg17_chr11_116211733_116212337_-\n+CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGC\n+TGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAA\n+AAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGT\n+GAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGG\n+AGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTC\n+CAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCC\n+ACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGC\n+GCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCG\n+CGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCA\n+CGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCG\n+CGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAG\n+GTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCA\n+GTGA\n+>hg17_chr11_1812377_1812407_+\n+ATGCTCCACCTGCATGGCTGGCAAACCATG\n+>hg17_chr12_38440094_38440321_-\n+GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATC\n+TATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATC\n+ACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAG\n+GGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCT\n+GACAATGATGCTTCTGATGTGGAATAA\n+>hg17_chr13_112381694_112381953_+\n+ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTA\n+CCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGA\n+AGATGGACCCGGCAGGTCTGGAGGGAGGCCCCCGTGATGAATCCCGTGAT\n+GAG'..b'TGAACACCTAGAAAAACCTAACAAATAG\n+>hg17_chr8_118881131_118881317_-\n+ACTTCTCGGGCTTCCCGTTGGGCTGACCCTGACCACTTTGCCCAGCGACA\n+GAGCTGCATGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCC\n+ACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATT\n+TTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA\n+>hg17_chr9_128764156_128764189_+\n+ATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG\n+>hg17_chr9_128787519_128789136_-\n+ATGACCCGAGAGTGCCCATCTCCGGCCCCGGGGCCTGGGGCTCCGCTGAG\n+TGGATCGGTGCTGGCAGAGGCGGCAGTAGTGTTTGCAGTGGTGCTGAGCA\n+TCCACGCAACCGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCA\n+GTGCAGGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGG\n+AAGCGCCGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTATTGCCCG\n+CCTCCATGGTCATGCCTTTGCTTGGACTAGTCATGAAGGAGCGGTGCCAG\n+ACTGCTGGGAACCCGTTCTTTGAGCGTTTTGGCATTGTGGTGGCAGCCAC\n+TGGCATGGCAGTGGCCCTCTTCTCATCAGTGTTGGCGCTCGGCATCACTC\n+GCCCAGTGCCAACCAACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTT\n+ATCATTTATATCATGAAGCACTCGTTGAGCGTGGGGGAGGTGATCGAAGT\n+CCTGGAAGTCCTTCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACC\n+TGCTGCCCCGCTGCTTCACCCCTGGTGAGGCACTGCTGGTATTGGGTGGC\n+ATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGTGGA\n+AAGTCAGGGGGACCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGA\n+TGGTACTCATGGGCATTTTCTTCAGCACTCTGTTTGTCTTCATGGACTCA\n+GGCACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGAG\n+CCTTGGTGTGGTCCTACCCTGGCTGCACCGGCTCATCCGCAGGAATCCCC\n+TGCTCTGGCTTCTTCAGTTTCTCTTCCAGACAGACACCCGCATCTACCTC\n+CTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTA\n+CCAGAATGCCAAGCGGTCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCA\n+CCATCGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCA\n+GGTATCATCTTTGACCGGCCACTGCTCTATGTAGCCGCCACTGTATGCCT\n+GGCGGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCTT\n+TGGGTCACACTCTACGGAGCTTCCTGTCCCTTTTTCTGGATGAACGAGAC\n+AGTGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCT\n+TCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGAG\n+GAGCCAGGGCCCTCGTCCCCTATGCCGGTGTCCTGGCTGTGGGTGTGGGT\n+GATACTGTGGCCTCCATCTTCGGTAGCACCATGGGGGAGATCCGCTGGCC\n+TGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCGCAGA\n+TCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAAC\n+TACAGTTATGCTTGGATTTTGGGGTCCATCAGCACTGTGTCCCTCCTGGA\n+AGCATACACTACACAGATAGACAATCTCCTTCTGCCTCTCTACCTCCTGA\n+TATTGCTGATGGCCTAG\n+>hg17_chr9_128882427_128882523_+\n+ATGGCGTTCCGGAGGGCCGAGGGCACGTCTATGATCCAGGCCCTGGCCAT\n+GACGGTGGCCGAGATCCCCGTGTTCCTGTACACGACGTTTGGGCAG\n+>hg17_chr9_128937229_128937445_-\n+GTCCCTGCCAAGACAGACTGTGTCATGTTCTTCGGGCCCGTGGTCCCCGA\n+CGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCC\n+TGTCGGCCTACAACAGCTGCGCGGAGACCAACGCCGCCCGCCTGGCGCAT\n+TACCTGGAGAAGGCGCTCCTGGACATGCGTGCCCTGCTGCAGAGCCACCC\n+CCGGGCCAAGCTCTGA\n+>hg17_chrX_122745047_122745924_+\n+ATGACTTTTAACAGTTTTGAAGGATCTAAAACTTGTGTACCTGCAGACAT\n+CAATAAGGAAGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTG\n+CTAATTTTCCAAGTGGTAGTCCTGTTTCAGCATCAACACTGGCACGAGCA\n+GGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCA\n+TGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACA\n+GGAAAGTATCCCCAAATTGCAGATTTATCAACGGCTTTTATCTTGAAAAT\n+AGTGCCACGCAGTCTACAAATTCTGGTATCCAGAATGGTCAGTACAAAGT\n+TGAAAACTATCTGGGAAGCAGAGATCATTTTGCCTTAGACAGGCCATCTG\n+AGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCA\n+GACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATT\n+AAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGT\n+TAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGC\n+TTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTG\n+GTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGA\n+ATCTTAATATTCGAAGTGAATCTGATGCTGTGAGTTCTGATAGGAATTTC\n+CCAAATTCAACAAATCTTCCAAGAAATCCATCCATGGCAGATTATGAAGC\n+ACGGATCTTTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGC\n+TTGCAAGAGCTGGATTTTATGCTTTAG\n+>hg17_chrX_152648964_152649196_-\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGG\n+ACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGC\n+GTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGG\n+CAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACTT\n+CCCCCATCAACCCTGCCGTGGCCCTAGAATAG\n+>hg17_chrX_152691446_152691471_+\n+ATGCTCATGGCGTCCACCACTTCCG\n+>hg17_chrX_152694029_152694263_-\n+GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC\n+CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG\n+GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA\n+GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC\n+CCAGGGCCTAGACACGACCCCCAAGCCACACTGA\n'
b
diff -r d8cc2c8eef14 -r de2db1bdfbf8 test-data/fasta_tool_compute_length_1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_tool_compute_length_1.out Wed Nov 11 12:13:18 2015 -0500
b
@@ -0,0 +1,18 @@
+EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ 54
+EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ 187
+EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_ 115
+EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_ 95
+EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_ 115
+EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_ 116
+EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_ 82
+EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_ 47
+EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_ 83
+EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_ 69
+EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_ 222
+EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_ 83
+EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_ 54
+EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_ 57
+EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_ 64
+EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_ 54
+EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_ 60
+EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_ 78
b
diff -r d8cc2c8eef14 -r de2db1bdfbf8 test-data/fasta_tool_compute_length_2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_tool_compute_length_2.out Wed Nov 11 12:13:18 2015 -0500
b
@@ -0,0 +1,65 @@
+hg17_chr1_147962192_147962580_- 388
+hg17_chr1_147984545_147984630_+ 85
+hg17_chr1_148078400_148078582_- 182
+hg17_chr1_148185136_148185276_+ 140
+hg17_chr10_55251623_55253124_- 1501
+hg17_chr11_116124407_116124501_- 94
+hg17_chr11_116206508_116206563_+ 55
+hg17_chr11_116211733_116212337_- 604
+hg17_chr11_1812377_1812407_+ 30
+hg17_chr12_38440094_38440321_- 227
+hg17_chr13_112381694_112381953_+ 259
+hg17_chr14_98710240_98712285_- 2045
+hg17_chr15_41486872_41487060_- 188
+hg17_chr15_41673708_41673857_+ 149
+hg17_chr15_41679161_41679250_- 89
+hg17_chr15_41826029_41826196_+ 167
+hg17_chr16_142908_143003_+ 95
+hg17_chr16_179963_180135_- 172
+hg17_chr16_244413_244681_+ 268
+hg17_chr16_259268_259383_- 115
+hg17_chr18_23786114_23786321_- 207
+hg17_chr18_59406881_59407046_+ 165
+hg17_chr18_59455932_59456337_- 405
+hg17_chr18_59600586_59600754_+ 168
+hg17_chr19_59068595_59069564_+ 969
+hg17_chr19_59236026_59236146_- 120
+hg17_chr19_59297998_59298008_+ 10
+hg17_chr19_59302168_59302288_- 120
+hg17_chr2_118288583_118288668_+ 85
+hg17_chr2_118394148_118394202_- 54
+hg17_chr2_220190202_220190242_+ 40
+hg17_chr2_220229609_220230869_- 1260
+hg17_chr20_33330413_33330423_- 10
+hg17_chr20_33513606_33513792_+ 186
+hg17_chr20_33579500_33579527_- 27
+hg17_chr20_33593260_33593348_+ 88
+hg17_chr21_32707032_32707192_+ 160
+hg17_chr21_32869641_32870022_- 381
+hg17_chr21_33321040_33322012_+ 972
+hg17_chr21_33744994_33745040_- 46
+hg17_chr22_30120223_30120265_+ 42
+hg17_chr22_30160419_30160661_- 242
+hg17_chr22_30665273_30665360_+ 87
+hg17_chr22_30939054_30939266_- 212
+hg17_chr5_131424298_131424460_+ 162
+hg17_chr5_131556601_131556672_- 71
+hg17_chr5_131621326_131621419_+ 93
+hg17_chr5_131847541_131847666_- 125
+hg17_chr6_108299600_108299744_- 144
+hg17_chr6_108594662_108594687_+ 25
+hg17_chr6_108640045_108640151_- 106
+hg17_chr6_108722976_108723115_+ 139
+hg17_chr7_113660517_113660685_+ 168
+hg17_chr7_116512159_116512389_- 230
+hg17_chr7_116714099_116714152_+ 53
+hg17_chr7_116945541_116945787_- 246
+hg17_chr8_118881131_118881317_- 186
+hg17_chr9_128764156_128764189_+ 33
+hg17_chr9_128787519_128789136_- 1617
+hg17_chr9_128882427_128882523_+ 96
+hg17_chr9_128937229_128937445_- 216
+hg17_chrX_122745047_122745924_+ 877
+hg17_chrX_152648964_152649196_- 232
+hg17_chrX_152691446_152691471_+ 25
+hg17_chrX_152694029_152694263_- 234
b
diff -r d8cc2c8eef14 -r de2db1bdfbf8 test-data/fasta_tool_compute_length_3.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_tool_compute_length_3.out Wed Nov 11 12:13:18 2015 -0500
b
@@ -0,0 +1,18 @@
+EYKX4VC01B65GS 54
+EYKX4VC01BNCSP 187
+EYKX4VC01CD9FT 115
+EYKX4VC01B8FW0 95
+EYKX4VC01BCGYW 115
+EYKX4VC01AZXC6 116
+EYKX4VC01CATH5 82
+EYKX4VC01BCEIV 47
+EYKX4VC01BWERM 83
+EYKX4VC01BT2O7 69
+EYKX4VC01BO0UO 222
+EYKX4VC01CBCPK 83
+EYKX4VC01B474S 54
+EYKX4VC01BB4QL 57
+EYKX4VC01BJ37M 64
+EYKX4VC01BV9R8 54
+EYKX4VC01CEPP8 60
+EYKX4VC01BTLME 78