# HG changeset patch
# User galaxyp
# Date 1432977054 14400
# Node ID e3a05965ca0cfbf351c0f834c139c9f9853efcbc

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv commit d8b91dbe304c99bb5a46da25a5820005cde105c5-dirty

diff -r 000000000000 -r e3a05965ca0c spectrast2tsv.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast2tsv.xml	Sat May 30 05:10:54 2015 -0400
@@ -0,0 +1,137 @@
+<tool id="gp_spectrast2tsv" name="Spectrast to TSV" version="0.1.0">
+    <description>Filter from spectraST files to swath input files</description>
+    <requirements>
+        <requirement type="package" version="0.3.2">msproteomicstools</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command>
+<![CDATA[
+        #set $input_files = list()
+        #for $counter,$filename in enumerate($inputs):
+            #set $tmp = "./%s.sptxt" % $counter;
+            ln -s "$filename" "$tmp";
+            #silent $input_files.append($tmp)
+        #end for
+
+        spectrast2tsv.py
+            #if $fasta:
+                -f ${fasta}
+            #end if
+            -a ${output}
+            -q "\${GALAXY_SLOTS:-24}"
+            $d
+            $e
+            -n $n
+            -o $o
+            #if $mass_modifs:
+                -g "#echo ','.join([$param.mass_modif for $param in $mass_modifs])#"
+            #end if
+            -p $p
+            #if $ion_series:
+                -s "#echo ','.join([$param.ion for $param in $ion_series])#"
+            #end if
+            -t $time_scale
+            #if $labeling_file:
+                -i $labeling_file
+            #end if
+            -k $oformat
+            #if $l_lower and $l_upper:
+                -l "$l_lower,$l_upper"
+            #end if
+            #if $mods_file:
+                -m $mods_file
+            #end if
+            #if $u:
+                -u $u
+            #end if
+            #if $swaths_file:
+                -w $swaths_file
+            #end if
+            -x "$x"
+            -y $y
+            #echo '" "'.join($input_files)#
+]]>
+    </command>
+    <inputs>
+        <param name="inputs" format="txt" type="data" multiple="True" label="Spectrast files" help="" />
+        <param name="mods_file" format="txt" type="data" optional="True" label="File with the modifications delta mass" help="(-m)" />
+        <param name="labeling_file" format="txt" type="data" optional="True"
+            label="File containing the amino acid isotopic labeling mass shifts" help="If this option is used, heavy transitions will be generated. (-i)" />
+        <param name="fasta" format="fasta" type="data" optional="True" label="Fasta file to relate peptides to their proteins" help="" />
+        <param name="swaths_file" format="txt" type="data" optional="True"
+            label="File containing the swath ranges" help="This is used to remove transitions with Q3 falling in the swath mass range. (-w)" />
+        <param name="d" type="boolean" truevalue="-d" falsevalue="" checked="False"
+            label="Remove duplicate masses from labeling" help="(-d)" />
+        <param name="e" type="boolean" truevalue="-e" falsevalue="" checked="False"
+            label="Use theoretical mass" help="(-e)" />
+        <param name="o" type="integer" value="3" label="Min number of reported ions per peptide/z" help="(-o)" />
+        <param name="n" type="integer" value="20" label="Max number of reported ions per peptide/z" help="(-n)" />
+
+        <param name="l_lower" type="integer" optional="True" value="" label="Lower mass limit of fragment ions"
+            help="You need to specify the upper limit as well, if you specify a lower limit. (-l)" />
+        <param name="l_upper" type="integer" optional="True" value="" label="Upper mass limit of fragment ions"
+            help="You need to specify the lower limit as well, if you specify a upper limit. (-l)" />
+
+        <param name="u" type="integer" optional="True" value="" label="Use this unimod code as a switching modification" help="Useful for phosphorylations. (-u)" />
+
+        <repeat name="mass_modifs" title="List of allowed fragment mass modifications"
+            help="Useful for phosphorylation and neutral losses (-g)">
+            <param name="mass_modif" type="float" value="" label="Fragment mass modifications" />
+        </repeat>
+        <param name="p" type="float" value="0.05" label="Maximum error allowed at the annotation of a fragment ion" help="(-p)" />
+
+        <repeat name="ion_series" title="List of ion series to be used"
+            help="(-s)">
+            <param name="ion" type="text" value="" label="Ion series" />
+        </repeat>
+        <param name="time_scale" type="select" label="Time scale">
+            <option value="minutes">Minutes</option>
+            <option value="seconds" selected="True">Seconds</option>
+        </param>
+        <param name="oformat" type="select" label="Output format">
+            <option value="openswath">OpenSwath</option>
+            <option value="peakview" selected="True">Peakview</option>
+        </param>
+        <param name="x" type="text" value="1,2" label="Fragment ion charge states allowed" help="(-x)"/>
+        <param name="y" type="integer" value="2"
+            label="When using a switching modification, this determines the UIS order to be calculated"
+            help="If -1 is set, all transitions for each isoform will be reported. (-y)" />
+
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="testlib.sptxt" ftype="txt" />
+            <param name="time_scale" value="minutes" />
+            <param name="oformat" value="openswath" />
+            <output name="output" file="spectrast2tsv_1_openswath_out.csv" ftype="tabular" />
+        </test>
+        <test>
+            <param name="inputs" value="testlib.sptxt" ftype="txt" />
+            <param name="labeling_file" value="labeling_file.txt" ftype="txt" />
+            <param name="time_scale" value="minutes" />
+            <param name="oformat" value="openswath" />
+            <output name="output" file="spectrast2tsv_2_openswath_out.csv" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Filter from spectraST files to swath input files.
+
+
+]]>
+    </help>
+    <citations>
+    </citations>
+</tool>
diff -r 000000000000 -r e3a05965ca0c test-data/labeling_file.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/labeling_file.txt	Sat May 30 05:10:54 2015 -0400
@@ -0,0 +1,4 @@
+# Labeling file, contains AA and mass shift
+K	8.014199	13C(6) 15N(2) Silac label
+R	10.008269	13C(6) 15N(4) Silac label
+
diff -r 000000000000 -r e3a05965ca0c test-data/spectrast2tsv_1_openswath_out.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spectrast2tsv_1_openswath_out.csv	Sat May 30 05:10:54 2015 -0400
@@ -0,0 +1,41 @@
+PrecursorMz	ProductMz	Tr_recalibrated	transition_name	CE	LibraryIntensity	transition_group_id	decoy	PeptideSequence	ProteinName	Annotation	FullUniModPeptideName	PrecursorCharge	PeptideGroupLabel	UniprotID	FragmentType	FragmentCharge	FragmentSeriesNumber	LabelType
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+1080.5866	1547.7921	103.50166666666668	44_y16_1_FAIPAINVTSSSTAVAALEAAR_2	-1	5462.2	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y16/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	16	light
+1080.5866	1233.6333	103.50166666666668	33_y13_1_FAIPAINVTSSSTAVAALEAAR_2	-1	4287.7	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y13/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	13	light
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+1080.5866	701.3857	103.50166666666668	20_y7_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2333.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y7/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	7	light
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+1080.5866	914.9837	103.50166666666668	25_y19_2_FAIPAINVTSSSTAVAALEAAR_2	-1	2305.2	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y19^2/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	2	19	light
+1080.5866	317.1925	103.50166666666668	8_y3_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2146.7	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y3/-0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	3	light
+1080.5866	86.0974	103.50166666666668	2_immonium0_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2116.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	IIA/0.00,IIA/0.00,IIA/0.00,IIA/0.00,ILA/0.00,ILA/0.00,INA/-0.96,INA/-0.96	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	immonium	1	0	light
+1080.5866	1059.5675	103.50166666666668	29_y11_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1859.7	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y11/-0.01,p-44^2/0.98	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	11	light
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+1080.5866	175.119	103.50166666666668	4_y1_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1740.9	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y1/0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	1	light
+1080.5866	191.1182	103.50166666666668	5_a2_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1561.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	a2/0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	a	1	2	light
+1080.5866	972.5362	103.50166666666668	28_y10_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1301.0	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y10/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	10	light
+1080.5866	871.4911	103.50166666666668	24_y9_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1283.8	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y9/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	9	light
+1080.5866	630.3522	103.50166666666668	19_y6_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1209.8	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y6/-0.00,a13^2/-0.99	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	6	light
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+1080.5866	446.2322	103.50166666666668	12_y4_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1084.8	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y4/-0.00,b9-35^2/-0.52	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	4	light
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+592.8115	557.2613	67.73333333333333	67_y10_2_AAELDVLNDPK_2	-1	598.7	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y10^2/-0.03	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	2	10	light
+592.8115	359.1833	67.73333333333333	61_y3_1_AAELDVLNDPK_2	-1	588.5	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y3/-0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	3	light
diff -r 000000000000 -r e3a05965ca0c test-data/spectrast2tsv_2_openswath_out.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spectrast2tsv_2_openswath_out.csv	Sat May 30 05:10:54 2015 -0400
@@ -0,0 +1,76 @@
+PrecursorMz	ProductMz	Tr_recalibrated	transition_name	CE	LibraryIntensity	transition_group_id	decoy	PeptideSequence	ProteinName	Annotation	FullUniModPeptideName	PrecursorCharge	PeptideGroupLabel	UniprotID	FragmentType	FragmentCharge	FragmentSeriesNumber	LabelType
+1080.5866	1334.6793	103.50166666666668	36_y14_1_FAIPAINVTSSSTAVAALEAAR_2	-1	10000.0	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y14/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	14	light
+1085.5907345	1344.687569	103.50166666666668	36_y14_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	10000.0	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y14/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	14	heavy
+1080.5866	1547.7921	103.50166666666668	44_y16_1_FAIPAINVTSSSTAVAALEAAR_2	-1	5462.2	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y16/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	16	light
+1085.5907345	1557.8003689999998	103.50166666666668	44_y16_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	5462.2	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y16/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	16	heavy
+1080.5866	1233.6333	103.50166666666668	33_y13_1_FAIPAINVTSSSTAVAALEAAR_2	-1	4287.7	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y13/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	13	light
+1085.5907345	1243.641569	103.50166666666668	33_y13_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	4287.7	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y13/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	13	heavy
+1080.5866	219.1128	103.50166666666668	6_b2_1_FAIPAINVTSSSTAVAALEAAR_2	-1	3759.1	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	b2/-0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	b	1	2	light
+1085.5907345	219.1128	103.50166666666668	6_b2_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	3759.1	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	b2/-0.00	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	b	1	2	heavy
+1080.5866	1146.6016	103.50166666666668	31_y12_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2441.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y12/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	12	light
+1085.5907345	1156.609869	103.50166666666668	31_y12_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	2441.6	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y12/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	12	heavy
+1080.5866	701.3857	103.50166666666668	20_y7_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2333.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y7/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	7	light
+1085.5907345	711.3939690000001	103.50166666666668	20_y7_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	2333.6	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y7/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	7	heavy
+1080.5866	500.283	103.50166666666668	15_b5_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2313.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	b5/-0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	b	1	5	light
+1085.5907345	500.283	103.50166666666668	15_b5_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	2313.6	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	b5/-0.00	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	b	1	5	heavy
+1080.5866	914.9837	103.50166666666668	25_y19_2_FAIPAINVTSSSTAVAALEAAR_2	-1	2305.2	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y19^2/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	2	19	light
+1085.5907345	919.9878345	103.50166666666668	25_y19_2_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	2305.2	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y19^2/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	2	19	heavy
+1080.5866	317.1925	103.50166666666668	8_y3_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2146.7	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y3/-0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	3	light
+1085.5907345	327.200769	103.50166666666668	8_y3_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	2146.7	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y3/-0.00	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	3	heavy
+1080.5866	86.0974	103.50166666666668	2_immonium0_1_FAIPAINVTSSSTAVAALEAAR_2	-1	2116.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	IIA/0.00,IIA/0.00,IIA/0.00,IIA/0.00,ILA/0.00,ILA/0.00,INA/-0.96,INA/-0.96	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	immonium	1	0	light
+1080.5866	1059.5675	103.50166666666668	29_y11_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1859.7	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y11/-0.01,p-44^2/0.98	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	11	light
+1085.5907345	1069.575769	103.50166666666668	29_y11_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1859.7	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y11/-0.01,p-44^2/0.98	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	11	heavy
+1080.5866	1828.9618	103.50166666666668	49_y19_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1744.1	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y19/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	19	light
+1085.5907345	1838.970069	103.50166666666668	49_y19_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1744.1	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y19/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	19	heavy
+1080.5866	175.119	103.50166666666668	4_y1_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1740.9	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y1/0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	1	light
+1085.5907345	185.127269	103.50166666666668	4_y1_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1740.9	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y1/0.00	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	1	heavy
+1080.5866	191.1182	103.50166666666668	5_a2_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1561.6	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	a2/0.00	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	a	1	2	light
+1080.5866	972.5362	103.50166666666668	28_y10_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1301.0	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y10/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	10	light
+1085.5907345	982.544469	103.50166666666668	28_y10_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1301.0	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y10/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	10	heavy
+1080.5866	871.4911	103.50166666666668	24_y9_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1283.8	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y9/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	9	light
+1085.5907345	881.499369	103.50166666666668	24_y9_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1283.8	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y9/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	9	heavy
+1080.5866	630.3522	103.50166666666668	19_y6_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1209.8	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y6/-0.00,a13^2/-0.99	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	6	light
+1085.5907345	640.3604690000001	103.50166666666668	19_y6_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1209.8	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y6/-0.00,a13^2/-0.99	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	6	heavy
+1080.5866	800.4553	103.50166666666668	22_y8_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1209.7	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y8/-0.01,b17^2/-0.98	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	8	light
+1085.5907345	810.463569	103.50166666666668	22_y8_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1209.7	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y8/-0.01,b17^2/-0.98	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	8	heavy
+1080.5866	446.2322	103.50166666666668	12_y4_1_FAIPAINVTSSSTAVAALEAAR_2	-1	1084.8	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y4/-0.00,b9-35^2/-0.52	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	4	light
+1085.5907345	456.24046899999996	103.50166666666668	12_y4_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	1084.8	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y4/-0.00,b9-35^2/-0.52	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	4	heavy
+1080.5866	1660.8772	103.50166666666668	47_y17_1_FAIPAINVTSSSTAVAALEAAR_2	-1	892.9	1_FAIPAINVTSSSTAVAALEAAR_2	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y17/-0.01	FAIPAINVTSSSTAVAALEAAR	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	17	light
+1085.5907345	1670.8854689999998	103.50166666666668	47_y17_1_FAIPAINVTSSSTAVAALEAAR_2heavy	-1	892.9	1_FAIPAINVTSSSTAVAALEAAR_2heavy	0	FAIPAINVTSSSTAVAALEAAR	1/YKL060C	y17/-0.01	FAIPAINVTSSSTAVAALEAAR(13C(6) 15N(4) Silac label)	2	1_FAIPAINVTSSSTAVAALEAAR_2	1/YKL060C	y	1	17	heavy
+592.8115	244.166	67.73333333333333	58_y2_1_AAELDVLNDPK_2	-1	10000.0	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y2/0.00,a3/0.04	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	2	light
+596.8185995	252.180199	67.73333333333333	58_y2_1_AAELDVLNDPK_2heavy	-1	10000.0	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y2/0.00,a3/0.04	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	2	heavy
+592.8115	272.1222	67.73333333333333	59_b3_1_AAELDVLNDPK_2	-1	7172.4	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	b3/-0.00,y5-44^2/0.45,y5-45^2/0.97	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	3	light
+596.8185995	272.1222	67.73333333333333	59_b3_1_AAELDVLNDPK_2heavy	-1	7172.4	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	b3/-0.00,y5-44^2/0.45,y5-45^2/0.97	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	3	heavy
+592.8115	586.325	67.73333333333333	69_y5_1_AAELDVLNDPK_2	-1	5992.7	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y5/0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	5	light
+596.8185995	594.339199	67.73333333333333	69_y5_1_AAELDVLNDPK_2heavy	-1	5992.7	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y5/0.01	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	5	heavy
+592.8115	800.3955	67.73333333333333	74_y7_1_AAELDVLNDPK_2	-1	5532.3	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y7/-0.02	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	7	light
+596.8185995	808.4096989999999	67.73333333333333	74_y7_1_AAELDVLNDPK_2heavy	-1	5532.3	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y7/-0.02	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	7	heavy
+592.8115	143.0799	67.73333333333333	56_b2_1_AAELDVLNDPK_2	-1	5273.3	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	b2/-0.00	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	2	light
+596.8185995	143.0799	67.73333333333333	56_b2_1_AAELDVLNDPK_2heavy	-1	5273.3	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	b2/-0.00	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	2	heavy
+592.8115	913.4868	67.73333333333333	75_y8_1_AAELDVLNDPK_2	-1	3314.2	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y8/-0.01,a9/0.02	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	8	light
+596.8185995	921.500999	67.73333333333333	75_y8_1_AAELDVLNDPK_2heavy	-1	3314.2	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y8/-0.01,a9/0.02	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	8	heavy
+592.8115	473.2253	67.73333333333333	64_y4_1_AAELDVLNDPK_2	-1	1982.7	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y4/-0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	4	light
+596.8185995	481.239499	67.73333333333333	64_y4_1_AAELDVLNDPK_2heavy	-1	1982.7	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y4/-0.01	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	4	heavy
+592.8115	685.3942	67.73333333333333	73_y6_1_AAELDVLNDPK_2	-1	1967.0	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y6/0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	6	light
+596.8185995	693.4083989999999	67.73333333333333	73_y6_1_AAELDVLNDPK_2heavy	-1	1967.0	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y6/0.01	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	6	heavy
+592.8115	592.8243	67.73333333333333	71_p0_2_AAELDVLNDPK_2	-1	1925.2	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	p^2/0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	p	2	0	light
+592.8115	115.0858	67.73333333333333	55_a2_1_AAELDVLNDPK_2	-1	1917.0	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	a2/-0.00,b3-44^2/0.52	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	a	1	2	light
+592.8115	1042.535	67.73333333333333	78_y9_1_AAELDVLNDPK_2	-1	1265.4	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y9/-0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	9	light
+596.8185995	1050.549199	67.73333333333333	78_y9_1_AAELDVLNDPK_2heavy	-1	1265.4	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y9/-0.01	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	9	heavy
+592.8115	86.0978	67.73333333333333	53_immonium0_1_AAELDVLNDPK_2	-1	1028.0	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	ILA/0.00,ILA/0.00,ILA/0.00,ILA/0.00	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	immonium	1	0	light
+592.8115	72.0801	67.73333333333333	52_b1_1_AAELDVLNDPK_2	-1	891.7	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	b1/0.04,b2^2/0.04,IVA/-0.00,IVA/-0.00	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	1	light
+596.8185995	72.0801	67.73333333333333	52_b1_1_AAELDVLNDPK_2heavy	-1	891.7	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	b1/0.04,b2^2/0.04,IVA/-0.00,IVA/-0.00	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	1	heavy
+592.8115	385.2171	67.73333333333333	62_b4_1_AAELDVLNDPK_2	-1	852.7	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	b4/0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	4	light
+596.8185995	385.2171	67.73333333333333	62_b4_1_AAELDVLNDPK_2heavy	-1	852.7	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	b4/0.01	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	4	heavy
+592.8115	500.2331	67.73333333333333	65_b5_1_AAELDVLNDPK_2	-1	803.0	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	b5/-0.00,y9-44^2/0.45,y9-45^2/0.97	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	5	light
+596.8185995	500.2331	67.73333333333333	65_b5_1_AAELDVLNDPK_2heavy	-1	803.0	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	b5/-0.00,y9-44^2/0.45,y9-45^2/0.97	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	5	heavy
+592.8115	147.1098	67.73333333333333	57_y1_1_AAELDVLNDPK_2	-1	766.4	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y1/-0.00	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	1	light
+596.8185995	155.123999	67.73333333333333	57_y1_1_AAELDVLNDPK_2heavy	-1	766.4	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y1/-0.00	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	1	heavy
+592.8115	599.3251	67.73333333333333	72_b6_1_AAELDVLNDPK_2	-1	653.8	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	b6/0.02	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	6	light
+596.8185995	599.3251	67.73333333333333	72_b6_1_AAELDVLNDPK_2heavy	-1	653.8	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	b6/0.02	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	b	1	6	heavy
+592.8115	343.1639	67.73333333333333	60_y6_2_AAELDVLNDPK_2	-1	638.2	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y6^2/-0.03,a7^2/0.46	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	2	6	light
+596.8185995	347.1709995	67.73333333333333	60_y6_2_AAELDVLNDPK_2heavy	-1	638.2	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y6^2/-0.03,a7^2/0.46	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	2	6	heavy
+592.8115	557.2613	67.73333333333333	67_y10_2_AAELDVLNDPK_2	-1	598.7	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y10^2/-0.03	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	2	10	light
+596.8185995	561.2683995	67.73333333333333	67_y10_2_AAELDVLNDPK_2heavy	-1	598.7	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y10^2/-0.03	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	2	10	heavy
+592.8115	359.1833	67.73333333333333	61_y3_1_AAELDVLNDPK_2	-1	588.5	2_AAELDVLNDPK_2	0	AAELDVLNDPK	1/YPR041W	y3/-0.01	AAELDVLNDPK	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	3	light
+596.8185995	367.197499	67.73333333333333	61_y3_1_AAELDVLNDPK_2heavy	-1	588.5	2_AAELDVLNDPK_2heavy	0	AAELDVLNDPK	1/YPR041W	y3/-0.01	AAELDVLNDPK(13C(6) 15N(2) Silac label)	2	2_AAELDVLNDPK_2	1/YPR041W	y	1	3	heavy
diff -r 000000000000 -r e3a05965ca0c test-data/testlib.sptxt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testlib.sptxt	Sat May 30 05:10:54 2015 -0400
@@ -0,0 +1,324 @@
+### SequestConsensusFiltered.sptxt  (Text version of SequestConsensusFiltered.splib)
+### SpectraST (version 4.0, TPP v4.5 RAPTURE rev 1, Build 201111141620 (MinGW))
+### 
+### COMPILE FROM "z:/html/Sorcerer_Searches/1201_YeastPostDiauxic/SequestConsensusLib.splib" ; FILTER for Protein!~reverse_
+### > SequestConsensusLib.splib : COMPILE FROM "/mnt/u07/lgillet/html/Sorcerer_Searches/1201_YeastPostDiauxic/SequestConsensusLib2.splib"  [CONSENSUS;r=1;I=;_QUO=0.6;_XNR=100;_WGT=SN;_DIS=TRUE;_XPK=150;_XPU=300;_BDN=FALSE;_TBD=FALSE]
+### > > SequestConsensusLib2.splib : IMPORT FROM PepXML "/mnt/u07/lgillet/html/Sorcerer_Searches/1201_YeastPostDiauxic/interact-SequestAllCombined.pep.xml", (SEQUEST against "/IMSB/users/lgillet/html/databases/SGD_decoy.fasta" (AA); ) [P=0.7;n=;g=FALSE;o=FALSE;I=;_RNT=0;_RDR=100000;_DCN=0;_NAA=6;_NPK=10;_MDF=9999;_CEN=FALSE;_XAN=FALSE;_BRK=FALSE;_BRM=FALSE]
+### ===
+Name: FAIPAINVTSSSTAVAALEAAR/2
+LibID: 3829
+MW: 2161.1731
+PrecursorMZ: 1080.5866
+Status: Normal
+FullName: K.FAIPAINVTSSSTAVAALEAAR.D/2
+Comment: AvePrecursorMz=1081.2350 BestRawSpectrum=lgillet_L120122_003.21975.21975 BinaryFileOffset=24442137 CollisionEnergy=0.0 ConsFracAssignedPeaks=0.720 DeltaCn=0.6150 DotConsensus=0.93,0.01;0/100 FracUnassigned=0.38,2/5;0.33,5/20;0.35,328/558 Inst=0 MassDiff=-0.0281 MassDiffCounts=1/0:100 MaxRepSN=31.9 Mods=0 NAA=22 NMC=0 NTT=2 Nreps=100/200 OrigMaxIntensity=9.7e+03 Parent=1080.59 Pep=Tryptic PrecursorIntensity=0 Prob=1.0000 ProbRange=1,1,1,1 Protein=1/YKL060C RepFracAssignedPeaks=0.433 RepNumPeaks=455.3/66.5 RetentionTime=6210.1,8377.0,5782.0 SN=200.0 Sample=1/_mnt_u07_lgillet_html_Sorcerer_Searches_1201_YeastPostDiauxic_interact-SequestAllCombined,100,200 Se=1^S100:dc=0.6250/0.0232,fv=7.2567/0.2167,pb=1.0000/0.0000,xc=4.6179/0.1759 Spec=Consensus TotalIonCurrent=1.8e+05 XCorr=5.1460
+NumPeaks: 150
+70.0666	1347.0	IPA/0.00,IPA/0.00,y1-35^2/-0.48	100/60 0.0013|0.29
+86.0974	2116.6	IIA/0.00,IIA/0.00,IIA/0.00,IIA/0.00,ILA/0.00,ILA/0.00,INA/-0.96,INA/-0.96	100/60 0.0014|0.26
+120.0812	737.8	a1/0.00,IFA/0.00,IFA/0.00	100/60 0.0019|0.33
+141.1028	1862.0	y3-35^2/-0.48	100/60 0.0015|0.24
+157.1336	386.9	y1-18/0.03	100/60 0.0060|0.38
+158.0930	357.7	y1-17/0.00,b3-17^2/0.00	100/60 0.0027|0.40
+169.0976	8114.0	?	100/60 0.0013|0.24
+175.1190	1740.9	y1/0.00	100/60 0.0017|0.29
+185.1272	413.9	?	100/60 0.0091|0.33
+186.1238	1035.1	?	100/60 0.0024|0.31
+191.1182	1561.6	a2/0.00	100/60 0.0021|0.26
+211.1433	414.0	y2-35/0.02	100/60 0.0073|0.34
+212.1036	340.2	y2-35i/-0.02	99/60 0.0039|0.37
+214.1188	856.4	y4-18^2/-0.50,y4-17^2/-0.99	100/60 0.0031|0.29
+219.1128	3759.1	b2/-0.00	100/60 0.0018|0.27
+228.1344	1305.7	y2-18/-0.01	100/60 0.0029|0.29
+238.1186	368.5	?	98/60 0.0045|0.39
+245.1286	497.6	?	100/60 0.0041|0.38
+246.1566	447.3	y2/0.00	100/60 0.0044|0.34
+254.1865	1300.0	?	100/60 0.0030|0.27
+282.1809	5129.8	y3-35/0.02	100/60 0.0021|0.26
+283.1403	495.2	y3-35i/-0.02	100/60 0.0043|0.34
+287.1749	639.3	?	98/60 0.0039|0.32
+297.1564	353.5	y6-36^2/-0.52	84/60 0.0056|0.37
+299.1732	585.8	y3-18/-0.01,b6-17^2/0.50	99/60 0.0073|0.36
+299.1927	316.3	?	77/60 0.0170|0.41
+314.1772	345.0	?	85/60 0.0075|0.39
+315.1662	353.7	b3-17/-0.00	84/60 0.0054|0.37
+316.1644	944.5	y6^2/0.48	100/60 0.0040|0.31
+317.1925	2146.7	y3/-0.00	100/60 0.0037|0.29
+327.2019	485.9	y7-46^2/-1.00	97/60 0.0051|0.37
+332.1963	828.6	b3/-0.00,y7-36^2/-0.99	100/60 0.0044|0.31
+351.2019	609.3	y7^2/0.00,a7^2/0.99	100/60 0.0053|0.35
+351.2025	308.8	?	61/60 0.0146|0.39
+353.2174	482.9	?	94/60 0.0054|0.36
+359.2052	338.8	?	90/60 0.0069|0.37
+365.1826	391.7	b7^2/0.97	91/60 0.0071|0.43
+368.2269	589.2	?	99/60 0.0057|0.33
+379.1965	752.3	y8-44^2/0.46	100/60 0.0068|0.30
+379.2018	384.9	?	74/60 0.0159|0.43
+382.2086	454.2	y8-36^2/-0.52	93/60 0.0075|0.34
+385.2066	326.3	?	80/60 0.0077|0.44
+387.2003	1500.0	?	100/60 0.0051|0.29
+387.2042	632.6	?	77/60 0.0172|0.49
+396.2220	5492.6	b8-34^2/-0.50	100/60 0.0030|0.29
+396.2351	1376.3	[b8-34^2/-0.4830]	64/60 0.0219|0.74
+401.2511	360.8	y8^2/0.52,a4/-0.00,y4-44/-0.99	89/60 0.0107|0.38
+429.2366	368.2	y4-18i/0.01	85/60 0.0190|0.36
+429.2466	669.5	b4/-0.00,y4-17/0.04	99/60 0.0073|0.37
+432.2236	325.1	?	84/60 0.0065|0.43
+446.2322	1084.8	y4/-0.00,b9-35^2/-0.52	100/60 0.0068|0.33
+446.2370	527.1	?	91/60 0.0183|0.41
+450.2678	488.4	a9^2/-0.00	100/60 0.0090|0.38
+467.2946	1322.7	?	100/60 0.0069|0.31
+467.2967	641.3	?	95/60 0.0196|0.41
+472.2875	746.7	a5/-0.00	100/60 0.0066|0.36
+472.2908	366.2	?	85/60 0.0190|0.40
+478.2631	629.5	y10-17^2/-0.00,y10-18^2/0.49	100/60 0.0089|0.35
+478.2670	359.1	?	82/60 0.0176|0.40
+495.2901	3061.2	?	100/60 0.0064|0.31
+495.2909	1196.3	?	90/60 0.0237|0.55
+495.2951	633.9	?	64/60 0.0317|0.63
+500.2830	2313.6	b5/-0.00	100/60 0.0064|0.30
+500.2847	1023.7	[b5/-0.0020]	97/60 0.0216|0.49
+500.2898	507.0	?	71/60 0.0338|0.55
+559.3143	885.9	y5/-0.01	100/60 0.0097|0.39
+559.3181	485.7	?	97/60 0.0214|0.36
+578.3248	452.2	b12-34^2/0.53	99/60 0.0096|0.43
+579.3080	314.1	?	93/60 0.0131|0.48
+596.3325	621.3	b6-17/-0.01	100/60 0.0110|0.37
+596.3406	374.0	?	92/60 0.0206|0.42
+597.2992	339.4	b6-17i/-0.05	88/60 0.0118|0.43
+613.3619	672.5	b6/-0.01,y6-17/0.03	100/60 0.0115|0.35
+613.3633	409.4	?	91/60 0.0223|0.38
+630.3522	1209.8	y6/-0.00,a13^2/-0.99	100/60 0.0105|0.30
+630.3527	667.2	?	100/60 0.0226|0.38
+630.3535	398.6	?	87/60 0.0371|0.46
+683.3679	316.1	y7-18/-0.02,y7-17/-1.00,b7-45/0.98	97/60 0.0125|0.44
+701.3857	2333.6	y7/-0.01	100/60 0.0093|0.32
+701.3952	1097.1	[y7/0.0011]	100/60 0.0259|0.45
+701.3959	387.1	?	65/60 0.0517|0.49
+701.3970	658.0	?	93/60 0.0401|0.58
+713.3887	356.3	b15-34^2/0.02,b15-35^2/0.51	100/60 0.0140|0.38
+800.4541	738.6	?	100/60 0.0260|0.31
+800.4553	1209.7	y8/-0.01,b17^2/-0.98	100/60 0.0126|0.38
+800.4649	472.7	?	96/60 0.0394|0.39
+826.4792	323.3	b8/-0.00,y9-46/0.99	100/60 0.0163|0.34
+871.4911	1283.8	y9/-0.01	100/60 0.0117|0.38
+871.4918	717.2	?	100/60 0.0300|0.31
+871.4992	500.5	?	97/60 0.0416|0.39
+871.5051	317.0	?	78/60 0.0536|0.38
+914.9837	2305.2	y19^2/-0.01	100/60 0.0129|0.36
+914.9837	1173.8	[y19^2/-0.0081]	99/60 0.0296|0.40
+914.9888	633.6	?	93/60 0.0453|0.57
+971.5266	327.4	y20^2/-0.01,b21-44^2/-0.01,b21-45^2/0.51,b21-46^2/1.00	99/60 0.0197|0.53
+972.5362	1301.0	y10/-0.01	100/60 0.0171|0.31
+972.5401	811.6	?	100/60 0.0278|0.38
+972.5490	488.4	?	98/60 0.0445|0.42
+972.5517	335.8	?	85/60 0.0596|0.42
+1059.5675	1859.7	y11/-0.01,p-44^2/0.98	100/60 0.0157|0.37
+1059.5729	462.8	?	94/60 0.0651|0.44
+1059.5773	1162.7	[y11/-0.0020]	100/60 0.0297|0.34
+1059.5827	712.3	?	100/60 0.0484|0.49
+1059.6196	328.7	?	71/60 0.0635|0.43
+1146.6016	2441.6	y12/-0.01	100/60 0.0147|0.34
+1146.6040	1404.8	[y12/-0.0073]	100/60 0.0351|0.35
+1146.6122	561.4	?	96/60 0.0696|0.52
+1146.6140	857.0	?	100/60 0.0525|0.47
+1146.6408	374.4	?	78/60 0.0787|0.49
+1233.6333	4287.7	y13/-0.01	100/60 0.0147|0.34
+1233.6336	482.9	?	86/60 0.0974|0.56
+1233.6440	2217.8	[y13/0.0007]	100/60 0.0372|0.45
+1233.6554	1299.6	[y13/0.0120]	100/60 0.0589|0.52
+1233.6706	725.1	?	98/60 0.0761|0.56
+1290.6551	376.9	b13/0.98,y14-44/-0.05	100/60 0.0263|0.37
+1316.6707	414.8	y14-18/-0.01,y14-17/-0.99,b14-45/0.98	100/60 0.0274|0.34
+1334.6793	10000.0	y14/-0.01	100/60 0.0148|0.10
+1334.7118	681.0	?	87/60 0.1195|0.83
+1334.7152	4324.5	[y14/0.0242]	100/60 0.0405|0.65
+1334.7219	1160.4	[y14/0.0309]	96/60 0.0999|0.90
+1334.7245	2026.3	[y14/0.0335]	99/60 0.0730|0.81
+1334.6894	8199.7	y15	62/60 0.0589|0.79
+1335.6790	603.4	y14i/-0.01	100/60 0.0214|0.33
+1335.6818	433.3	?	99/60 0.0390|0.34
+1433.7455	2049.3	y15/-0.01	100/60 0.0198|0.34
+1433.7536	871.8	?	100/60 0.0599|0.42
+1433.7620	1355.9	[y15/0.0026]	100/60 0.0324|0.33
+1433.7635	395.5	?	92/60 0.0977|0.45
+1433.7645	573.6	?	99/60 0.0755|0.43
+1529.7799	445.5	y16-18/-0.01	98/60 0.0360|0.46
+1530.7651	309.5	b16/-0.05,y16-17/-0.01	97/60 0.0347|0.39
+1547.7921	5462.2	y16/-0.01	100/60 0.0170|0.37
+1547.8069	2683.6	[y16/0.0045]	100/60 0.0422|0.39
+1547.8226	592.4	?	97/60 0.1173|0.67
+1547.8261	1599.7	[y16/0.0238]	100/60 0.0616|0.50
+1547.8293	912.5	?	100/60 0.0890|0.63
+1547.8712	413.8	?	87/60 0.1209|0.71
+1548.7932	411.4	y16i/-0.01	100/60 0.0275|0.35
+1660.8728	434.2	?	100/60 0.0630|0.34
+1660.8740	598.4	?	100/60 0.0425|0.30
+1660.8772	892.9	y17/-0.01	100/60 0.0299|0.37
+1660.8870	332.6	?	91/60 0.0779|0.37
+1731.9090	419.3	y18/-0.01	100/60 0.0313|0.31
+1731.9153	311.0	?	100/60 0.0488|0.32
+1828.8525	336.2	?	86/60 0.0332|0.50
+1828.9618	1744.1	y19/-0.01	100/60 0.0272|0.36
+1828.9639	1172.5	[y19/-0.0123]	100/60 0.0436|0.35
+1828.9747	859.4	?	100/60 0.0630|0.40
+1828.9854	541.7	?	100/60 0.0923|0.48
+1829.0936	333.9	?	81/60 0.0271|0.47
+
+Name: AAELDVLNDPK/2
+LibID: 43
+MW: 1185.6230
+PrecursorMZ: 592.8115
+Status: Normal
+FullName: K.AAELDVLNDPK.I/2
+Comment: AvePrecursorMz=593.1632 BinaryFileOffset=265269 CollisionEnergy=0.0 DeltaCn=0.4290 FracUnassigned=0.21,1/5;0.45,11/20;0.37,76/150 MassDiff=-0.0185 Mods=0 NAA=11 NMC=0 NTT=2 Nreps=1/1 OrigMaxIntensity=3.8e+03 Parent=592.811 Pep=Tryptic PrecursorIntensity=0 Prob=1.0000 Protein=1/YPR041W RawSpectrum=lgillet_L120124_003.14730.14730 RetentionTime=4064.0,4064.0,4064.0 Sample=1/_mnt_u07_lgillet_html_Sorcerer_Searches_1201_YeastPostDiauxic_interact-SequestAllCombined,1,1 Se=1^S1:pb=1.0000/0,fv=5.1761/0,xc=3.2380/0,dc=0.4290/0 Spec=Single TotalIonCurrent=7.1e+04 XCorr=3.2380
+NumPeaks: 150
+70.0641	638.2	IPA/-0.00,IPA/-0.00	
+72.0801	891.7	b1/0.04,b2^2/0.04,IVA/-0.00,IVA/-0.00	
+84.0454	429.0	?	
+84.0798	408.1	?	
+86.0978	1028.0	ILA/0.00,ILA/0.00,ILA/0.00,ILA/0.00	
+102.0511	1028.0	IEA/-0.00,IEA/-0.00	
+115.0798	567.6	?	
+115.0858	1917.0	a2/-0.00,b3-44^2/0.52	
+120.0802	481.3	?	
+129.1009	905.0	y1-18/-0.00	
+130.0850	287.7	y1-17/-0.00	
+136.0736	5076.9	b3^2/-0.49	
+143.0799	5273.3	b2/-0.00	
+147.1098	766.4	y1/-0.00	
+147.1159	300.8	?	
+147.1210	337.4	?	
+173.0927	397.3	?	
+175.1058	361.0	b4-35^2/-0.48	
+185.0906	287.7	b4-17^2/0.50	
+185.1685	308.7	?	
+187.1067	1666.2	?	
+197.1268	729.8	?	
+201.0825	951.8	y2-44/0.91	
+201.0920	549.3	?	
+201.1194	303.8	?	
+203.1012	306.7	y2-44i/0.93	
+207.1127	4645.6	?	
+207.1334	285.4	?	
+209.1337	287.7	y2-35/0.01	
+215.1011	695.8	y4-46^2/0.98	
+215.1386	1171.9	y4-44^2/0.01,y4-45^2/0.53	
+225.1228	831.8	?	
+226.1169	379.2	?	
+226.1532	1449.1	y2-18/-0.00,b3-46/0.03	
+226.1667	541.5	?	
+229.1131	392.4	y2-17i/-0.03,y4-17^2/0.51,b5-44^2/0.49	
+235.1067	2668.1	?	
+243.1081	303.4	?	
+243.1326	638.2	?	
+244.1660	10000.0	y2/0.00,a3/0.04	
+246.1826	389.7	y2i/0.02	
+272.1222	7172.4	b3/-0.00,y5-44^2/0.45,y5-45^2/0.97	
+286.1353	358.4	y5-17^2/0.99,a6^2/-0.02	
+309.1011	308.7	?	
+326.1323	303.4	y6-35^2/0.45,y6-36^2/0.95	
+328.1793	499.6	?	
+328.1941	515.3	?	
+340.1472	870.5	b4-46i/-0.06	
+340.1662	353.1	?	
+342.1845	290.3	y3-17/0.02,b4-44/0.97	
+343.1639	638.2	y6^2/-0.03,a7^2/0.46	
+344.1558	293.0	y3-17i/-0.01	
+347.2317	387.1	b7-18^2/-0.46,b7-17^2/-0.95	
+350.1367	3434.5	b4-35/-0.03	
+357.2157	504.5	b7^2/0.52,a4/0.00	
+358.1589	392.4	a4i/-0.05	
+358.1775	287.7	?	
+359.1833	588.5	y3/-0.01	
+359.2043	536.3	a4i/-0.01	
+369.1523	343.0	b4-17/0.97	
+385.1973	677.5	?	
+385.2171	852.7	b4/0.01	
+393.2210	284.5	?	
+397.2202	306.0	?	
+411.2214	1080.3	?	
+421.1901	481.3	?	
+421.2112	1062.0	?	
+429.1844	329.3	y4-44/-0.06,y4-45/0.97	
+439.1921	285.1	y4-35/0.99	
+439.2207	928.6	y8-36^2/-0.02,y8-35^2/-0.51	
+442.2353	612.1	?	
+449.1896	303.4	?	
+449.2064	593.5	y8-17^2/0.47,y8-18^2/0.96,b9-44^2/-0.03,b9-45^2/0.48,b9-46^2/0.98	
+452.1973	387.0	?	
+456.1894	614.2	y4-17/-0.02,b5-44/-0.06	
+456.2136	582.8	y4-18i/-0.01	
+457.2404	494.2	y8^2/-0.01,a9^2/0.01	
+473.2253	1982.7	y4/-0.01	
+473.2412	1365.4	a5i/0.00	
+473.2734	594.1	?	
+486.2174	290.3	?	
+491.2238	345.6	?	
+500.2331	803.0	b5/-0.00,y9-44^2/0.45,y9-45^2/0.97	
+500.2489	483.9	?	
+521.7752	303.4	y9^2/0.00	
+528.2515	307.7	b10+18^2/-0.51	
+552.2946	347.6	?	
+554.2903	429.0	b6-46/0.99	
+557.2613	598.7	y10^2/-0.03	
+557.2947	303.4	?	
+569.2977	392.4	p-46^2/-0.51,y5-17/0.00,y5-18/0.99	
+572.2834	488.8	a6i/-0.03	
+581.2803	306.0	?	
+581.3084	313.3	b6-18/0.02,b6-17/-0.97	
+586.2896	1697.6	[y5/-0.0299]	
+586.3250	5992.7	y5/0.01	
+586.3703	337.4	?	
+589.2850	627.8	?	
+589.3185	2158.0	?	
+589.3454	1488.4	?	
+589.3769	355.7	?	
+592.3492	413.9	?	
+592.7869	1184.9	[p^2/-0.0246]	
+592.8243	1925.2	p^2/0.01	
+599.2787	282.5	?	
+599.3063	530.9	?	
+599.3251	653.8	b6/0.02	
+670.3287	437.4	?	
+670.3558	355.7	?	
+685.3626	1831.0	a7/0.97	
+685.3942	1967.0	y6/0.01	
+685.4188	465.6	?	
+685.4262	410.7	?	
+685.4452	285.1	?	
+701.3481	284.8	?	
+736.3894	7658.9	?	
+736.4460	939.1	?	
+737.3785	318.2	?	
+737.4271	379.3	?	
+781.3696	337.6	b8-45/-0.04,b8-46/0.94	
+799.3571	303.4	a8/0.92	
+800.3607	1140.5	[y7/-0.0541]	
+800.3955	5532.3	y7/-0.02	
+800.4310	5092.9	a8i/1.00	
+800.4727	1035.8	[y7/0.0579]	
+801.4191	306.0	y7i/0.00	
+835.4294	308.5	?	
+835.4499	368.8	?	
+835.4684	711.5	?	
+835.4857	855.3	?	
+913.4274	353.1	?	
+913.4537	918.1	?	
+913.4868	3314.2	y8/-0.01,a9/0.02	
+913.5197	2393.4	[y8/0.0208]	
+941.4506	324.4	b9/-0.01	
+950.4389	797.8	?	
+950.4761	1566.8	?	
+950.5020	1627.0	?	
+950.5334	1062.0	?	
+1021.5166	426.4	b10-17/0.03	
+1021.5525	423.8	?	
+1024.5153	397.6	y9-18/-0.02	
+1042.5045	850.1	?	
+1042.5350	1265.4	y9/-0.01	
+1042.5577	1046.3	[y9/0.0162]	
+1042.6211	449.9	?	
+1147.5754	350.2	?	
+1147.5819	370.9	?	
+1166.6080	415.9	?	
+1184.6034	2288.8	?	
diff -r 000000000000 -r e3a05965ca0c tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat May 30 05:10:54 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="msproteomicstools" version="0.3.2">
+        <repository changeset_revision="4381e493affd" name="package_python_2_7_msproteomicstools_0_3_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>